From 2dce48c6ceb990aab3f3aa1c5a22c8552e9017d6 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 28 Sep 2026 12:26:11 -0400 Subject: [PATCH 01/14] chore: tidy repo layout (Phase 1 of 2026-09-28 tidy plan) Per Dr. Osumi-Sutherland's feedback, reports/ now holds current outputs only. - Archive the Sept 2026 resolver experiments (evaluation-alias/-legacy, resolver-refinement, regression-triage, regression-followup, baseline JSON, enhanced batch TSV) under archive/2026-09_resolver_experiments/, with a README summarizing what they showed. Keep only README/.md/.tsv summaries; the large JSON/HTML (~24 MB) is recoverable from 4dfc726 and f1e0772, as the archive README documents. - Drop 4 byte-identical legacy .md/.tsv copies (SHA-256 checked) and point their links at evaluation-legacy/. - Move planning docs to docs/planning/ and reports/literature/ to literature/. - Add reports/README.md (one row per file: producer, curated vs generated). - Add the Notes.md sheet link to README and its quick reference to MARKER_SYNTAX.md (Notes.md itself not yet removed). - Update paths in CLAUDE.md, README, ROADMAP, skills, curated TSVs (path prefix only), the CD8 review_ref, and let the audit dashboard link literature/ and archive/ paths. - Add tests/test_doc_links.py: all relative links in hand-written docs resolve. No mapping decisions, CL IDs, quotes or citations changed. Co-Authored-By: Claude Opus 5.5 --- .claude/skills/mapping-audit/SKILL.md | 2 +- .../pro-marker-species-support/SKILL.md | 6 +- .claude/skills/roadmap-status-sync/SKILL.md | 6 +- .claude/skills/soulcap-cl-matching/SKILL.md | 2 +- CLAUDE.md | 13 +- MARKER_SYNTAX.md | 12 + README.md | 32 +- ROADMAP.md | 6 +- .../2026-09_resolver_experiments/README.md | 52 + .../candidate_cl_mappings_enhanced.tsv | 0 .../evaluation-alias/matcher_evaluation.md | 0 .../evaluation-alias/matcher_evaluation.tsv | 0 .../evaluation-legacy/matcher_evaluation.md | 0 .../evaluation-legacy/matcher_evaluation.tsv | 0 .../regression-followup/README.md | 2 +- .../corrected/matcher_evaluation.md | 0 .../corrected/matcher_evaluation.tsv | 0 .../regression-followup/mapping_review.tsv | 0 .../regression-triage/README.md | 2 +- .../regression-triage/regression_triage.md | 0 .../regression-triage/regression_triage.tsv | 0 .../resolver-refinement/README.md | 11 +- .../audit/audit_summary.md | 0 .../resolver-refinement/enhanced.sssom.md | 0 .../enhanced.sssom.provenance.json | 0 .../resolver-refinement/enhanced.sssom.tsv | 0 .../enhanced/matcher_evaluation.md | 0 .../enhanced/matcher_evaluation.tsv | 0 .../planning}/fall_2026_semester_plan.html | 0 .../planning}/fall_2026_semester_plan.md | 0 .../planning}/fall_2026_semester_plan.pdf | Bin .../planning}/fall_2026_sprint_backlog.md | 8 +- .../b_cell_markers.md | 0 .../literature => literature}/dc_markers.md | 0 .../gdt_mait_markers.md | 0 .../literature => literature}/ilc_markers.md | 0 .../literature => literature}/inkt_markers.md | 0 .../nk_cell_markers.md | 0 .../t_cell_markers.md | 0 reports/README.md | 72 + reports/candidate_cl_mappings_narrative.md | 6 +- reports/cl_term_issues.md | 2 +- .../evaluation-alias/matcher_evaluation.json | 83216 ------ .../evaluation-legacy/matcher_evaluation.json | 14487 - reports/gaps.tsv | 2 +- reports/matcher_evaluation_baseline.json | 12326 - reports/pro_marker_species_support.tsv | 116 +- .../corrected/matcher_evaluation.json | 97822 ------- .../legacy/matcher_evaluation.json | 14489 - .../legacy/matcher_evaluation.md | 195 - .../legacy/matcher_evaluation.tsv | 81 - .../regression-triage/regression_triage.json | 216298 --------------- .../audit/audit_dashboard.html | 87 - .../resolver-refinement/audit/audit_data.json | 151903 ---------- .../enhanced/matcher_evaluation.json | 93319 ------- .../legacy/matcher_evaluation.json | 14489 - .../legacy/matcher_evaluation.md | 195 - .../legacy/matcher_evaluation.tsv | 81 - .../pre_refinement_evaluation.json | 35723 --- src/soulcap_cl_mapping/audit.py | 2 +- src/soulcap_cl_mapping/marker_resolution.py | 4 +- tests/test_doc_links.py | 76 + 62 files changed, 328 insertions(+), 734817 deletions(-) create mode 100644 archive/2026-09_resolver_experiments/README.md rename {reports => archive/2026-09_resolver_experiments}/candidate_cl_mappings_enhanced.tsv (100%) rename {reports => archive/2026-09_resolver_experiments}/evaluation-alias/matcher_evaluation.md (100%) rename {reports => archive/2026-09_resolver_experiments}/evaluation-alias/matcher_evaluation.tsv (100%) rename {reports => archive/2026-09_resolver_experiments}/evaluation-legacy/matcher_evaluation.md (100%) rename {reports => archive/2026-09_resolver_experiments}/evaluation-legacy/matcher_evaluation.tsv (100%) rename {reports => archive/2026-09_resolver_experiments}/regression-followup/README.md (98%) rename {reports => archive/2026-09_resolver_experiments}/regression-followup/corrected/matcher_evaluation.md (100%) rename {reports => archive/2026-09_resolver_experiments}/regression-followup/corrected/matcher_evaluation.tsv (100%) rename {reports => archive/2026-09_resolver_experiments}/regression-followup/mapping_review.tsv (100%) rename {reports => archive/2026-09_resolver_experiments}/regression-triage/README.md (92%) rename {reports => archive/2026-09_resolver_experiments}/regression-triage/regression_triage.md (100%) rename {reports => archive/2026-09_resolver_experiments}/regression-triage/regression_triage.tsv (100%) rename {reports => archive/2026-09_resolver_experiments}/resolver-refinement/README.md (70%) rename {reports => archive/2026-09_resolver_experiments}/resolver-refinement/audit/audit_summary.md (100%) rename {reports => archive/2026-09_resolver_experiments}/resolver-refinement/enhanced.sssom.md (100%) rename {reports => archive/2026-09_resolver_experiments}/resolver-refinement/enhanced.sssom.provenance.json (100%) rename {reports => archive/2026-09_resolver_experiments}/resolver-refinement/enhanced.sssom.tsv (100%) rename {reports => archive/2026-09_resolver_experiments}/resolver-refinement/enhanced/matcher_evaluation.md (100%) rename {reports => archive/2026-09_resolver_experiments}/resolver-refinement/enhanced/matcher_evaluation.tsv (100%) rename {reports => docs/planning}/fall_2026_semester_plan.html (100%) rename {reports => docs/planning}/fall_2026_semester_plan.md (100%) rename {reports => docs/planning}/fall_2026_semester_plan.pdf (100%) rename {reports => docs/planning}/fall_2026_sprint_backlog.md (97%) rename {reports/literature => literature}/b_cell_markers.md (100%) rename {reports/literature => literature}/dc_markers.md (100%) rename {reports/literature => literature}/gdt_mait_markers.md (100%) rename {reports/literature => literature}/ilc_markers.md (100%) rename {reports/literature => literature}/inkt_markers.md (100%) rename {reports/literature => literature}/nk_cell_markers.md (100%) rename {reports/literature => literature}/t_cell_markers.md (100%) create mode 100644 reports/README.md delete mode 100644 reports/evaluation-alias/matcher_evaluation.json delete mode 100644 reports/evaluation-legacy/matcher_evaluation.json delete mode 100644 reports/matcher_evaluation_baseline.json delete mode 100644 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b/.claude/skills/mapping-audit/SKILL.md index 7bb070b..23b194d 100644 --- a/.claude/skills/mapping-audit/SKILL.md +++ b/.claude/skills/mapping-audit/SKILL.md @@ -34,7 +34,7 @@ wants to know if any existing mapping is now stale. CL ID's current marker-axiom support as `confirmed` (directly asserted), `inferred_only`, or `no_marker_axiom`, from `reports/cl_pro_relationships.tsv`. -- `reports/literature/*.md` and `reports/pro_marker_species_support.tsv` — the +- `literature/*.md` and `reports/pro_marker_species_support.tsv` — the literature side of the evidence a mapping might rely on, especially for species-specific marker claims. - `uv run soulcap-match --req-excl ... --ideal-excl ... --req-pheno ... diff --git a/.claude/skills/pro-marker-species-support/SKILL.md b/.claude/skills/pro-marker-species-support/SKILL.md index ce4805b..69ef282 100644 --- a/.claude/skills/pro-marker-species-support/SKILL.md +++ b/.claude/skills/pro-marker-species-support/SKILL.md @@ -30,7 +30,7 @@ axioms are added. already carries a species qualifier (`(mouse)`/`(human)`). Run via `uv run python -c "..."` or a short driver script — not a CLI (deliberately; see the module docstring). -- `reports/literature/*.md` — the Milestone 2 literature reports. **Check +- `literature/*.md` — the Milestone 2 literature reports. **Check these first, always.** They already contain verbatim-quoted, hook-validated evidence for 7 cell families (NK, ILC, DC, iNKT, T cell, B cell, gdT/MAIT), and reusing a quote from here is strictly better than a fresh search: it's @@ -72,7 +72,7 @@ refreshing rather than re-running everything. For each pair (or each CL cell type's group of pairs, sharing a seed set): -1. **Search the relevant `reports/literature/*.md` file** for the marker's +1. **Search the relevant `literature/*.md` file** for the marker's CD synonym or PR label. If a verbatim blockquote already covers it, reuse that quote and citation directly — `evidence_source: m2_literature_report`. 2. **If Asta is reachable and no M2 coverage exists**, run `citation-traversal` @@ -124,7 +124,7 @@ Append to `reports/pro_marker_species_support.tsv` | `evidence_source` | `m2_literature_report` / `citation_traversal` / `europepmc_search` / `none`. | | `citation` | Author/year/PMID/DOI, plus a trailing `-- ` caveat clause when the quote's context doesn't exactly match the pair's cell type/subset (e.g. a naive-T marker's only evidence coming from a Treg paper) — say so rather than let the row imply a cleaner match than it is. | | `quote` | The verbatim substring itself. | -| `source_ref` | `reports/literature/.md` for M2 reuse, an EuropePMC article URL for a fresh search, or `reports/citation_traversal//` for a traversal — or, for `insufficient_evidence`, a one-line note on what was tried. | +| `source_ref` | `literature/.md` for M2 reuse, an EuropePMC article URL for a fresh search, or `reports/citation_traversal//` for a traversal — or, for `insufficient_evidence`, a one-line note on what was tried. | ## Step 5 — flag real findings diff --git a/.claude/skills/roadmap-status-sync/SKILL.md b/.claude/skills/roadmap-status-sync/SKILL.md index 7b7a949..1c6e4dd 100644 --- a/.claude/skills/roadmap-status-sync/SKILL.md +++ b/.claude/skills/roadmap-status-sync/SKILL.md @@ -24,7 +24,7 @@ changes a milestone's completion state. - `uv run soulcap-sync` — re-pull the Google Sheet before checking anything that depends on its current column set (this is a network call and overwrites the gitignored `data/` cache — safe, but mention you're doing it). -- File/row counts under `marker_mappings/`, `reports/`, `reports/literature/`. +- File/row counts under `marker_mappings/`, `reports/`, `literature/`. - `gh issue view ` — for the CL term corrections table, whose "Status" column tracks upstream `obophenotype/cell-ontology` issues that this repo doesn't control the resolution of. @@ -37,7 +37,7 @@ disk, every time: | Milestone | Evidence to check | How to read it | |---|---|---| | M1 — marker → protein → gene | `marker_mappings/marker_protein_gene.csv` exists and has rows | Empty/missing → ⬜. Has rows but visibly incomplete (spot-check a few marker tokens from `data/marker_combinations.csv` against it) → 🟡. Covers essentially all distinct tokens → ✅. | -| M2 — literature support | Count `reports/literature/*.md` files against the distinct `Category` values in `data/citation_mgr.csv` (re-sync first if `data/` looks stale) | 0 files → ⬜. Some but not all categories covered → 🟡 (state the fraction, e.g. "8/14"). All categories covered → ✅. | +| M2 — literature support | Count `literature/*.md` files against the distinct `Category` values in `data/citation_mgr.csv` (re-sync first if `data/` looks stale) | 0 files → ⬜. Some but not all categories covered → 🟡 (state the fraction, e.g. "8/14"). All categories covered → ✅. | | M3 — audit curated mappings | Whether the Google Sheet now has dedicated broad/exact-match and comment columns beyond today's `Type of Match` (assay-type, not CL-match-type), `OLS CL identifier`, and `CL Mapping Notes` — check the freshly-synced sheet's actual column headers, don't assume from the column *names* alone (`Type of Match` sounds relevant but is not the same field per the roadmap's own note) | Columns still absent → stays ⛔, but if the `mapping-audit` skill has since made a drift/evidence-based audit possible without those columns, say so explicitly rather than leaving it a flat "blocked with nothing happening." | | M4 — candidate mappings | Row count in `reports/candidate_cl_mappings.sssom.tsv` (minus header) against total rows in `data/marker_combinations.csv` (minus header) | Partial coverage → 🟡 with the fraction. All SOULCAP rows covered (including documented "no reasonable match" cases logged in `gaps.tsv`, which count as resolved, not missing) → ✅. | | CL term corrections table | `gh issue view ` for each row's linked repo issue, and the upstream `obophenotype/cell-ontology` issue if linked | If the upstream issue is closed/merged, the table's "Status" cell is stale — update it. | @@ -72,7 +72,7 @@ same way when an upstream issue has moved. - M2's category list comes from `data/citation_mgr.csv`'s `Category` column, which mixes true cell-type families (NK cell, B cell, monocyte, ...) with at least one cross-cutting method category (`immunoprofiling`) that doesn't map - to a single `reports/literature/*.md` file — don't count it against M2's + to a single `literature/*.md` file — don't count it against M2's denominator; use judgment on any other ambiguous category the same way. - A "done" `data/` count is only as fresh as the last `uv run soulcap-sync` — always re-sync before trusting M2/M3/M4 numbers if the last sync date is diff --git a/.claude/skills/soulcap-cl-matching/SKILL.md b/.claude/skills/soulcap-cl-matching/SKILL.md index c6b819b..e066ea0 100644 --- a/.claude/skills/soulcap-cl-matching/SKILL.md +++ b/.claude/skills/soulcap-cl-matching/SKILL.md @@ -127,7 +127,7 @@ format (one `##` section per cell type or closely related family): agreement, and calling out anything that had to be verified by hand> **Evidence:** +literature/, `soulcap-match` rank/score> ``` If a candidate is genuinely uncertain (e.g. the SOULCAP profile doesn't test diff --git a/CLAUDE.md b/CLAUDE.md index d2553f9..cb22633 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -58,10 +58,15 @@ AST in `marker_syntax.py`, compiled/evaluated by `phenotype.py`. | [README.md](README.md) | Project overview + setup (UV, Asta token). | | `CLAUDE.md` | This file — guidance for Claude. | | [ROADMAP.md](ROADMAP.md) | Planned work / milestones and their deliverables and dependencies. | -| [Notes.md](Notes.md) | Scratch notes on data sources + a marker-syntax quick reference. | +| [Notes.md](Notes.md) | Superseded: its sheet link is now in README.md and its quick reference in MARKER_SYNTAX.md. Pending removal. | | [MARKER_SYNTAX.md](MARKER_SYNTAX.md) | **Canonical spec** of the marker expression language (human-readable guide + EBNF). Cite this for anything parsing/validating marker strings. | -| [reports/](reports/) | Analysis reports. `marker_string_issues.md` is the curated review; `marker_validation.md` is **auto-generated** by the EBNF validator on each sync. `cl_pro_relationships.md`/`.tsv` are **auto-generated** by `soulcap-cl-pro` from Ubergraph. `cl_term_issues.md` tracks proposed CL corrections found during mapping work. `candidate_cl_mappings.md` is the Milestone 4 deliverable — proposed SOULCAP→CL mappings with rationale and evidence. `candidate_cl_mappings_batch.tsv`/`candidate_cl_mappings_agreement.tsv` are **auto-generated** by `soulcap-match --batch [--lexical]` (issue #6) — a marker-axiom-only pass and a marker/lexical agreement pass across every SOULCAP cell type; treat as an unreviewed draft shortlist (conflicts must be checked), not curated output. `candidate_cl_mappings.sssom.tsv` is **auto-generated** by `soulcap-sssom` from the curated `CURATED_MAPPINGS` table in `sssom_export.py` (kept in sync by hand with `candidate_cl_mappings.md`) — standard SSSOM format, with `confidence`/`comment` derived from whether the match is backed by a directly-asserted CL marker axiom, an inferred-only one, or none at all (lexical/name match only). `gaps.tsv` is a curated, hand-maintained log of cases where SOULCAP has no reasonable CL match, CL conflicts with a marker panel, CL has an axiom gap, or the sheet itself has a data problem — separate from the mapping table; matching GitHub issues use the `gap` label (`.github/ISSUE_TEMPLATE/mapping_gap.yml`). `pro_marker_species_support.tsv` is the issue #11 deliverable — for each (CL cell type, general PRO marker) pair SOULCAP's mappings actually touch, whether literature supports the marker as human, mouse, or both, or `insufficient_evidence`; built by the `pro-marker-species-support` skill, every quote verified verbatim against its source before writing. `fall_2026_sprint_backlog.md` is the sprint-level breakdown of [ROADMAP.md](ROADMAP.md)'s Fall 2026 (Oct–Dec) working plan, prepared for Dr. Diehl — hand-maintained, not regenerable; update it as items complete or scope is renegotiated, don't treat it as a generated report. New reports go here. `reports/citation_traversal/` holds gitignored, regenerable snippet caches + summaries from the `citation-traversal` skill. | -| [cell_type_reviews/](cell_type_reviews/README.md) | **One review file per SOULCAP cell type** (tracked, curated — not a regenerable cache): definition, marker→protein, verbatim literature support, CL comparison, proposed verdict, uncertainty flags. Start from `_template.md` and keep the folder README's index in sync. Only reviews flagged **uncertain** go to Dr. Diehl for expert review. Scaffolded 2026-09-23, no reviews written yet; its relationship to the existing `reports/literature/` Milestone 2 output is still being confirmed with Dr. Diehl — see ROADMAP.md before assuming one supersedes the other. | +| [reports/](reports/README.md) | **Current outputs only.** Every file is listed in [reports/README.md](reports/README.md) with its producer and whether it is curated or generated. Curated (hand-maintained): `gaps.tsv`, `cl_term_issues.md`, `marker_string_issues.md`, `pro_marker_species_support.tsv` (issue #11, built by the `pro-marker-species-support` skill), `proposed_marker_fixes.xlsx`, `candidate_cl_mappings_narrative.md`. Generated (don't hand-edit): `candidate_cl_mappings.md`/`.sssom.tsv` (`soulcap-sssom`, from `mappings/curated_mappings.tsv`), `candidate_cl_mappings_batch.tsv`/`_agreement.tsv` (`soulcap-match --batch [--lexical]`, unreviewed draft shortlists), `audit_*` (`soulcap-audit`), `matcher_evaluation.*` (`soulcap-evaluate`), `marker_resolution_audit.*` (`soulcap-resolution-audit`), `marker_validation.md` (`soulcap-sync`/`soulcap-validate`), `cl_pro_relationships.md`/`.tsv` (`soulcap-cl-pro`, Ubergraph), `cl_lexical_cache.json` (`soulcap-cache-terms`). `reports/citation_traversal/` holds gitignored snippet caches from the `citation-traversal` skill. | +| [cell_type_reviews/](cell_type_reviews/README.md) | **One review file per SOULCAP cell type** (tracked, curated — not a regenerable cache): definition, marker→protein, verbatim literature support, CL comparison, proposed verdict, uncertainty flags. Start from `_template.md` and keep the folder README's index in sync. Only reviews flagged **uncertain** go to Dr. Diehl for expert review. Scaffolded 2026-09-23, no reviews written yet; its relationship to the existing [`literature/`](literature/) Milestone 2 output is still being confirmed with Dr. Diehl — see ROADMAP.md before assuming one supersedes the other. | +| [mappings/](mappings/README.md) | Curated mapping decisions (`curated_mappings.tsv`), permanent local entity IDs (`soulcap_entities.tsv`), and matcher benchmark files. The decision source of truth for this repo. | +| `marker_mappings/` | Token → PRO/UniProt/gene registry (`marker_protein_gene.csv`), per-token resolution policy (`marker_resolution.tsv`), token list, and PRO→UniProt overrides. Tracked, curated. | +| [literature/](literature/) | Milestone 2 literature evidence (verbatim quotes with citations), one file per cell-type family. Moved from `reports/literature/` on 2026-09-28. | +| [docs/planning/](docs/planning/) | Planning documents: `fall_2026_sprint_backlog.md` (hand-maintained sprint breakdown of ROADMAP.md; update as items complete, not a generated report) and the Sept 21 `fall_2026_semester_plan` draft (`.md`, `.pdf`, `.html`). | +| [archive/](archive/2026-09_resolver_experiments/README.md) | Finished one-off experiments, one dated folder each with a README. Not current output; nothing regenerates it. | | `src/soulcap_cl_mapping/` | All Python code. `sync_sheets.py` → `soulcap-sync`; `marker_syntax.py` → `soulcap-validate` (EBNF validator); `snippet_cache.py` → `soulcap-cache`; `report_validator.py` → `soulcap-validate-report`; `cl_pro.py` → `soulcap-cl-pro` (CL→PR relationships via Ubergraph SPARQL); `cl_match.py` → `soulcap-match` (marker-axiom + lexical CL candidate scoring, single-profile or `--batch`); `oak_match.py` → `soulcap-oak-match` (OAK sqlite-backed lexical/synonym CL search — downloads/caches a local CL database on first use, ~100MB); `sssom_export.py` → `soulcap-sssom` (curated mappings → SSSOM TSV, with confidence derived from CL marker-axiom assertion status); `pro_species_support.py` (scopes CL PRO markers needing species-specificity literature support — no CLI, called as a library from the `pro-marker-species-support` skill); `europepmc_search.py` → `soulcap-europepmc` (free, keyless Europe PMC search — fallback literature source when the Asta MCP server isn't reachable); `pubmed_search.py` → `soulcap-pubmed` (NCBI E-utilities search — reads `PUBMED_API_KEY` from `.env` if set for the higher rate limit, otherwise works keyless; use when a task specifically needs NCBI's own index/query syntax rather than Europe PMC's mirror of it). | | `tests/` | Unit tests (mirror `src/` layout). | | `.claude/skills/` | Project skills — see [citation-traversal](.claude/skills/citation-traversal/SKILL.md), `ontology-term-lookup`, [pro-marker-species-support](.claude/skills/pro-marker-species-support/SKILL.md), [gap-issue-filing](.claude/skills/gap-issue-filing/SKILL.md), [roadmap-status-sync](.claude/skills/roadmap-status-sync/SKILL.md), and [mapping-audit](.claude/skills/mapping-audit/SKILL.md). | @@ -76,7 +81,7 @@ from here and the README so locations stay consistent. Do not scatter documents at the repo root. The September 21 Fall 2026 planning draft for Dr. Diehl is -`reports/fall_2026_semester_plan.md`, with matching `.pdf` and `.html` versions. +`docs/planning/fall_2026_semester_plan.md`, with matching `.pdf` and `.html` versions. It summarizes recent work and proposes weekly deliverables and agent task instructions. It does not replace the existing sprint backlog or establish new scientific approvals or collaborator commitments without agreement. diff --git a/MARKER_SYNTAX.md b/MARKER_SYNTAX.md index 8eb0c00..40b8ebd 100644 --- a/MARKER_SYNTAX.md +++ b/MARKER_SYNTAX.md @@ -12,6 +12,18 @@ marker columns of the **`Marker Combinations`** sheet: It has two parts: a [human-readable guide](#1-human-readable-guide) and a [formal grammar](#2-formal-grammar-ebnf). They describe the same language. +## Quick reference + +``` +live/ selection for live cells, not a marker +(x|y) x OR y +space AND +[ ] and ( ) grouping (contents AND- or OR-joined); a postfix after a closing + bracket applies to the whole group, e.g. [A B]- = NOT(A AND B) +postfixes -, +, lo, hi, int, +/- (= low to undetectable) +/ OR delimiter on a postfix, e.g. -/lo +``` + --- ## 1. Human-readable guide diff --git a/README.md b/README.md index a41d79a..b603d82 100644 --- a/README.md +++ b/README.md @@ -35,13 +35,13 @@ the life sciences. Milestones and their status live in [ROADMAP.md](ROADMAP.md). The current semester's sprint-level breakdown (sub-tasks, acceptance criteria, and what's blocked on someone outside the repo) is -[reports/fall_2026_sprint_backlog.md](reports/fall_2026_sprint_backlog.md). +[docs/planning/fall_2026_sprint_backlog.md](docs/planning/fall_2026_sprint_backlog.md). The September 21 discussion draft for Dr. Diehl expands this into a plain-language October–December plan, recent-work summary, weekly schedule, -and agent task instructions: [PDF](reports/fall_2026_semester_plan.pdf), -[editable Markdown](reports/fall_2026_semester_plan.md), or -[browser version](reports/fall_2026_semester_plan.html). +and agent task instructions: [PDF](docs/planning/fall_2026_semester_plan.pdf), +[editable Markdown](docs/planning/fall_2026_semester_plan.md), or +[browser version](docs/planning/fall_2026_semester_plan.html). Its workload and review targets are proposed for approval, not confirmed commitments. ## Setup @@ -181,8 +181,8 @@ mapping evidence, SSSOM export, and the audit now share the same resolver when `--marker-map` is explicitly enabled for each command; defaults remain legacy. ```bash -uv run soulcap-match --batch --marker-map marker_mappings/marker_protein_gene.csv --term-cache reports/cl_lexical_cache.json --batch-out reports/candidate_cl_mappings_enhanced.tsv -uv run soulcap-evaluate --marker-map marker_mappings/marker_protein_gene.csv --term-cache reports/cl_lexical_cache.json --baseline reports/matcher_evaluation_baseline.json +uv run soulcap-match --batch --marker-map marker_mappings/marker_protein_gene.csv --term-cache reports/cl_lexical_cache.json --batch-out reports/candidate_cl_mappings_enhanced.tsv # archived Sept run: archive/2026-09_resolver_experiments/ +uv run soulcap-evaluate --marker-map marker_mappings/marker_protein_gene.csv --term-cache reports/cl_lexical_cache.json --baseline SAVED_BASELINE.json --out-dir reports/evaluation-next uv run soulcap-audit ``` @@ -214,7 +214,9 @@ the affected policy and its fingerprint; do not simply refresh hashes to bypass Resolution paths are recorded in candidate evidence; withheld cases are listed in evaluation JSON under `marker_resolution_issues`. -Isolate resolver changes from lexical coverage and inspect detailed differences: +Isolate resolver changes from lexical coverage and inspect detailed differences. +The September 2026 run of these commands is archived in +[archive/2026-09_resolver_experiments/resolver-refinement/](archive/2026-09_resolver_experiments/resolver-refinement/README.md): ```bash uv run soulcap-resolution-audit @@ -250,8 +252,8 @@ profiles remain unscored. Single-profile CLI searches use `--subset` or `--paren The evaluation distinguishes targets absent from the global index from targets present but not retrieved for a row. Candidate-source labels, lexical evidence, and protein-resolution paths are exported in batch TSV and evaluation JSON. -The original baseline is preserved in `reports/matcher_evaluation_baseline.json`; -controlled runs are in `reports/evaluation-legacy/` and `reports/evaluation-alias/`. +The original baseline and the controlled legacy/alias runs are archived in +[archive/2026-09_resolver_experiments/](archive/2026-09_resolver_experiments/README.md) (summaries only; JSON recoverable from git history). Mode/input changes make comparisons descriptive rather than equivalent-condition regression tests. Broader coverage alone does not establish better ranking. @@ -261,8 +263,9 @@ regression tests. Broader coverage alone does not establish better ranking. uv run python -m soulcap_cl_mapping.regression_triage ``` -Writes [regression_triage.md](reports/regression-triage/regression_triage.md), -JSON evidence, and a per-case TSV under `reports/regression-triage/`. Optional +Writes `regression_triage.md`, JSON evidence, and a per-case TSV under +`reports/regression-triage/` (not currently committed; the September 2026 run is +[archived](archive/2026-09_resolver_experiments/regression-triage/README.md)). Optional `--root` and `--out-dir` select another snapshot or report location. This is a diagnostic tool, not a production matcher mode: it does not change policies, mapping decisions, scoring weights, or existing audit/evaluation reports. @@ -278,7 +281,8 @@ the provisional targets or establish biological correctness of a policy. ## Input data The single source of truth is a -Google Sheet (ask for access) +[Google Sheet](https://docs.google.com/spreadsheets/d/1uWwczLxgbpWMmXycL8Thq5NVExzlib4A/edit) +(ask for edit access). Key tabs: @@ -419,7 +423,7 @@ are retained in the registry's `legacy_subject_id` column. ## Evidence-reviewed regression follow-up -The [steps 3–6 follow-up](reports/regression-followup/README.md) reviews the +The [steps 3–6 follow-up](archive/2026-09_resolver_experiments/regression-followup/README.md) reviews the three lost top-five targets, retains a narrowly scoped whole-CD8 surface assertion in opt-in policy mode, and records controlled before/after results. Top-five provisional agreement remains 16/80; this is not a validated ranking @@ -452,7 +456,7 @@ uncertainty trigger (weak literature, a conflict with CL axioms, no exact CL ter etc.) are sent for expert review; confident mappings go straight into the Google Sheet. See the folder README for the workflow, statuses, and template. Scaffolded 2026-09-23 — no reviews written yet, and how it relates to the existing -`reports/literature/` Milestone 2 reports is still being confirmed with Dr. Diehl +[`literature/`](literature/) Milestone 2 reports is still being confirmed with Dr. Diehl (see [ROADMAP.md](ROADMAP.md)). ## Skills & literature workflows diff --git a/ROADMAP.md b/ROADMAP.md index bc9587f..d288a9d 100644 --- a/ROADMAP.md +++ b/ROADMAP.md @@ -36,7 +36,7 @@ working on any task. For the Oct–Dec 2026 execution plan against these milestones — broken into sprint-level sub-tasks, acceptance criteria, and who each item is blocked -on — see [reports/fall_2026_sprint_backlog.md](reports/fall_2026_sprint_backlog.md). +on — see [docs/planning/fall_2026_sprint_backlog.md](docs/planning/fall_2026_sprint_backlog.md). Status legend: ⬜ not started · 🟡 in progress · ✅ done · ⛔ blocked. @@ -128,7 +128,7 @@ type as claimed. - Distinguish "no supporting evidence found" from "evidence found" — never invent support. -**Deliverable:** a set of markdown reports under `reports/literature/` (e.g. one +**Deliverable:** a set of markdown reports under `literature/` (moved from `reports/literature/` on 2026-09-28) (e.g. one per cell type or per marker), each listing markers, verified supporting quotes, and citations. @@ -213,5 +213,5 @@ upstream to `obophenotype/cell-ontology`. before relying on automated parsing for M1/M3/M4. - **Folders to standardise:** - `marker_mappings/` — curated mapping CSVs (tracked). - - `reports/literature/` — M2 literature reports. + - `literature/` — M2 literature reports. - `reports/` — analysis/audit reports (M3, M4). diff --git a/archive/2026-09_resolver_experiments/README.md b/archive/2026-09_resolver_experiments/README.md new file mode 100644 index 0000000..fb89953 --- /dev/null +++ b/archive/2026-09_resolver_experiments/README.md @@ -0,0 +1,52 @@ +# Resolver experiments, September 2026 + +Historical comparison runs from 2026-09-10 to 2026-09-18, moved here from +`reports/` on 2026-09-28. They explain why the opt-in token-to-PRO resolver +(`--marker-map`) is **not** the default. Nothing here is a current output, and +nothing here is regenerated by any command. The reproduce commands inside the +sub-READMEs show the original `reports/...` paths they were run with. + +## What the experiments showed + +1. **Stricter marker resolution lowered agreement with the provisional + mappings.** With the same 80 provisional cases and 826-term axiom index, + top-5 agreement fell from 19/80 (legacy) to 16/80 (explicit-policy + resolver), and mean reciprocal rank fell from 0.152 to 0.108. + See [resolver-refinement/](resolver-refinement/README.md). +2. **The drop came from evidence the stricter rules removed**, not from the + alias additions or duplicate-clause fixes. Withholding generic CD3/CD8 + component assertions lost support for the expected targets and removed + contradictions that had been keeping implausible competitors (e.g. + CL:0002000) out of the top ranks. See [regression-triage/](regression-triage/README.md). +3. **One narrow correction was kept.** CL asserts the *whole* CD8 coreceptor + (PR:000025402) on CL:0000625, which is a different case from inferring a + complex from its alpha chain. The rule `whole_cd8_surface_positive_v1` in + `src/soulcap_cl_mapping/marker_resolution.py` restores it in opt-in mode + only. Top-5 agreement stayed at 16/80, so this is not a validated ranking + improvement. See [regression-followup/](regression-followup/README.md). + +All of these metrics measure agreement with **provisional** (unreviewed) +mappings. None of them measures biological accuracy. + +## Contents + +| Folder / file | What it is | +|---|---| +| [evaluation-legacy/](evaluation-legacy/matcher_evaluation.md) | Controlled legacy-mode evaluation (2026-09-10). Canonical copy of the legacy `.md`/`.tsv`. | +| [evaluation-alias/](evaluation-alias/matcher_evaluation.md) | Alias/protein-aware evaluation (marker resolution on, no lexical expansion, 2026-09-10). Its `.md` is byte-identical to the legacy one because the headline metrics did not change; the per-case `.tsv` differs. | +| [resolver-refinement/](resolver-refinement/README.md) | Legacy vs explicit-policy resolver comparison (2026-09-11), plus the enhanced SSSOM export and audit summary. | +| [regression-triage/](regression-triage/README.md) | Eight-way offline diagnostic isolating which resolver change caused the ranking regression (2026-09-18). | +| [regression-followup/](regression-followup/README.md) | Evidence review of the three lost top-5 targets and the scoped CD8 correction (2026-09-18). | +| [candidate_cl_mappings_enhanced.tsv](candidate_cl_mappings_enhanced.tsv) | Batch candidate list from `soulcap-match --batch --marker-map` (opt-in mode). | + +## What was removed on 2026-09-28 + +To keep the repository small, only the human-readable summaries (`.md`, `.tsv`, +READMEs) were kept. These were removed from the tree and can be recovered from +git history: + +| Removed | Recover with | +|---|---| +| All `matcher_evaluation.json` files, `regression_triage.json`, the resolver-refinement audit dashboard/JSON, `pre_refinement_evaluation.json` | `git show 4dfc726:reports/` | +| `matcher_evaluation_baseline.json` (the original pre-resolver baseline) | `git show f1e0772:reports/matcher_evaluation_baseline.json` | +| `regression-followup/legacy/` and `resolver-refinement/legacy/` `.md`/`.tsv` | Byte-identical to `evaluation-legacy/` (SHA-256 checked) | diff --git a/reports/candidate_cl_mappings_enhanced.tsv b/archive/2026-09_resolver_experiments/candidate_cl_mappings_enhanced.tsv similarity index 100% rename from reports/candidate_cl_mappings_enhanced.tsv rename to archive/2026-09_resolver_experiments/candidate_cl_mappings_enhanced.tsv diff --git a/reports/evaluation-alias/matcher_evaluation.md b/archive/2026-09_resolver_experiments/evaluation-alias/matcher_evaluation.md similarity index 100% rename from reports/evaluation-alias/matcher_evaluation.md rename to archive/2026-09_resolver_experiments/evaluation-alias/matcher_evaluation.md diff --git a/reports/evaluation-alias/matcher_evaluation.tsv b/archive/2026-09_resolver_experiments/evaluation-alias/matcher_evaluation.tsv similarity index 100% rename from reports/evaluation-alias/matcher_evaluation.tsv rename to archive/2026-09_resolver_experiments/evaluation-alias/matcher_evaluation.tsv diff --git a/reports/evaluation-legacy/matcher_evaluation.md b/archive/2026-09_resolver_experiments/evaluation-legacy/matcher_evaluation.md similarity index 100% rename from reports/evaluation-legacy/matcher_evaluation.md rename to archive/2026-09_resolver_experiments/evaluation-legacy/matcher_evaluation.md diff --git a/reports/evaluation-legacy/matcher_evaluation.tsv b/archive/2026-09_resolver_experiments/evaluation-legacy/matcher_evaluation.tsv similarity index 100% rename from reports/evaluation-legacy/matcher_evaluation.tsv rename to archive/2026-09_resolver_experiments/evaluation-legacy/matcher_evaluation.tsv diff --git a/reports/regression-followup/README.md b/archive/2026-09_resolver_experiments/regression-followup/README.md similarity index 98% rename from reports/regression-followup/README.md rename to archive/2026-09_resolver_experiments/regression-followup/README.md index 0e94396..944e5cd 100644 --- a/reports/regression-followup/README.md +++ b/archive/2026-09_resolver_experiments/regression-followup/README.md @@ -96,7 +96,7 @@ tie bounds are 59–139 for the first two and 114–120 for the third. These are change is not evidence of general improvement. Legacy mode remains the default. - [Corrected evaluation](corrected/matcher_evaluation.md) -- [Fresh legacy control](legacy/matcher_evaluation.md) +- [Fresh legacy control](../evaluation-legacy/matcher_evaluation.md) (this run's `.md`/`.tsv` were byte-identical to `evaluation-legacy/` and were deduplicated on 2026-09-28) - [Archived strict-before evaluation](../resolver-refinement/enhanced/matcher_evaluation.md) - [Earlier eight-way regression triage](../regression-triage/README.md) diff --git a/reports/regression-followup/corrected/matcher_evaluation.md b/archive/2026-09_resolver_experiments/regression-followup/corrected/matcher_evaluation.md similarity index 100% rename from reports/regression-followup/corrected/matcher_evaluation.md rename to archive/2026-09_resolver_experiments/regression-followup/corrected/matcher_evaluation.md diff --git a/reports/regression-followup/corrected/matcher_evaluation.tsv b/archive/2026-09_resolver_experiments/regression-followup/corrected/matcher_evaluation.tsv similarity index 100% rename from reports/regression-followup/corrected/matcher_evaluation.tsv rename to archive/2026-09_resolver_experiments/regression-followup/corrected/matcher_evaluation.tsv diff --git a/reports/regression-followup/mapping_review.tsv b/archive/2026-09_resolver_experiments/regression-followup/mapping_review.tsv similarity index 100% rename from reports/regression-followup/mapping_review.tsv rename to archive/2026-09_resolver_experiments/regression-followup/mapping_review.tsv diff --git a/reports/regression-triage/README.md b/archive/2026-09_resolver_experiments/regression-triage/README.md similarity index 92% rename from reports/regression-triage/README.md rename to archive/2026-09_resolver_experiments/regression-triage/README.md index 190d9da..0079563 100644 --- a/reports/regression-triage/README.md +++ b/archive/2026-09_resolver_experiments/regression-triage/README.md @@ -44,7 +44,7 @@ Production scoring, biological policies, mappings, and existing exports were not changed by this investigation. - [Full report: eight runs, boundary cases, and all rank changes](regression_triage.md) -- [JSON: profiles, targets, competitor scores, axiom and policy evidence, paired factor effects, hashes](regression_triage.json) +- JSON: profiles, targets, competitor scores, axiom and policy evidence, paired factor effects, hashes. Removed from the tree on 2026-09-28 to save space; recover with `git show 4dfc726:reports/regression-triage/regression_triage.json` - [TSV: every case's rank in every run](regression_triage.tsv) Reproduce with `uv run python -m soulcap_cl_mapping.regression_triage`. diff --git a/reports/regression-triage/regression_triage.md b/archive/2026-09_resolver_experiments/regression-triage/regression_triage.md similarity index 100% rename from reports/regression-triage/regression_triage.md rename to archive/2026-09_resolver_experiments/regression-triage/regression_triage.md diff --git a/reports/regression-triage/regression_triage.tsv b/archive/2026-09_resolver_experiments/regression-triage/regression_triage.tsv similarity index 100% rename from reports/regression-triage/regression_triage.tsv rename to archive/2026-09_resolver_experiments/regression-triage/regression_triage.tsv diff --git a/reports/resolver-refinement/README.md b/archive/2026-09_resolver_experiments/resolver-refinement/README.md similarity index 70% rename from reports/resolver-refinement/README.md rename to archive/2026-09_resolver_experiments/resolver-refinement/README.md index 73eba39..ec8b8b1 100644 --- a/reports/resolver-refinement/README.md +++ b/archive/2026-09_resolver_experiments/resolver-refinement/README.md @@ -17,18 +17,19 @@ withholds component/family/reagent assertions and incompatible protein identitie it also fixes compatible duplicate alias ownership and double-counted clauses. The generic comparison marks mode/input differences as non-equivalent by design. -The [per-marker audit](../marker_resolution_audit.md) reports six normalized +The [per-marker audit](../../../reports/marker_resolution_audit.md) reports six normalized marker groups gaining axiom links and eleven losing links. None of the 80 mapping-level support status categories changed, although their detailed evidence and candidate rankings can differ. Inspect the JSON evidence before accepting any representation or ranking change. -- [Legacy evaluation](legacy/matcher_evaluation.md) +- [Legacy evaluation](../evaluation-legacy/matcher_evaluation.md) (byte-identical copy; deduplicated 2026-09-28) - [Enhanced evaluation](enhanced/matcher_evaluation.md) - [Enhanced mapping review](enhanced.sssom.md) -- [Enhanced audit dashboard](audit/audit_dashboard.html) -- `pre_refinement_evaluation.json` preserves the prior combined lexical/alias run; - it is not the controlled legacy comparator used above. +- [Enhanced audit summary](audit/audit_summary.md) (dashboard HTML/JSON removed 2026-09-28; recover with `git show 4dfc726:reports/resolver-refinement/audit/audit_dashboard.html`) +- `pre_refinement_evaluation.json` preserved the prior combined lexical/alias run; + it is not the controlled legacy comparator used above. Removed 2026-09-28; recover with + `git show 4dfc726:reports/resolver-refinement/pre_refinement_evaluation.json`. Source data, existing marker identifiers, mapping decisions, and the default SSSOM export were not changed. Enhanced SSSOM and its input-hash manifest are diff --git a/reports/resolver-refinement/audit/audit_summary.md b/archive/2026-09_resolver_experiments/resolver-refinement/audit/audit_summary.md similarity index 100% rename from reports/resolver-refinement/audit/audit_summary.md rename to archive/2026-09_resolver_experiments/resolver-refinement/audit/audit_summary.md diff --git a/reports/resolver-refinement/enhanced.sssom.md b/archive/2026-09_resolver_experiments/resolver-refinement/enhanced.sssom.md similarity index 100% rename from reports/resolver-refinement/enhanced.sssom.md rename to archive/2026-09_resolver_experiments/resolver-refinement/enhanced.sssom.md diff --git a/reports/resolver-refinement/enhanced.sssom.provenance.json b/archive/2026-09_resolver_experiments/resolver-refinement/enhanced.sssom.provenance.json similarity index 100% rename from reports/resolver-refinement/enhanced.sssom.provenance.json rename to archive/2026-09_resolver_experiments/resolver-refinement/enhanced.sssom.provenance.json diff --git a/reports/resolver-refinement/enhanced.sssom.tsv b/archive/2026-09_resolver_experiments/resolver-refinement/enhanced.sssom.tsv similarity index 100% rename from reports/resolver-refinement/enhanced.sssom.tsv rename to archive/2026-09_resolver_experiments/resolver-refinement/enhanced.sssom.tsv diff --git a/reports/resolver-refinement/enhanced/matcher_evaluation.md b/archive/2026-09_resolver_experiments/resolver-refinement/enhanced/matcher_evaluation.md similarity index 100% rename from reports/resolver-refinement/enhanced/matcher_evaluation.md rename to archive/2026-09_resolver_experiments/resolver-refinement/enhanced/matcher_evaluation.md diff --git a/reports/resolver-refinement/enhanced/matcher_evaluation.tsv b/archive/2026-09_resolver_experiments/resolver-refinement/enhanced/matcher_evaluation.tsv similarity index 100% rename from reports/resolver-refinement/enhanced/matcher_evaluation.tsv rename to archive/2026-09_resolver_experiments/resolver-refinement/enhanced/matcher_evaluation.tsv diff --git a/reports/fall_2026_semester_plan.html b/docs/planning/fall_2026_semester_plan.html similarity index 100% rename from reports/fall_2026_semester_plan.html rename to docs/planning/fall_2026_semester_plan.html diff --git a/reports/fall_2026_semester_plan.md b/docs/planning/fall_2026_semester_plan.md similarity index 100% rename from reports/fall_2026_semester_plan.md rename to docs/planning/fall_2026_semester_plan.md diff --git a/reports/fall_2026_semester_plan.pdf b/docs/planning/fall_2026_semester_plan.pdf similarity index 100% rename from reports/fall_2026_semester_plan.pdf rename to docs/planning/fall_2026_semester_plan.pdf diff --git a/reports/fall_2026_sprint_backlog.md b/docs/planning/fall_2026_sprint_backlog.md similarity index 97% rename from reports/fall_2026_sprint_backlog.md rename to docs/planning/fall_2026_sprint_backlog.md index 845f806..9164667 100644 --- a/reports/fall_2026_sprint_backlog.md +++ b/docs/planning/fall_2026_sprint_backlog.md @@ -3,7 +3,7 @@ Sprint-level breakdown of the Fall 2026 (Oct–Dec) working plan prepared for Dr. Alexander Diehl, baselined 2026-09-18. Every item from that plan is expanded into concrete sub-tasks with acceptance criteria, grounded in -[ROADMAP.md](../ROADMAP.md), [gaps.tsv](gaps.tsv), and issues #5, #6, #7, +[ROADMAP.md](../../ROADMAP.md), [gaps.tsv](../../reports/gaps.tsv), and issues #5, #6, #7, #12, #13, #14 as they stood on that date. **No scope beyond those sources** — this is a task breakdown of already-agreed work, not a new plan. An interactive version of this backlog also exists as a published Claude @@ -139,7 +139,7 @@ evidence review; curator sign-off pending" — three flagged mappings and five marker-representation holds, none of them a coding task. 1. Walk a curator through the three flagged cases in - `reports/regression-followup/mapping_review.tsv`: SC000063 (CL:0000625, + `archive/2026-09_resolver_experiments/regression-followup/mapping_review.tsv`: SC000063 (CL:0000625, Broad — lineage mismatch), SC000067 (CL:0000625, Exact — OR-gate equivalence unconfirmed), SC000073 (CL:0000803, Exact — missing tissue context). @@ -195,7 +195,7 @@ lane per the existing division of labor. Monocyte doubles as evidence for reachable, falling back to `soulcap-europepmc` when it isn't. 3. Mine the `OMIPs` tab as a secondary source when the reference set alone comes up short. -4. Write `reports/literature/_markers.md` with verbatim, +4. Write `literature/_markers.md` with verbatim, source-checked quotes — the PreToolUse hook blocks the write if any quote isn't in the snippet cache. 5. For monocyte specifically: cross-reference #12's requested corrections @@ -313,7 +313,7 @@ September's snapshot as the standing reference. `audit_summary.md`, and `audit_data.json`. 2. Re-run `uv run soulcap-evaluate` for a refreshed matcher evaluation report. 3. Diff both against the September baselines in - `reports/regression-followup/` and `reports/resolver-refinement/` — any + `archive/2026-09_resolver_experiments/regression-followup/` and `archive/2026-09_resolver_experiments/resolver-refinement/` — any metric regression must be explained, not silently accepted. **Acceptance criteria:** dashboard and evaluation artifacts carry a December diff --git a/reports/literature/b_cell_markers.md b/literature/b_cell_markers.md similarity index 100% rename from reports/literature/b_cell_markers.md rename to literature/b_cell_markers.md diff --git a/reports/literature/dc_markers.md b/literature/dc_markers.md similarity index 100% rename from reports/literature/dc_markers.md rename to literature/dc_markers.md diff --git a/reports/literature/gdt_mait_markers.md b/literature/gdt_mait_markers.md similarity index 100% rename from reports/literature/gdt_mait_markers.md rename to literature/gdt_mait_markers.md diff --git a/reports/literature/ilc_markers.md b/literature/ilc_markers.md similarity index 100% rename from reports/literature/ilc_markers.md rename to literature/ilc_markers.md diff --git a/reports/literature/inkt_markers.md b/literature/inkt_markers.md similarity index 100% rename from reports/literature/inkt_markers.md rename to literature/inkt_markers.md diff --git a/reports/literature/nk_cell_markers.md b/literature/nk_cell_markers.md similarity index 100% rename from reports/literature/nk_cell_markers.md rename to literature/nk_cell_markers.md diff --git a/reports/literature/t_cell_markers.md b/literature/t_cell_markers.md similarity index 100% rename from reports/literature/t_cell_markers.md rename to literature/t_cell_markers.md diff --git a/reports/README.md b/reports/README.md new file mode 100644 index 0000000..fb5def3 --- /dev/null +++ b/reports/README.md @@ -0,0 +1,72 @@ +# reports/ + +Current outputs only. Every tracked file in this folder is listed below. +Old experiment runs live in [archive/](../archive/2026-09_resolver_experiments/README.md), +literature evidence in [literature/](../literature/), and planning documents in +[docs/planning/](../docs/planning/). + +**Generated** files are rewritten by the command shown; never hand-edit them. +**Curated** files are maintained by hand (or by a skill) and cannot be regenerated. + +## Mapping proposals + +| File | What it is | Produced by | Type | +|---|---|---|---| +| [candidate_cl_mappings.sssom.tsv](candidate_cl_mappings.sssom.tsv) | Proposed SOULCAP→CL mappings in standard SSSOM format, with per-mapping marker evidence as JSON in `comment` | `uv run soulcap-sssom` (from [mappings/curated_mappings.tsv](../mappings/curated_mappings.tsv)) | Generated | +| [candidate_cl_mappings.md](candidate_cl_mappings.md) | Readable view of the same rows (Milestone 4 deliverable) | `uv run soulcap-sssom` | Generated | +| [candidate_cl_mappings.sssom.provenance.json](candidate_cl_mappings.sssom.provenance.json) | SHA-256 hashes of the inputs used for the export | `uv run soulcap-sssom` | Generated | +| [candidate_cl_mappings_narrative.md](candidate_cl_mappings_narrative.md) | Pre-migration rationale and sheet-confirmation notes, kept for provenance | Hand-written (frozen archive of old rationale) | Curated | +| [candidate_cl_mappings_batch.tsv](candidate_cl_mappings_batch.tsv) | Marker-axiom-only candidate shortlist for every SOULCAP row. Unreviewed draft | `uv run soulcap-match --batch` | Generated | +| [candidate_cl_mappings_agreement.tsv](candidate_cl_mappings_agreement.tsv) | Marker vs lexical agreement shortlist. **Stale**: predates the parser/identity migration; regenerate before use | `uv run soulcap-match --batch --lexical` | Generated | + +## Audit and evaluation + +| File | What it is | Produced by | Type | +|---|---|---|---| +| [audit_dashboard.html](audit_dashboard.html) | Offline, filterable dashboard of entities, proposals, findings, marker coverage, gaps and provenance | `uv run soulcap-audit` | Generated | +| [audit_summary.md](audit_summary.md) | Text summary of the same audit | `uv run soulcap-audit` | Generated | +| [audit_data.json](audit_data.json) | Data behind the dashboard | `uv run soulcap-audit` | Generated | +| [matcher_evaluation.md](matcher_evaluation.md) / `.tsv` / `.json` | How well the matcher retrieves the proposed CL targets (provisional agreement, not accuracy) | `uv run soulcap-evaluate` | Generated | +| [marker_resolution_audit.md](marker_resolution_audit.md) / `.tsv` / `.json` | Effect of the per-token resolution policies in [marker_mappings/marker_resolution.tsv](../marker_mappings/marker_resolution.tsv) on axiom links and mapping evidence | `uv run soulcap-resolution-audit` | Generated | + +`uv run python -m soulcap_cl_mapping.regression_triage` writes to +`reports/regression-triage/` by default. No current run is committed; the +September 2026 run is [archived](../archive/2026-09_resolver_experiments/regression-triage/README.md). + +## Source data checks and SOULCAP feedback + +| File | What it is | Produced by | Type | +|---|---|---|---| +| [marker_validation.md](marker_validation.md) | Marker strings that fail the EBNF grammar | `uv run soulcap-sync` or `uv run soulcap-validate` | Generated | +| [marker_string_issues.md](marker_string_issues.md) | Reviewed list of marker-string errors and inconsistencies in the sheet | Hand-written | Curated | +| [proposed_marker_fixes.xlsx](proposed_marker_fixes.xlsx) | Proposed corrections to send to SOULCAP | Hand-written | Curated | + +## Cell Ontology reference snapshots + +These are generated, but they are inputs to other code and need network access +(or a specific local database) to rebuild, so they stay committed. + +| File | What it is | Produced by | Type | +|---|---|---|---| +| [cl_pro_relationships.tsv](cl_pro_relationships.tsv) | One row per (CL cell type, relation, PRO marker) axiom | `uv run soulcap-cl-pro` (Ubergraph SPARQL) | Generated snapshot | +| [cl_pro_relationships.md](cl_pro_relationships.md) | Readable view: each CL cell type with its PRO markers grouped by sense | `uv run soulcap-cl-pro` | Generated snapshot | +| [cl_lexical_cache.json](cl_lexical_cache.json) | Active CL labels and exact synonyms for offline lexical matching | `uv run soulcap-cache-terms` (local OAK database) | Generated snapshot | + +## Gaps and upstream issues + +| File | What it is | Produced by | Type | +|---|---|---|---| +| [gaps.tsv](gaps.tsv) | Cases with no good CL match, CL/marker conflicts, CL axiom gaps, or sheet data problems. Filed as GitHub issues by the `gap-issue-filing` skill | Hand-maintained | Curated | +| [cl_term_issues.md](cl_term_issues.md) | Proposed Cell Ontology corrections found during mapping | Hand-maintained | Curated | +| [pro_marker_species_support.tsv](pro_marker_species_support.tsv) | Whether literature supports each CL PRO marker as human, mouse, or both (issue #11) | `pro-marker-species-support` skill, quotes verified verbatim | Curated | + +## Not tracked + +`reports/citation_traversal/` holds snippet caches and summaries from the +`citation-traversal` skill. It is gitignored and regenerable. + +## Adding a file here + +Put a new output here only if it is a current result that people should read. +Add a row to this README in the same commit. One-off experiments go in +`archive/_/` with their own README. diff --git a/reports/candidate_cl_mappings_narrative.md b/reports/candidate_cl_mappings_narrative.md index 8144958..dfa6b81 100644 --- a/reports/candidate_cl_mappings_narrative.md +++ b/reports/candidate_cl_mappings_narrative.md @@ -46,7 +46,7 @@ mapping — it reflects a real CL gap (see below), not a poor match. - Literature: "Natural killer cells are prototypic members of the innate lymphoid cell (ILC) family and characterized in humans by expression of the phenotypic marker CD56 in the absence of CD3." — Van Acker HH et al. 2017 - (PMID:28791027) — [reports/literature/nk_cell_markers.md](literature/nk_cell_markers.md) + (PMID:28791027) — [literature/nk_cell_markers.md](../literature/nk_cell_markers.md) **CL gap flagged:** `CL:0000623` asserts no positive marker axiom at all (only CD14-/CD19-/CD3-/CD20- negatives), even though CD56 positivity is the @@ -75,7 +75,7 @@ negative-exclusion markers; the CD16-negative axiom aligns with SOULCAP's **Evidence:** Marker→gene as above (CD56 → NCAM1); CD16 → FCGR3A (see [marker_mappings/marker_protein_gene.csv](../marker_mappings/marker_protein_gene.csv)). Literature distinguishing CD56bright/CD56dim NK subsets: -[reports/literature/nk_cell_markers.md](literature/nk_cell_markers.md). +[literature/nk_cell_markers.md](../literature/nk_cell_markers.md). --- @@ -104,7 +104,7 @@ yet based on current `cl_pro_relationships` data. Flagged for follow-up, not yet logged as a formal CL gap. **Evidence:** Marker→gene as above; literature on CD16+CD56dim cytotoxic NK -subset: [reports/literature/nk_cell_markers.md](literature/nk_cell_markers.md). +subset: [literature/nk_cell_markers.md](../literature/nk_cell_markers.md). --- diff --git a/reports/cl_term_issues.md b/reports/cl_term_issues.md index 8c0ef14..10e3165 100644 --- a/reports/cl_term_issues.md +++ b/reports/cl_term_issues.md @@ -80,7 +80,7 @@ cells. ### Natural killer cell missing CD56 marker axiom — CL:0000623 **Repo issue:** not yet filed -**Reference:** SOULCAP `NK` row ([data/marker_combinations.csv](../data/marker_combinations.csv), regenerate via `uv run soulcap-sync`); literature in [reports/literature/nk_cell_markers.md](literature/nk_cell_markers.md) +**Reference:** SOULCAP `NK` row ([data/marker_combinations.csv](../data/marker_combinations.csv), regenerate via `uv run soulcap-sync`); literature in [literature/nk_cell_markers.md](../literature/nk_cell_markers.md) **Status:** Drafted during Milestone 4 candidate mapping work — not yet filed as a repo issue #### CL:0000623 — "natural killer cell" diff --git a/reports/evaluation-alias/matcher_evaluation.json b/reports/evaluation-alias/matcher_evaluation.json deleted file mode 100644 index 6757c43..0000000 --- a/reports/evaluation-alias/matcher_evaluation.json +++ /dev/null @@ -1,83216 +0,0 @@ -{ - "schema_version": 1, - "generated_utc": "2026-09-10T19:46:00.594110+00:00", - "inputs": { - "data/marker_combinations.csv": "29b476e499ac402094b3dbccc410d052010a9b804ca9865e2624dda3ba9bfc44", - "mappings/soulcap_entities.tsv": "b7d312081b5279669599ead19d3d201a1003ff4978eb814302f16c9783b659a8", - "mappings/curated_mappings.tsv": "2ce1d078ed3d374b0c96d04184bb3520d37a1970415ad08584e33bc26e31434e", - "reports/cl_pro_relationships.tsv": "293edb6a7dc435caf9d85a758425be9305eb4eb00c877074fdec4593ef0d1b3c", - "benchmark": "bb1ab9905205a1ab8738b6e9da0a8db382ad3a778eae1103a1279a75335aa706", - "marker_map": "4d1982db77c57a9a9e43b1fc883c5b0b32f0d69184e081764880baacb37992b7" - }, - "benchmark_path": "C:\\Users\\s28al\\SOULCAP_CL_Mapping\\mappings\\matcher_benchmark.tsv", - "matcher": { - "version": "0.1.0", - "source_hashes": { - "cl_match.py": "1bec5e9d880cfd34574ae55dfde29d4b62c745e9649a9b5d292d5697d848649f", - "phenotype.py": "6d3e7e59b884365fa48596fe1365b8630053b70a6259bb0e8f42413a55a9514a", - "marker_syntax.py": "e40620b1d804eec3c1f05251716092abd7f5a273e11ba91ce61a3345b1872ade", - "registry.py": "a225ca650e0278378566bf7134b3d8daa33dabee0c61c3d479d8affddf7a25fd", - "evaluation.py": "ad643e2b29d58e07d3e16b9c8aca15723f160cad346c751597cf52dec9526b25", - "audit.py": "86a7f3978446fe1122eec579b5a4c41ea3adf0086b5bcb642c195104e4125d4d", - "candidate_index.py": "b8ede03e76d0df09fd8735d1d45178c77a977c6ae40a61c38478bbb4be737ddc" - } - }, - "config": { - "ks": [ - 1, - 3, - 5 - ], - "ranking": "production order, including disqualified candidates", - "ties": "primary metrics use production order; bounds report tie sensitivity", - "denominator": "all cohort cases, including unscorable profiles and absent targets", - "marker_resolution": true, - "local_lexical": false, - "lexical_limit": 20, - "lexical_min_jaccard": 0.5 - }, - "candidate_count": 826, - "marker_resolution_issues": [ - { - "marker": "CD1D-A-GALCER", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "CD57", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "HLA-DR", - "reason": "complex_or_reagent", - "pro_ids": [ - "PR:000002015" - ] - }, - { - "marker": "IGA", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "IGD", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "IGE", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "IGG", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "IGM", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "MR1", - "reason": "complex_or_reagent", - "pro_ids": [ - "PR:Q95460" - ] - }, - { - "marker": "TCR", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "TCRAB", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "TCRGD", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "TETRAMER", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "V", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "DELTA", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "DELTA1", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "GAMMA", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "CCR4", - "reason": "ambiguous_alias", - "owners": [ - "CCR4", - "CD194" - ] - }, - { - "marker": "CD194", - "reason": "ambiguous_alias", - "owners": [ - "CCR4", - "CD194" - ] - }, - { - "marker": "CCR6", - "reason": "ambiguous_alias", - "owners": [ - "CCR6", - "CD196" - ] - }, - { - "marker": "CD196", - "reason": "ambiguous_alias", - "owners": [ - "CCR6", - "CD196" - ] - }, - { - "marker": "CD183", - "reason": "ambiguous_alias", - "owners": [ - "CD183", - "CXCR3" - ] - }, - { - "marker": "CXCR3", - "reason": "ambiguous_alias", - "owners": [ - "CD183", - "CXCR3" - ] - }, - { - "marker": "CD185", - "reason": "ambiguous_alias", - "owners": [ - "CD185", - "CXCR5" - ] - }, - { - "marker": "CXCR5", - "reason": "ambiguous_alias", - "owners": [ - "CD185", - "CXCR5" - ] - } - ], - "cases": [ - { - "case_id": "provisional/SOULCAP:SC000001/Exact", - "cohort": "provisional", - "subject_id": "SOULCAP:SC000001", - "match_type": "Exact", - "targets": [ - "CL:0000623" - ], - "evidence_reference": "mappings/curated_mappings.tsv", - "uncertain": false, - "rank": 6, - "rank_best": 6, - "rank_worst": 32, - "missing_targets": [], - "candidates": [ - { - "cl_id": "CL:0002338", - "label": "CD56-positive, CD161-positive immature natural killer cell, human", - "score": 23, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD34-", - "CD3-", - "CD19-", - "CD56+ (1 of 2 alt.)" - ], - "gaps": [ - "CD45+", - "CD127-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD123-", - "CD33-/CD64- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 3, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001003", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD34", - "tokens": [ - "CD34" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001003", - "tokens": [ - "CD34" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3", - "tokens": [ - "CD3" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001020", - "tokens": [ - "CD3" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001289", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001889", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD14", - "tokens": [ - "CD14" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001889", - "tokens": [ - "CD14" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001024", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001381", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD122", - "tokens": [ - "CD122" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001874", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:000002065", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD117", - "tokens": [ - "CD117" - ] - }, - { - "via": "pro_id", - "pr": "PR:000002065", - "tokens": [ - "CD117" - ] - } - ] - } - ] - }, - { - "cl_id": "CL:0000938", - "label": "CD16-negative, CD56-bright natural killer cell, human", - "score": 19, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD3-", - "CD19-", - "CD56+ (hi) (1 of 2 alt.)" - ], - "gaps": [ - "CD34-", - "CD45+", - "CD127-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD123-", - "CD33-/CD64- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 3, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001024", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3", - "tokens": [ - "CD3" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001020", - "tokens": [ - "CD3" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001289", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - }, - { - "sense": "negative", - 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CL:0000623 reports/cl_pro_relationships.md; reports/literature/nk_cell_markers.md; reports/cl_term_issues.md#natural-killer-cell-missing-cd56-marker-axiom--cl0000623 open (not yet filed) 2026-07-22 +NK Natural Killer Cell cl_axiom_gap CL:0000623 asserts only negative exclusion markers (CD14-/CD19-/CD3-/CD20-); the field-standard defining positive marker CD56 is absent from its own axioms, though present on its child terms. CL:0000623 reports/cl_pro_relationships.md; literature/nk_cell_markers.md; reports/cl_term_issues.md#natural-killer-cell-missing-cd56-marker-axiom--cl0000623 open (not yet filed) 2026-07-22 NK1 / NK3 Natural Killer Cell 1 / Natural Killer Cell 3 cl_axiom_gap CL:0000939 (CD16-positive, CD56-dim NK cell, human) does not distinguish CD57-negative (NK1) from CD57-positive (NK3) substates; both SOULCAP rows currently map to the same CL term at Broad match type. CL:0000939 reports/candidate_cl_mappings_narrative.md#ctnk--nk1--nk3--cytotoxic-natural-killer-cell-cd16-positive open (not yet filed) 2026-07-22 ILC1 Innate Lymphoid Cell 1 cl_axiom_gap No human-specific "group 1 innate lymphoid cell" CL term exists, unlike group 2 (CL:0001081) and group 3 (CL:0001078); confirmed by direct OLS4 search returning zero hits for the human-qualified query. CL:0001067 reports/cl_term_issues.md#missing-human-specific-group-1-innate-lymphoid-cell-term filed_as_issue https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/14 2026-07-23 Transitional Transitional B cell no_reasonable_cl_match SOULCAP row has all four marker columns (Required/Ideal exclusion, Required/Ideal phenotypic markers) completely empty in the master sheet — there is no marker definition to match against at all, so no CL candidate can be derived from markers. Distinct from the more specific "T3" (Transitional B cell 3) row, which does have marker data. (none) reports/candidate_cl_mappings_batch.tsv (note column); data/marker_combinations.csv open (not yet filed) 2026-07-24 diff --git a/reports/matcher_evaluation_baseline.json b/reports/matcher_evaluation_baseline.json deleted file mode 100644 index b99d684..0000000 --- a/reports/matcher_evaluation_baseline.json +++ /dev/null @@ -1,12326 +0,0 @@ -{ - "schema_version": 1, - "generated_utc": "2026-09-10T19:23:45.791616+00:00", - "inputs": { - "data/marker_combinations.csv": "29b476e499ac402094b3dbccc410d052010a9b804ca9865e2624dda3ba9bfc44", - "mappings/soulcap_entities.tsv": "b7d312081b5279669599ead19d3d201a1003ff4978eb814302f16c9783b659a8", - "mappings/curated_mappings.tsv": "2ce1d078ed3d374b0c96d04184bb3520d37a1970415ad08584e33bc26e31434e", - "reports/cl_pro_relationships.tsv": "293edb6a7dc435caf9d85a758425be9305eb4eb00c877074fdec4593ef0d1b3c", - "benchmark": "bb1ab9905205a1ab8738b6e9da0a8db382ad3a778eae1103a1279a75335aa706" - }, - "benchmark_path": "C:\\Users\\s28al\\SOULCAP_CL_Mapping\\mappings\\matcher_benchmark.tsv", - 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], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false - }, - { - "cl_id": "CL:0002343", - "label": "decidual natural killer cell, human", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false - } - ], - "target_results": [ - { - "cl_id": "CL:0000913", - "label": "effector memory CD8-positive, alpha-beta T cell", - "score": 3, - "matched": [], - "gaps": [ - "CD14-/CD33-/CD64- (no axiom on any alt.)", - "CD19-/CD20- (no axiom on any alt.)", - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 3, - "disqualified": false, - "rank": 239, - "rank_best": 238, - "rank_worst": 247 - } - ], - "status": "below_top_5", - "note": "" - }, - { - "case_id": "provisional/SOULCAP:SC000103/Exact", - "cohort": "provisional", - "subject_id": "SOULCAP:SC000103", - "match_type": "Exact", - "targets": [ - "CL:4030002" - ], - "evidence_reference": "mappings/curated_mappings.tsv", - "uncertain": false, - "rank": null, - "rank_best": null, - "rank_worst": null, - "missing_targets": [ - "CL:4030002" - ], - "candidates": [ - { - "cl_id": "CL:0001057", - "label": "myeloid dendritic cell, human", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false - }, - { - "cl_id": "CL:0002000", - "label": "Kit-positive erythroid progenitor cell", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false - }, - { - "cl_id": "CL:0000938", - "label": "CD16-negative, CD56-bright natural killer cell, human", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false - }, - { - "cl_id": "CL:0001024", - "label": "CD34-positive, CD38-negative hematopoietic stem cell", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false - }, - { - "cl_id": "CL:0002343", - "label": "decidual natural killer cell, human", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false - } - ], - "target_results": [], - "status": "target_not_in_index", - "note": "" - } - ], - "metrics": { - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.1524095320342756, - "statuses": { - "below_top_5": 42, - "hit_at_5": 19, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0875, - "hit_at_1_optimistic": 0.125, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.15, - "hit_at_3_optimistic": 0.2, - "hit_at_3_pessimistic": 0.0875, - "hit_at_5": 0.2375, - "hit_at_5_optimistic": 0.275, - "hit_at_5_pessimistic": 0.1 - } - }, - "by_relation": { - "reviewed/Exact": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Broad": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Exact": { - "cases": 50, - "mrr": 0.15217520145714408, - "statuses": { - "below_top_5": 26, - "hit_at_5": 12, - "invalid_profile": 6, - "target_not_in_index": 6 - }, - "cases_with_missing_targets": 8, - "top1_disqualified": 0, - "hit_at_1": 0.08, - "hit_at_1_optimistic": 0.14, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.16, - "hit_at_3_optimistic": 0.18, - "hit_at_3_pessimistic": 0.08, - "hit_at_5": 0.24, - "hit_at_5_optimistic": 0.24, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Broad": { - "cases": 30, - "mrr": 0.1528000829961614, - "statuses": { - "hit_at_5": 7, - "below_top_5": 16, - "target_not_in_index": 7 - }, - "cases_with_missing_targets": 7, - "top1_disqualified": 0, - "hit_at_1": 0.1, - "hit_at_1_optimistic": 0.1, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.13333333333333333, - "hit_at_3_optimistic": 0.23333333333333334, - "hit_at_3_pessimistic": 0.1, - "hit_at_5": 0.23333333333333334, - "hit_at_5_optimistic": 0.3333333333333333, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - } - } -} diff --git a/reports/pro_marker_species_support.tsv b/reports/pro_marker_species_support.tsv index 6af1f8b..4bfcec1 100644 --- a/reports/pro_marker_species_support.tsv +++ b/reports/pro_marker_species_support.tsv @@ -1,10 +1,10 @@ cl_id cl_label pr_id pr_label cd_synonym species_support evidence_source citation quote source_ref -CL:0000623 natural killer cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303). reports/literature/nk_cell_markers.md -CL:0000623 natural killer cell PR:000001889 CD14 molecule CD14 (label) human m2_literature_report Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes reports/literature/nk_cell_markers.md -CL:0000624 CD4-positive, alpha-beta T cell PR:000025402 T cell receptor co-receptor CD8 CD8 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ reports/literature/t_cell_markers.md -CL:0000624 CD4-positive, alpha-beta T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ reports/literature/t_cell_markers.md -CL:0000625 CD8-positive, alpha-beta T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8+/CD4−/CCR7+/CD45RA+ reports/literature/t_cell_markers.md -CL:0000625 CD8-positive, alpha-beta T cell PR:000025402 T cell receptor co-receptor CD8 CD8 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8+/CD4−/CCR7+/CD45RA+ reports/literature/t_cell_markers.md +CL:0000623 natural killer cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303). literature/nk_cell_markers.md +CL:0000623 natural killer cell PR:000001889 CD14 molecule CD14 (label) human m2_literature_report Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes literature/nk_cell_markers.md +CL:0000624 CD4-positive, alpha-beta T cell PR:000025402 T cell receptor co-receptor CD8 CD8 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ literature/t_cell_markers.md +CL:0000624 CD4-positive, alpha-beta T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ literature/t_cell_markers.md +CL:0000625 CD8-positive, alpha-beta T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8+/CD4−/CCR7+/CD45RA+ literature/t_cell_markers.md +CL:0000625 CD8-positive, alpha-beta T cell PR:000025402 T cell receptor co-receptor CD8 CD8 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8+/CD4−/CCR7+/CD45RA+ literature/t_cell_markers.md CL:0000771 eosinophil PR:000001254 C-C chemokine receptor type 1 CD191 (exact) insufficient_evidence none CD191/CCR1 not among the markers studied in PMID:38666394 (CCR3/CD193 is, but not CCR1); no other eosinophil-specific CD191 evidence found via targeted EuropePMC search. CL:0000771 eosinophil PR:000001255 C-C chemokine receptor type 3 CD193 (exact) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 CL:0000771 eosinophil PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 @@ -12,18 +12,18 @@ CL:0000771 eosinophil PR:000001343 CD69 molecule CD69 (label) human europepmc_se CL:0000771 eosinophil PR:000005178 CD9 molecule CD9 (label) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 CL:0000775 neutrophil PR:000001479 low affinity immunoglobulin gamma Fc region receptor II CD32 (broad) human europepmc_search Su K et al. 2007 (PMID:17312177; DOI:10.4049/jimmunol.178.5.3272) -- FcγRIIb (CD32B) expression profiling in human circulating leukocytes we found that FcgammaRIIb is expressed on the cell surface of circulating B lymphocytes, monocytes, neutrophils, myeloid dendritic cells (DCs), and at very low levels on plasmacytoid DCs from some donors https://europepmc.org/article/MED/17312177 CL:0000775 neutrophil PR:000001879 leukosialin CD43 (related) insufficient_evidence none CD43 not found in any targeted EuropePMC search in a human-neutrophil-specific context ('CD43 leukosialin human neutrophil' returned unrelated papers). -CL:0000786 plasma cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired reports/literature/b_cell_markers.md -CL:0000786 plasma cell PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired reports/literature/b_cell_markers.md -CL:0000787 memory B cell PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) -- describes the plasmablast/plasma-cell transition boundary, not memory B cells directly, but confirms CD138 as a human B-lineage differentiation marker as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired reports/literature/b_cell_markers.md -CL:0000787 memory B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) Mature B cells typically express both CD19 and CD20. reports/literature/b_cell_markers.md -CL:0000788 naive B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**N**: CD19+ CD27− CD38− CD24− IgD+"" [naive B cell gating entry, Table 1]" reports/literature/b_cell_markers.md -CL:0000788 naive B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) Mature B cells typically express both CD19 and CD20. reports/literature/b_cell_markers.md -CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies. reports/literature/t_cell_markers.md -CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) human m2_literature_report Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies. reports/literature/t_cell_markers.md -CL:0000814 mature NK T cell PR:000001874 KLRB1-like protein human m2_literature_report Lal KG et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) we defined iNKT cell subsets by the co-expression of TCR Vα24 and Vβ11 among CD3+ cells, and further through their expression of CD4 and CD161 reports/literature/inkt_markers.md -CL:0000818 transitional stage B cell PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−) reports/literature/b_cell_markers.md -CL:0000818 transitional stage B cell PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−) reports/literature/b_cell_markers.md -CL:0000818 transitional stage B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none CD20 positivity on transitional B cells is not stated verbatim in reports/literature/b_cell_markers.md -- the report only confirms CD20 on 'mature B cells' generally (Griffin & Rothstein 2012), not the transitional stage specifically. +CL:0000786 plasma cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired literature/b_cell_markers.md +CL:0000786 plasma cell PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired literature/b_cell_markers.md +CL:0000787 memory B cell PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) -- describes the plasmablast/plasma-cell transition boundary, not memory B cells directly, but confirms CD138 as a human B-lineage differentiation marker as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired literature/b_cell_markers.md +CL:0000787 memory B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) Mature B cells typically express both CD19 and CD20. literature/b_cell_markers.md +CL:0000788 naive B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**N**: CD19+ CD27− CD38− CD24− IgD+"" [naive B cell gating entry, Table 1]" literature/b_cell_markers.md +CL:0000788 naive B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) Mature B cells typically express both CD19 and CD20. literature/b_cell_markers.md +CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies. literature/t_cell_markers.md +CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) human m2_literature_report Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies. literature/t_cell_markers.md +CL:0000814 mature NK T cell PR:000001874 KLRB1-like protein human m2_literature_report Lal KG et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) we defined iNKT cell subsets by the co-expression of TCR Vα24 and Vβ11 among CD3+ cells, and further through their expression of CD4 and CD161 literature/inkt_markers.md +CL:0000818 transitional stage B cell PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−) literature/b_cell_markers.md +CL:0000818 transitional stage B cell PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−) literature/b_cell_markers.md +CL:0000818 transitional stage B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none CD20 positivity on transitional B cells is not stated verbatim in literature/b_cell_markers.md -- the report only confirms CD20 on 'mature B cells' generally (Griffin & Rothstein 2012), not the transitional stage specifically. CL:0000860 classical monocyte PR:000001199 C-C chemokine receptor type 2 CD192 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. CL:0000860 classical monocyte PR:000001002 CD19 molecule CD19 (label) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. CL:0000860 classical monocyte PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. @@ -32,47 +32,47 @@ CL:0000875 non-classical monocyte PR:000001206 CX3C chemokine receptor 1 insuff CL:0000875 non-classical monocyte PR:000001002 CD19 molecule CD19 (label) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. CL:0000875 non-classical monocyte PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. CL:0000875 non-classical monocyte PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 reports/literature/t_cell_markers.md -CL:0000898 naive T cell PR:000001318 L-selectin CD62 (exact); CD62L (exact) human m2_literature_report Kamigaichi A et al. 2026 (PMID: 42047825; DOI: 10.1007/s00262-026-04357-4; PMC: PMC13125411) -- confirms CD62L used on human CD4+ T cells, though in a Th1 (not naive-T) context Th1 (CXCR3+CCR4−CCR6− CD62LlowCD4+ T cells) reports/literature/t_cell_markers.md -CL:0000898 naive T cell PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) insufficient_evidence none CD44 not mentioned anywhere in reports/literature/t_cell_markers.md; not found via a targeted EuropePMC search either ('CD44 human naive T cell surface marker' returned unrelated tissue-resident-memory/B-cell papers). -CL:0000898 naive T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ reports/literature/t_cell_markers.md -CL:0000898 naive T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ reports/literature/t_cell_markers.md -CL:0000898 naive T cell PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 reports/literature/t_cell_markers.md -CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 reports/literature/t_cell_markers.md -CL:0000904 central memory CD4-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA− reports/literature/t_cell_markers.md -CL:0000904 central memory CD4-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA− reports/literature/t_cell_markers.md -CL:0000905 effector memory CD4-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7−/CD45RA+ reports/literature/t_cell_markers.md -CL:0000905 effector memory CD4-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7−/CD45RA+ reports/literature/t_cell_markers.md -CL:0000907 central memory CD8-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ reports/literature/t_cell_markers.md -CL:0000907 central memory CD8-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ reports/literature/t_cell_markers.md -CL:0000913 effector memory CD8-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ reports/literature/t_cell_markers.md -CL:0000913 effector memory CD8-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ reports/literature/t_cell_markers.md -CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells. reports/literature/nk_cell_markers.md -CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) CD56bright human NK cells express high levels of CD62L (l-selectin) and CD94 but absent or low levels of CD16 and KIRs reports/literature/nk_cell_markers.md -CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000002015 MHC class II histocompatibility antigen alpha chain DRA human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1) reports/literature/nk_cell_markers.md -CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001319 SLAM family member 5 CD84 (exact) insufficient_evidence none No CD84-on-NK-cell evidence found in reports/literature/nk_cell_markers.md or a targeted EuropePMC search ('CD84 human natural killer cell surface marker' -- top hits were CD84 in MDSCs/breast cancer/CLL, none NK-specific). -CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells. reports/literature/nk_cell_markers.md -CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000002015 MHC class II histocompatibility antigen alpha chain DRA human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1) reports/literature/nk_cell_markers.md -CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) In contrast, CD56dim NK cells are CD16hi and express more KIRs but less CD94 and CD62L; they predominate in PB reports/literature/nk_cell_markers.md -CL:0000960 T3 B cell PR:000001318 L-selectin CD62 (exact); CD62L (exact) insufficient_evidence none CD62L not mentioned in the T3-transitional context in reports/literature/b_cell_markers.md (only mentioned for DN2 B cells: 'lack of CXCR5 and CD62L expression', Sachinidis 2021, a different B cell subset). -CL:0000960 T3 B cell PR:000001338 complement receptor type 2 CD21 (exact) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells reports/literature/b_cell_markers.md -CL:0000960 T3 B cell PR:000001880 low affinity immunoglobulin epsilon Fc receptor CD23 (exact); CD23A (related) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells reports/literature/b_cell_markers.md -CL:0000970 unswitched memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**M**: CD19+ CD27+ CD38−/lo"" [memory B cell gating entry]" reports/literature/b_cell_markers.md -CL:0000972 class switched memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**M**: CD19+ CD27+ CD38−/lo"" [memory B cell gating entry]" reports/literature/b_cell_markers.md -CL:0000980 plasmablast PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**ASC**: CD19+ CD27+ CD38hi"" and ""**M**: CD19+ CD27+ CD38−/lo"" and" reports/literature/b_cell_markers.md -CL:0000980 plasmablast PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**ASC**: CD19+ CD27+ CD38hi"" and ""**M**: CD19+ CD27+ CD38−/lo"" and" reports/literature/b_cell_markers.md -CL:0000980 plasmablast PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired reports/literature/b_cell_markers.md -CL:0000980 plasmablast PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**CD138neg ASC**: CD138−"" and ""**CD138pos ASC**: CD138+"" [gating labels distinguishing" reports/literature/b_cell_markers.md -CL:0000981 double negative memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Sachinidis A & Garyfallos A 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) Double negative (DN) B cells, also known as atypical memory B cells, constitute a B cell population that lacks expression of immunoglobulin D and CD27 memory marker. reports/literature/b_cell_markers.md -CL:0000990 conventional dendritic cell PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123− reports/literature/dc_markers.md -CL:0001058 plasmacytoid dendritic cell, human PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123− reports/literature/dc_markers.md -CL:0001058 plasmacytoid dendritic cell, human PR:000001889 CD14 molecule CD14 (label) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DCs were defined as live, LIN(CD3, CD19, CD56)−CD14−HLA-DR+ cells. reports/literature/dc_markers.md -CL:0001058 plasmacytoid dendritic cell, human PR:000001865 interleukin-3 receptor class 2 alpha chain CD123 (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) pDCs are CD11c− CD123+ cells best characterized for their type I interferon reports/literature/dc_markers.md -CL:0001065 innate lymphoid cell PR:000001002 CD19 molecule CD19 (label) human m2_literature_report Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696) Subsequently we gated out non‐relevant lineages using antibodies against CD3, CD4, TCRαβ, and TCRγδ (T cells), CD19 (B cells) CD14 (monocytes) FcRεR1a (mast cells), BDCA2 (pDCs), CD123 (pDCs, basophils), and CD34 (hematopoietic progenitors). reports/literature/ilc_markers.md -CL:0001065 innate lymphoid cell PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) human m2_literature_report Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696) We gated for lymphocytes, excluded doublets and dead cells and selected CD45+CD3− cells reports/literature/ilc_markers.md +CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 literature/t_cell_markers.md +CL:0000898 naive T cell PR:000001318 L-selectin CD62 (exact); CD62L (exact) human m2_literature_report Kamigaichi A et al. 2026 (PMID: 42047825; DOI: 10.1007/s00262-026-04357-4; PMC: PMC13125411) -- confirms CD62L used on human CD4+ T cells, though in a Th1 (not naive-T) context Th1 (CXCR3+CCR4−CCR6− CD62LlowCD4+ T cells) literature/t_cell_markers.md +CL:0000898 naive T cell PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) insufficient_evidence none CD44 not mentioned anywhere in literature/t_cell_markers.md; not found via a targeted EuropePMC search either ('CD44 human naive T cell surface marker' returned unrelated tissue-resident-memory/B-cell papers). +CL:0000898 naive T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ literature/t_cell_markers.md +CL:0000898 naive T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ literature/t_cell_markers.md +CL:0000898 naive T cell PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 literature/t_cell_markers.md +CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 literature/t_cell_markers.md +CL:0000904 central memory CD4-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA− literature/t_cell_markers.md +CL:0000904 central memory CD4-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA− literature/t_cell_markers.md +CL:0000905 effector memory CD4-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7−/CD45RA+ literature/t_cell_markers.md +CL:0000905 effector memory CD4-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7−/CD45RA+ literature/t_cell_markers.md +CL:0000907 central memory CD8-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ literature/t_cell_markers.md +CL:0000907 central memory CD8-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ literature/t_cell_markers.md +CL:0000913 effector memory CD8-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ literature/t_cell_markers.md +CL:0000913 effector memory CD8-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ literature/t_cell_markers.md +CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells. literature/nk_cell_markers.md +CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) CD56bright human NK cells express high levels of CD62L (l-selectin) and CD94 but absent or low levels of CD16 and KIRs literature/nk_cell_markers.md +CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000002015 MHC class II histocompatibility antigen alpha chain DRA human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1) literature/nk_cell_markers.md +CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001319 SLAM family member 5 CD84 (exact) insufficient_evidence none No CD84-on-NK-cell evidence found in literature/nk_cell_markers.md or a targeted EuropePMC search ('CD84 human natural killer cell surface marker' -- top hits were CD84 in MDSCs/breast cancer/CLL, none NK-specific). +CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells. literature/nk_cell_markers.md +CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000002015 MHC class II histocompatibility antigen alpha chain DRA human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1) literature/nk_cell_markers.md +CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) In contrast, CD56dim NK cells are CD16hi and express more KIRs but less CD94 and CD62L; they predominate in PB literature/nk_cell_markers.md +CL:0000960 T3 B cell PR:000001318 L-selectin CD62 (exact); CD62L (exact) insufficient_evidence none CD62L not mentioned in the T3-transitional context in literature/b_cell_markers.md (only mentioned for DN2 B cells: 'lack of CXCR5 and CD62L expression', Sachinidis 2021, a different B cell subset). +CL:0000960 T3 B cell PR:000001338 complement receptor type 2 CD21 (exact) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells literature/b_cell_markers.md +CL:0000960 T3 B cell PR:000001880 low affinity immunoglobulin epsilon Fc receptor CD23 (exact); CD23A (related) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells literature/b_cell_markers.md +CL:0000970 unswitched memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**M**: CD19+ CD27+ CD38−/lo"" [memory B cell gating entry]" literature/b_cell_markers.md +CL:0000972 class switched memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**M**: CD19+ CD27+ CD38−/lo"" [memory B cell gating entry]" literature/b_cell_markers.md +CL:0000980 plasmablast PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**ASC**: CD19+ CD27+ CD38hi"" and ""**M**: CD19+ CD27+ CD38−/lo"" and" literature/b_cell_markers.md +CL:0000980 plasmablast PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**ASC**: CD19+ CD27+ CD38hi"" and ""**M**: CD19+ CD27+ CD38−/lo"" and" literature/b_cell_markers.md +CL:0000980 plasmablast PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired literature/b_cell_markers.md +CL:0000980 plasmablast PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**CD138neg ASC**: CD138−"" and ""**CD138pos ASC**: CD138+"" [gating labels distinguishing" literature/b_cell_markers.md +CL:0000981 double negative memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Sachinidis A & Garyfallos A 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) Double negative (DN) B cells, also known as atypical memory B cells, constitute a B cell population that lacks expression of immunoglobulin D and CD27 memory marker. literature/b_cell_markers.md +CL:0000990 conventional dendritic cell PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123− literature/dc_markers.md +CL:0001058 plasmacytoid dendritic cell, human PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123− literature/dc_markers.md +CL:0001058 plasmacytoid dendritic cell, human PR:000001889 CD14 molecule CD14 (label) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DCs were defined as live, LIN(CD3, CD19, CD56)−CD14−HLA-DR+ cells. literature/dc_markers.md +CL:0001058 plasmacytoid dendritic cell, human PR:000001865 interleukin-3 receptor class 2 alpha chain CD123 (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) pDCs are CD11c− CD123+ cells best characterized for their type I interferon literature/dc_markers.md +CL:0001065 innate lymphoid cell PR:000001002 CD19 molecule CD19 (label) human m2_literature_report Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696) Subsequently we gated out non‐relevant lineages using antibodies against CD3, CD4, TCRαβ, and TCRγδ (T cells), CD19 (B cells) CD14 (monocytes) FcRεR1a (mast cells), BDCA2 (pDCs), CD123 (pDCs, basophils), and CD34 (hematopoietic progenitors). literature/ilc_markers.md +CL:0001065 innate lymphoid cell PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) human m2_literature_report Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696) We gated for lymphocytes, excluded doublets and dead cells and selected CD45+CD3− cells literature/ilc_markers.md CL:0002393 intermediate monocyte PR:000001002 CD19 molecule CD19 (label) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. CL:0002393 intermediate monocyte PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. CL:0002393 intermediate monocyte PR:000001199 C-C chemokine receptor type 2 CD192 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. CL:0002393 intermediate monocyte PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0002394 CD141-positive myeloid dendritic cell PR:000002105 thrombomodulin CD141 (exact) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DC1 corresponds to the cross-presenting CD141/BDCA-3+ cDC1, which is best marked by CLEC9A reports/literature/dc_markers.md -CL:0002399 CD1c-positive myeloid dendritic cell PR:000002027 T-cell surface glycoprotein CD1c CD1C (exact); CD1c (label) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DC2 and DC3 correspond to new subdivisions of the CD1C/BDCA-1+ cDC2 reports/literature/dc_markers.md +CL:0002394 CD141-positive myeloid dendritic cell PR:000002105 thrombomodulin CD141 (exact) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DC1 corresponds to the cross-presenting CD141/BDCA-3+ cDC1, which is best marked by CLEC9A literature/dc_markers.md +CL:0002399 CD1c-positive myeloid dendritic cell PR:000002027 T-cell surface glycoprotein CD1c CD1C (exact); CD1c (label) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DC2 and DC3 correspond to new subdivisions of the CD1C/BDCA-1+ cDC2 literature/dc_markers.md diff --git a/reports/regression-followup/corrected/matcher_evaluation.json b/reports/regression-followup/corrected/matcher_evaluation.json deleted file mode 100644 index 13cbca9..0000000 --- a/reports/regression-followup/corrected/matcher_evaluation.json +++ /dev/null @@ -1,97822 +0,0 @@ -{ - "schema_version": 1, - "generated_utc": "2026-09-18T21:08:23.198343+00:00", - "inputs": { - "data/marker_combinations.csv": "29b476e499ac402094b3dbccc410d052010a9b804ca9865e2624dda3ba9bfc44", - "mappings/soulcap_entities.tsv": "b7d312081b5279669599ead19d3d201a1003ff4978eb814302f16c9783b659a8", - "mappings/curated_mappings.tsv": "2ce1d078ed3d374b0c96d04184bb3520d37a1970415ad08584e33bc26e31434e", - "reports/cl_pro_relationships.tsv": "293edb6a7dc435caf9d85a758425be9305eb4eb00c877074fdec4593ef0d1b3c", - "benchmark": "bb1ab9905205a1ab8738b6e9da0a8db382ad3a778eae1103a1279a75335aa706", - "marker_policy": "317578b4b7fb1a9837b9a61fa85c2dc1ea6469eab4404b0435476ba4a12a1f84", - "marker_map": "4d1982db77c57a9a9e43b1fc883c5b0b32f0d69184e081764880baacb37992b7" - }, - "benchmark_path": "C:\\Users\\s28al\\SOULCAP_CL_Mapping\\mappings\\matcher_benchmark.tsv", - "matcher": { - "version": "0.1.0", - "source_hashes": { - "cl_match.py": "c810b988a7915b6bc2bf8ae3fa58a55986586d8c0b6734f6a84d9c3d7b4d1f73", - "phenotype.py": "6d3e7e59b884365fa48596fe1365b8630053b70a6259bb0e8f42413a55a9514a", - "marker_syntax.py": "e40620b1d804eec3c1f05251716092abd7f5a273e11ba91ce61a3345b1872ade", - "registry.py": "a225ca650e0278378566bf7134b3d8daa33dabee0c61c3d479d8affddf7a25fd", - "evaluation.py": "69dd3abd6c1bbf5a5ae453428269179a5cca8b991c1338bb51097dadf06555c5", - "audit.py": "4d2bfeff9583efd80c37d8fef51e06abb887410f4b9d88ce9b68bceace8bc9bb", - "candidate_index.py": "d4c58041cb4c4a4033d1457ae9f04d2e4d814a2d80469dd7aced2e696539e9a6", - "marker_resolution.py": "2a8245a656ca8d3e77c678b6d3adb3975ff6081de5586979a9a78283134ba7af" - } - }, - "config": { - "ks": [ - 1, - 3, - 5 - ], - "ranking": "production order, including disqualified candidates", - "ties": "primary metrics use production order; bounds report tie sensitivity", - "denominator": "all cohort cases, including unscorable profiles and absent targets", - "marker_resolution": true, - "resolution_policy": "explicit_v1", - "local_lexical": false, - "lexical_limit": 20, - "lexical_min_jaccard": 0.5 - }, - "candidate_count": 826, - "marker_resolution_issues": [ - { - "marker": "CD15", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required." - }, - { - "marker": "CD16", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required." - }, - { - "marker": "CD1D-A-GALCER", - "reason": "policy_withheld", - "representation": "reagent_gate", - "rationale": "Registry notes describe a reagent, lipid antigen, or carbohydrate epitope rather than a single protein." - }, - { - "marker": "CD3", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required." - }, - { - "marker": "CD57", - "reason": "policy_withheld", - "representation": "reagent_gate", - "rationale": "Registry notes describe a reagent, lipid antigen, or carbohydrate epitope rather than a single protein." - }, - { - "marker": "CD8", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required." - }, - { - "marker": "HLA-DR", - "reason": "policy_withheld", - "representation": "complex", - "rationale": "Registry notes describe an assembled or multi-gene marker; component PRO identity cannot establish whole-marker equivalence." - }, - { - "marker": "IGA", - "reason": "policy_withheld", - "representation": "protein_family", - "rationale": "Registry notes document a non-single-protein or pan-marker representation." - }, - { - "marker": "IGD", - "reason": "policy_withheld", - "representation": "protein_family", - "rationale": "Registry notes document a non-single-protein or pan-marker representation." - 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"candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - } - ], - "target_results": [ - { - "cl_id": "CL:0000913", - "label": "effector memory CD8-positive, alpha-beta T cell", - "score": 3, - "matched": [], - "gaps": [ - "CD14-/CD33-/CD64- (no axiom on any alt.)", - "CD19-/CD20- (no axiom on any alt.)", - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 3, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [], - "rank": 239, - "rank_best": 238, - "rank_worst": 247 - } - ], - "status": "below_top_5", - "note": "" - }, - { - "case_id": "provisional/SOULCAP:SC000103/Exact", - "cohort": "provisional", - "subject_id": "SOULCAP:SC000103", - "match_type": "Exact", - "targets": [ - "CL:4030002" - ], - "evidence_reference": "mappings/curated_mappings.tsv", - "uncertain": false, - "rank": null, - "rank_best": null, - "rank_worst": null, - "missing_targets": [ - "CL:4030002" - ], - "candidates": [ - { - "cl_id": "CL:0001057", - "label": "myeloid dendritic cell, human", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0002000", - "label": "Kit-positive erythroid progenitor cell", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0000938", - "label": "CD16-negative, CD56-bright natural killer cell, human", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0001024", - "label": "CD34-positive, CD38-negative hematopoietic stem cell", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0002343", - "label": "decidual natural killer cell, human", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - } - ], - "target_results": [], - "status": "target_not_in_index", - "note": "" - } - ], - "metrics": { - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.1524095320342756, - "statuses": { - "below_top_5": 42, - "hit_at_5": 19, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0875, - "hit_at_1_optimistic": 0.125, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.15, - "hit_at_3_optimistic": 0.2, - "hit_at_3_pessimistic": 0.0875, - "hit_at_5": 0.2375, - "hit_at_5_optimistic": 0.275, - "hit_at_5_pessimistic": 0.1 - } - }, - "by_relation": { - "reviewed/Exact": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Broad": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Exact": { - "cases": 50, - "mrr": 0.15217520145714408, - "statuses": { - "below_top_5": 26, - "hit_at_5": 12, - "invalid_profile": 6, - "target_not_in_index": 6 - }, - "cases_with_missing_targets": 8, - "top1_disqualified": 0, - "hit_at_1": 0.08, - "hit_at_1_optimistic": 0.14, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.16, - "hit_at_3_optimistic": 0.18, - "hit_at_3_pessimistic": 0.08, - "hit_at_5": 0.24, - "hit_at_5_optimistic": 0.24, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Broad": { - "cases": 30, - "mrr": 0.1528000829961614, - "statuses": { - "hit_at_5": 7, - "below_top_5": 16, - "target_not_in_index": 7 - }, - "cases_with_missing_targets": 7, - "top1_disqualified": 0, - "hit_at_1": 0.1, - "hit_at_1_optimistic": 0.1, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.13333333333333333, - "hit_at_3_optimistic": 0.23333333333333334, - "hit_at_3_pessimistic": 0.1, - "hit_at_5": 0.23333333333333334, - "hit_at_5_optimistic": 0.3333333333333333, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - } - } -} diff --git a/reports/regression-followup/legacy/matcher_evaluation.md b/reports/regression-followup/legacy/matcher_evaluation.md deleted file mode 100644 index 5ed8fdf..0000000 --- a/reports/regression-followup/legacy/matcher_evaluation.md +++ /dev/null @@ -1,195 +0,0 @@ -# Matcher evaluation - -Target retrieval only; provisional agreement is not validated accuracy. -All cohort cases remain in denominators, including invalid profiles and absent targets. -Primary ranks retain production tie ordering and disqualified candidates. Bounds show tie sensitivity. - -## Metrics - -```json -{ - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.1524095320342756, - "statuses": { - "below_top_5": 42, - "hit_at_5": 19, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0875, - "hit_at_1_optimistic": 0.125, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.15, - "hit_at_3_optimistic": 0.2, - "hit_at_3_pessimistic": 0.0875, - "hit_at_5": 0.2375, - "hit_at_5_optimistic": 0.275, - "hit_at_5_pessimistic": 0.1 - } -} -``` - -## Relation breakdown - -```json -{ - "reviewed/Exact": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Broad": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Exact": { - "cases": 50, - "mrr": 0.15217520145714408, - "statuses": { - "below_top_5": 26, - "hit_at_5": 12, - "invalid_profile": 6, - "target_not_in_index": 6 - }, - "cases_with_missing_targets": 8, - "top1_disqualified": 0, - "hit_at_1": 0.08, - "hit_at_1_optimistic": 0.14, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.16, - "hit_at_3_optimistic": 0.18, - "hit_at_3_pessimistic": 0.08, - "hit_at_5": 0.24, - "hit_at_5_optimistic": 0.24, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Broad": { - "cases": 30, - "mrr": 0.1528000829961614, - "statuses": { - "hit_at_5": 7, - "below_top_5": 16, - "target_not_in_index": 7 - }, - "cases_with_missing_targets": 7, - "top1_disqualified": 0, - "hit_at_1": 0.1, - "hit_at_1_optimistic": 0.1, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.13333333333333333, - "hit_at_3_optimistic": 0.23333333333333334, - "hit_at_3_pessimistic": 0.1, - "hit_at_5": 0.23333333333333334, - "hit_at_5_optimistic": 0.3333333333333333, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - } -} -``` - -See matcher_evaluation.tsv for per-case failures and matcher_evaluation.json for full evidence and provenance. diff --git a/reports/regression-followup/legacy/matcher_evaluation.tsv b/reports/regression-followup/legacy/matcher_evaluation.tsv deleted file mode 100644 index e878348..0000000 --- a/reports/regression-followup/legacy/matcher_evaluation.tsv +++ /dev/null @@ -1,81 +0,0 @@ -case_id cohort subject_id match_type targets status rank rank_best rank_worst missing_targets note candidates target_results -provisional/SOULCAP:SC000001/Exact provisional SOULCAP:SC000001 Exact "[""CL:0000623""]" below_top_5 6 6 32 [] "[{""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD56+ (1 of 2 alt.)""], ""gaps"": [""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 19, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (hi) (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 19, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim) (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 19, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (hi) (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 17, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD56+ (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000623"", ""label"": ""natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+/CD56:high (no axiom on any alt.)"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 6, ""rank_best"": 6, ""rank_worst"": 32}]" -provisional/SOULCAP:SC000002/Exact provisional SOULCAP:SC000002 Exact "[""CL:0000938""]" hit_at_5 1 1 2 [] "[{""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56:high (hi)"", ""CD16- (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56:high (hi)"", ""CD16- (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 19, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD56:high"", ""CD127-"", ""CD16-/CD16:low (no axiom on any alt.)"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000623"", ""label"": ""natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56:high"", ""CD127-"", ""CD16-/CD16:low (no axiom on any alt.)"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000823"", ""label"": ""immature natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56:high"", ""CD127-"", ""CD16-/CD16:low (no axiom on any alt.)"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56:high (hi)"", ""CD16- (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000003/Exact provisional SOULCAP:SC000003 Exact "[""CL:0000939""]" hit_at_5 1 1 2 [] "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim) (1 of 2 alt.)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD56+ (1 of 2 alt.)""], ""gaps"": [""CD45+"", ""CD127-"", ""CD16+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 17, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD56+ (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD45+"", ""CD127-"", ""CD16+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000623"", ""label"": ""natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+/CD56:high (no axiom on any alt.)"", ""CD127-"", ""CD16+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000823"", ""label"": ""immature natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+/CD56:high (no axiom on any alt.)"", ""CD127-"", ""CD16+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim) (1 of 2 alt.)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000004/Broad provisional SOULCAP:SC000004 Broad "[""CL:0000939""]" hit_at_5 1 1 2 [] "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD56+""], ""gaps"": [""CD45+"", ""CD127-"", ""CD16+"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 17, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD45+"", ""CD127-"", ""CD16+"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002346"", ""label"": ""Dx5-negative, NK1.1-positive immature natural killer cell, mouse"", ""score"": 16, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+"", ""CD127-"", ""CD16+"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002438"", ""label"": ""NK1.1-positive natural killer cell, mouse"", ""score"": 16, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+"", ""CD127-"", ""CD16+"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000005/Broad provisional SOULCAP:SC000005 Broad "[""CL:0000939""]" hit_at_5 1 1 2 [] "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD56+""], ""gaps"": [""CD45+"", ""CD127-"", ""CD16+"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 17, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD45+"", ""CD127-"", ""CD16+"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000623"", ""label"": ""natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+"", ""CD127-"", ""CD16+"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000823"", ""label"": ""immature natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+"", ""CD127-"", ""CD16+"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000006/Broad provisional SOULCAP:SC000006 Broad "[""CL:0001074""]" hit_at_5 3 3 3 [] "[{""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 15, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001076"", ""label"": ""NKp46-positive innate lymphoid cell, human"", ""score"": 15, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001074"", ""label"": ""CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human"", ""score"": 14, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 13, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001072"", ""label"": ""CD34-negative, CD117-positive innate lymphoid cell, human"", ""score"": 11, ""matched"": [""CD3-"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD56+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001074"", ""label"": ""CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human"", ""score"": 14, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 3, ""rank_best"": 3, ""rank_worst"": 3}]" -provisional/SOULCAP:SC000007/Exact provisional SOULCAP:SC000007 Exact "[""CL:0001065""]" below_top_5 155 155 159 [] "[{""cl_id"": ""CL:0000989"", ""label"": ""CD11c-low plasmacytoid dendritic cell"", ""score"": 23, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000992"", ""label"": ""immature CD11c-low plasmacytoid dendritic cell"", ""score"": 23, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000993"", ""label"": ""mature CD11c-low plasmacytoid dendritic cell"", ""score"": 23, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD123-""], ""gaps"": [""CD45+"", ""CD127+"", ""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002089"", ""label"": ""group 2 innate lymphoid cell, mouse"", ""score"": 23, ""matched"": [""CD33- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD127+""], ""gaps"": [""CD34-"", ""CD45+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001065"", ""label"": ""innate lymphoid cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD19-"", ""CD3-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD34-"", ""CD45+"", ""CD127+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 155, ""rank_best"": 155, ""rank_worst"": 159}]" -provisional/SOULCAP:SC000008/Exact provisional SOULCAP:SC000008 Exact "[""CL:0001067""]" below_top_5 161 150 165 [] "[{""cl_id"": ""CL:0000989"", ""label"": ""CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117-"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000992"", ""label"": ""immature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117-"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000993"", ""label"": ""mature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117-"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 27, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD56-"", ""CD123-""], ""gaps"": [""CD45+"", ""CD127+"", ""CD117-"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002089"", ""label"": ""group 2 innate lymphoid cell, mouse"", ""score"": 27, ""matched"": [""CD33- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD127+"", ""CD56-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD117-"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001067"", ""label"": ""group 1 innate lymphoid cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD19-"", ""CD3-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD34-"", ""CD45+"", ""CD127+"", ""CD56-"", ""CD117-"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 161, ""rank_best"": 150, ""rank_worst"": 165}]" -provisional/SOULCAP:SC000009/Exact provisional SOULCAP:SC000009 Exact "[""CL:0001081""]" below_top_5 26 25 32 [] "[{""cl_id"": ""CL:0002029"", ""label"": ""Fc-epsilon RIalpha-low mast cell progenitor"", ""score"": 29, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD117:low (dim) (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD127+"", ""CD294+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000989"", ""label"": ""CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117:low/CD117- (no axiom on any alt.)"", ""CD294+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000992"", ""label"": ""immature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117:low/CD117- (no axiom on any alt.)"", ""CD294+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000993"", ""label"": ""mature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117:low/CD117- (no axiom on any alt.)"", ""CD294+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 27, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD56-"", ""CD123-""], ""gaps"": [""CD45+"", ""CD127+"", ""CD117:low/CD117- (no axiom on any alt.)"", ""CD294+"", ""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001081"", ""label"": ""group 2 innate lymphoid cell, human"", ""score"": 23, ""matched"": [""CD3-"", ""CD19-"", ""CD3-"", ""CD127+"", ""CD294+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD34-"", ""CD45+"", ""CD56-"", ""CD117:low/CD117- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 26, ""rank_best"": 25, ""rank_worst"": 32}]" -provisional/SOULCAP:SC000010/Exact provisional SOULCAP:SC000010 Exact "[""CL:0001078""]" below_top_5 118 118 120 [] "[{""cl_id"": ""CL:0002029"", ""label"": ""Fc-epsilon RIalpha-low mast cell progenitor"", ""score"": 29, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD117+ (dim)""], ""gaps"": [""CD34-"", ""CD127+"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002344"", ""label"": ""CD56-negative, CD161-positive immature natural killer cell, human"", ""score"": 29, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000989"", ""label"": ""CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117+"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000992"", ""label"": ""immature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117+"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000993"", ""label"": ""mature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117+"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001078"", ""label"": ""group 3 innate lymphoid cell, human"", ""score"": 19, ""matched"": [""CD3-"", ""CD19-"", ""CD3-"", ""CD127+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD34-"", ""CD45+"", ""CD56:low/CD56- (no axiom on any alt.)"", ""CD117+"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 118, ""rank_best"": 118, ""rank_worst"": 120}]" -provisional/SOULCAP:SC000011/Exact provisional SOULCAP:SC000011 Exact "[""CL:0000990""]" below_top_5 18 15 21 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 21, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD3-"", ""CD19-"", ""CD56-"", ""CD127-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""CD11C:high"", ""HLA-DR+""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000782"", ""label"": ""myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002394"", ""label"": ""CD141-positive myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002399"", ""label"": ""CD1c-positive myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000990"", ""label"": ""conventional dendritic cell"", ""score"": 13, ""matched"": [""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD123:not:high/CD193- (no axiom on any alt.)"", ""CD123:not:high/CD303- (no axiom on any alt.)"", ""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 18, ""rank_best"": 15, ""rank_worst"": 21}]" -provisional/SOULCAP:SC000012/Exact provisional SOULCAP:SC000012 Exact "[""CL:0002394""]" hit_at_5 2 1 2 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD141+"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002394"", ""label"": ""CD141-positive myeloid dendritic cell"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD141+"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 21, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD3-"", ""CD19-"", ""CD56-"", ""CD127-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""CD11C:high"", ""HLA-DR+"", ""CD1C-"", ""CD141+"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000782"", ""label"": ""myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD141+"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0011031"", ""label"": ""monocyte-derived dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD141+"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0002394"", ""label"": ""CD141-positive myeloid dendritic cell"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD141+"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 2, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000013/Exact provisional SOULCAP:SC000013 Exact "[""CL:0002399""]" hit_at_5 2 1 2 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002399"", ""label"": ""CD1c-positive myeloid dendritic cell"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD1C+"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 21, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD3-"", ""CD19-"", ""CD56-"", ""CD127-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""CD11C:high"", ""HLA-DR+"", ""CD1C+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000782"", ""label"": ""myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002394"", ""label"": ""CD141-positive myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0002399"", ""label"": ""CD1c-positive myeloid dendritic cell"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD1C+"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 2, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000014/Exact provisional SOULCAP:SC000014 Exact "[""CL:0001058""]" below_top_5 34 27 42 [] "[{""cl_id"": ""CL:0000991"", ""label"": ""CD11c-negative plasmacytoid dendritic cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD303+ (1 of 3 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000994"", ""label"": ""immature CD11c-negative plasmacytoid dendritic cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD303+ (1 of 3 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000996"", ""label"": ""mature CD11c-negative plasmacytoid dendritic cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD303+ (1 of 3 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002008"", ""label"": ""CD34-positive, CD38-positive eosinophil progenitor cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD56-"", ""CD19-"", ""CD14-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD193-/FCER1A-/CD303+ (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002029"", ""label"": ""Fc-epsilon RIalpha-low mast cell progenitor"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD56-"", ""CD19-"", ""CD14-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD193-/FCER1A-/CD303+ (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001058"", ""label"": ""plasmacytoid dendritic cell, human"", ""score"": 12, ""matched"": [""CD3-"", ""CD56-"", ""CD19-"", ""CD14-""], ""gaps"": [""CD45+"", ""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD193-/FCER1A-/CD303+ (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 34, ""rank_best"": 27, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000015/Exact provisional SOULCAP:SC000015 Exact "[""CL:0000043""]" hit_at_5 3 3 7 [] "[{""cl_id"": ""CL:0000614"", ""label"": ""basophilic myelocyte"", ""score"": 18, ""matched"": [""CD3-"", ""CD33+ (1 of 2 alt.)"", ""CD193+ (hi) (1 of 4 alt.)"", ""CD56-"", ""CD19-"", ""CD16-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD14-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [""CD15-/CD66B- (all alt. conflict)""], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002008"", ""label"": ""CD34-positive, CD38-positive eosinophil progenitor cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD123+ (1 of 2 alt.)"", ""CD56-"", ""CD19-"", ""CD14-""], ""gaps"": [""CD193+/FCER1A+/HLA-DR-/CD303- (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000043"", ""label"": ""mature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD123+ (hi) (1 of 2 alt.)"", ""CD193+ (hi) (1 of 4 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000612"", ""label"": ""eosinophilic myelocyte"", ""score"": 17, ""matched"": [""CD3-"", ""CD33+ (1 of 2 alt.)"", ""CD193+ (1 of 4 alt.)"", ""CD56-"", ""CD19-"", ""CD16-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD14-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [""CD15-/CD66B- (all alt. conflict)""], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000767"", ""label"": ""basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD123+ (hi) (1 of 2 alt.)"", ""CD193+ (hi) (1 of 4 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000043"", ""label"": ""mature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD123+ (hi) (1 of 2 alt.)"", ""CD193+ (hi) (1 of 4 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 3, ""rank_best"": 3, ""rank_worst"": 7}]" -provisional/SOULCAP:SC000016/Exact provisional SOULCAP:SC000016 Exact "[""CL:0000043""]" hit_at_5 1 1 4 [] "[{""cl_id"": ""CL:0000043"", ""label"": ""mature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000767"", ""label"": ""basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000768"", ""label"": ""immature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000770"", ""label"": ""band form basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000942"", ""label"": ""thymic plasmacytoid dendritic cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD45+"", ""CD123+"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD193+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000043"", ""label"": ""mature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 4}]" -provisional/SOULCAP:SC000017/Exact provisional SOULCAP:SC000017 Exact "[""CL:0000576""]" invalid_profile "[""CL:0000576""]" invalid expression in Required exclusion: unexpected ')' in group [] [] -provisional/SOULCAP:SC000018/Exact provisional SOULCAP:SC000018 Exact "[""CL:0000860""]" invalid_profile [] invalid expression in Required exclusion: unexpected ')' in group [] [] -provisional/SOULCAP:SC000019/Exact provisional SOULCAP:SC000019 Exact "[""CL:0000875""]" invalid_profile [] invalid expression in Required exclusion: unexpected ')' in group [] [] -provisional/SOULCAP:SC000020/Exact provisional SOULCAP:SC000020 Exact "[""CL:0002393""]" invalid_profile [] invalid expression in Required exclusion: unexpected ')' in group [] [] -provisional/SOULCAP:SC000021/Exact provisional SOULCAP:SC000021 Exact "[""CL:0000775""]" below_top_5 9 7 16 [] "[{""cl_id"": ""CL:0000582"", ""label"": ""neutrophilic metamyelocyte"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD19-"", ""CD33+ (1 of 2 alt.)""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001021"", ""label"": ""CD34-positive, CD38-positive common lymphoid progenitor"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD14- (1 of 2 alt.)"", ""CD45+"", ""CD19-""], ""gaps"": [""CD123-"", ""CD15:high/CD66B+ (no axiom on any alt.)"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD14- (1 of 2 alt.)"", ""CD123-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD15:high/CD66B+ (no axiom on any alt.)"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD14- (1 of 2 alt.)"", ""CD123-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD15:high/CD66B+ (no axiom on any alt.)"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002029"", ""label"": ""Fc-epsilon RIalpha-low mast cell progenitor"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD14- (1 of 2 alt.)"", ""CD45+"", ""CD19-""], ""gaps"": [""CD123-"", ""CD15:high/CD66B+ (no axiom on any alt.)"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000775"", ""label"": ""neutrophil"", ""score"": 16, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 9, ""rank_best"": 7, ""rank_worst"": 16}]" -provisional/SOULCAP:SC000022/Exact provisional SOULCAP:SC000022 Exact "[""CL:0000771""]" hit_at_5 4 2 7 [] "[{""cl_id"": ""CL:0000612"", ""label"": ""eosinophilic myelocyte"", ""score"": 26, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD16-"", ""CD19-"", ""CD33+ (1 of 2 alt.)""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000041"", ""label"": ""mature eosinophil"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD16-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000580"", ""label"": ""neutrophilic myelocyte"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD16-"", ""CD19-"", ""CD33+ (1 of 2 alt.)""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD193+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000771"", ""label"": ""eosinophil"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD16-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000772"", ""label"": ""immature eosinophil"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD16-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000771"", ""label"": ""eosinophil"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD16-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 4, ""rank_best"": 2, ""rank_worst"": 7}]" -provisional/SOULCAP:SC000023/Exact provisional SOULCAP:SC000023 Exact "[""CL:0000236""]" target_not_in_index "[""CL:0000236""]" "[{""cl_id"": ""CL:0000819"", ""label"": ""B-1 B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000820"", ""label"": ""B-1a B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000821"", ""label"": ""B-1b B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000843"", ""label"": ""follicular B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000024/Exact provisional SOULCAP:SC000024 Exact "[""CL:0000946""]" target_not_in_index "[""CL:0000946""]" "[{""cl_id"": ""CL:0000949"", ""label"": ""IgD plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000950"", ""label"": ""IgE plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000980"", ""label"": ""plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000982"", ""label"": ""IgG plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000983"", ""label"": ""IgM plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000025/Exact provisional SOULCAP:SC000025 Exact "[""CL:0000980""]" hit_at_5 3 1 7 [] "[{""cl_id"": ""CL:0000949"", ""label"": ""IgD plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000950"", ""label"": ""IgE plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000980"", ""label"": ""plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000982"", ""label"": ""IgG plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000983"", ""label"": ""IgM plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000980"", ""label"": ""plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 3, ""rank_best"": 1, ""rank_worst"": 7}]" -provisional/SOULCAP:SC000026/Exact provisional SOULCAP:SC000026 Exact "[""CL:0000786""]" below_top_5 31 31 53 [] "[{""cl_id"": ""CL:0002047"", ""label"": ""fraction B precursor B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD45+"", ""CD19+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002049"", ""label"": ""fraction C precursor B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD45+"", ""CD19+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002050"", ""label"": ""fraction C' precursor B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD45+"", ""CD19+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002051"", ""label"": ""CD38-high pre-BCR positive cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD19+"", ""CD38:high (hi)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002052"", ""label"": ""fraction D precursor B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD45+"", ""CD19+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000786"", ""label"": ""plasma cell"", ""score"": 8, ""matched"": [""CD138+"", ""CD20-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD3-"", ""CD56-"", ""CD45+"", ""CD19+"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 31, ""rank_best"": 31, ""rank_worst"": 53}]" -provisional/SOULCAP:SC000028/Broad provisional SOULCAP:SC000028 Broad "[""CL:0000818""]" hit_at_5 1 1 6 [] "[{""cl_id"": ""CL:0000818"", ""label"": ""transitional stage B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000958"", ""label"": ""T1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000959"", ""label"": ""T2 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000960"", ""label"": ""T3 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:high/CD10:high (no axiom on any alt.)"", ""CD24:high"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000818"", ""label"": ""transitional stage B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 6}]" -provisional/SOULCAP:SC000029/Exact provisional SOULCAP:SC000029 Exact "[""CL:0000785""]" below_top_5 43 43 45 [] "[{""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002055"", ""label"": ""CD38-negative immature B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000785"", ""label"": ""mature B cell"", ""score"": 10, ""matched"": [""CD3-"", ""CD19+ (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20+""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 43, ""rank_best"": 43, ""rank_worst"": 45}]" -provisional/SOULCAP:SC000030/Exact provisional SOULCAP:SC000030 Exact "[""CL:0000960""]" below_top_5 20 13 26 [] "[{""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24+"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24+"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10:low (no axiom on any alt.)"", ""CD24+"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10:low (no axiom on any alt.)"", ""CD24+"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002054"", ""label"": ""fraction E immature B cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+"", ""CD127-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low/CD38-/CD10:low (no axiom on any alt.)"", ""IGD+"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000960"", ""label"": ""T3 B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+ (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low (hi)/CD38- (hi)/CD10:low (no axiom on any alt.)"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 20, ""rank_best"": 13, ""rank_worst"": 26}]" -provisional/SOULCAP:SC000031/Exact provisional SOULCAP:SC000031 Exact "[""CL:0000788""]" hit_at_5 5 5 8 [] "[{""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000788"", ""label"": ""naive B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000788"", ""label"": ""naive B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 5, ""rank_best"": 5, ""rank_worst"": 8}]" -provisional/SOULCAP:SC000032/Exact provisional SOULCAP:SC000032 Exact "[""CL:0000981""]" hit_at_5 5 5 8 [] "[{""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 5, ""rank_best"": 5, ""rank_worst"": 8}]" -provisional/SOULCAP:SC000033/Broad provisional SOULCAP:SC000033 Broad "[""CL:0000981""]" below_top_5 12 12 19 [] "[{""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 23, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002055"", ""label"": ""CD38-negative immature B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD21+ (dim)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24+"", ""IGD-"", ""CD21+"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000843"", ""label"": ""follicular B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000959"", ""label"": ""T2 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+ (hi)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low (hi)/CD38- (hi)/CD10- (no axiom on any alt.)"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21+"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 12, ""rank_best"": 12, ""rank_worst"": 19}]" -provisional/SOULCAP:SC000034/Broad provisional SOULCAP:SC000034 Broad "[""CL:0000981""]" hit_at_5 4 4 6 [] "[{""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002103"", ""label"": ""IgG-positive double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 4, ""rank_best"": 4, ""rank_worst"": 6}]" -provisional/SOULCAP:SC000035/Broad provisional SOULCAP:SC000035 Broad "[""CL:0000981""]" hit_at_5 5 5 12 [] "[{""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000958"", ""label"": ""T1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+ (hi)"", ""CD21-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low (hi)/CD38- (hi)/CD10- (no axiom on any alt.)"", ""IGD-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 5, ""rank_best"": 5, ""rank_worst"": 12}]" -provisional/SOULCAP:SC000036/Broad provisional SOULCAP:SC000036 Broad "[""CL:0000981""]" below_top_5 12 12 19 [] "[{""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 23, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002055"", ""label"": ""CD38-negative immature B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD21+ (dim)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24+"", ""IGD-"", ""CD21+"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000843"", ""label"": ""follicular B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000959"", ""label"": ""T2 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+ (hi)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low (hi)/CD38- (hi)/CD10- (no axiom on any alt.)"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21+"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 12, ""rank_best"": 12, ""rank_worst"": 19}]" -provisional/SOULCAP:SC000037/Exact provisional SOULCAP:SC000037 Exact "[""CL:0000787""]" below_top_5 39 39 42 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002108"", ""label"": ""CD38-negative IgG memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002111"", ""label"": ""CD38-negative unswitched memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002115"", ""label"": ""B220-positive CD38-positive unswitched memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000787"", ""label"": ""memory B cell"", ""score"": 12, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 39, ""rank_best"": 39, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000039/Exact provisional SOULCAP:SC000039 Exact "[""CL:0000970""]" below_top_5 13 13 14 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 25, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 25, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002111"", ""label"": ""CD38-negative unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002115"", ""label"": ""B220-positive CD38-positive unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002116"", ""label"": ""B220-low CD38-positive unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000970"", ""label"": ""unswitched memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 13, ""rank_best"": 13, ""rank_worst"": 14}]" -provisional/SOULCAP:SC000040/Exact provisional SOULCAP:SC000040 Exact "[""CL:0000971""]" below_top_5 33 33 39 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002108"", ""label"": ""CD38-negative IgG memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002111"", ""label"": ""CD38-negative unswitched memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002115"", ""label"": ""B220-positive CD38-positive unswitched memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000971"", ""label"": ""IgM memory B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 33, ""rank_best"": 33, ""rank_worst"": 39}]" -provisional/SOULCAP:SC000041/Exact provisional SOULCAP:SC000041 Exact "[""CL:0000972""]" below_top_5 14 13 18 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 25, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 25, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002111"", ""label"": ""CD38-negative unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002115"", ""label"": ""B220-positive CD38-positive unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002116"", ""label"": ""B220-low CD38-positive unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000972"", ""label"": ""class switched memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 14, ""rank_best"": 13, ""rank_worst"": 18}]" -provisional/SOULCAP:SC000042/Exact provisional SOULCAP:SC000042 Exact "[""CL:0000973""]" below_top_5 18 17 19 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002118"", ""label"": ""CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002120"", ""label"": ""CD24-positive CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002121"", ""label"": ""CD24-negative CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000973"", ""label"": ""IgA memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 18, ""rank_best"": 17, ""rank_worst"": 19}]" -provisional/SOULCAP:SC000043/Exact provisional SOULCAP:SC000043 Exact "[""CL:0000979""]" below_top_5 18 17 22 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002118"", ""label"": ""CD38-negative IgG-negative class switched memory B cell"", ""score"": 22, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002120"", ""label"": ""CD24-positive CD38-negative IgG-negative class switched memory B cell"", ""score"": 22, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002121"", ""label"": ""CD24-negative CD38-negative IgG-negative class switched memory B cell"", ""score"": 22, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000979"", ""label"": ""IgG memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 18, ""rank_best"": 17, ""rank_worst"": 22}]" -provisional/SOULCAP:SC000044/Exact provisional SOULCAP:SC000044 Exact "[""CL:0000948""]" below_top_5 17 17 19 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002118"", ""label"": ""CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002120"", ""label"": ""CD24-positive CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002121"", ""label"": ""CD24-negative CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000948"", ""label"": ""IgE memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 17, ""rank_best"": 17, ""rank_worst"": 19}]" -provisional/SOULCAP:SC000045/Exact provisional SOULCAP:SC000045 Exact "[""CL:0000084""]" target_not_in_index "[""CL:0000084""]" "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000786"", ""label"": ""plasma cell"", ""score"": 5, ""matched"": [""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000046/Broad provisional SOULCAP:SC000046 Broad "[""CL:4052055""]" below_top_5 34 2 34 [] "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD56+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000570"", ""label"": ""parafollicular cell"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 34, ""rank_best"": 2, ""rank_worst"": 34}]" -provisional/SOULCAP:SC000047/Broad provisional SOULCAP:SC000047 Broad "[""CL:4052055""]" below_top_5 42 13 42 [] "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002430"", ""label"": ""CD4-intermediate, CD8-positive double-positive thymocyte"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002431"", ""label"": ""CD4-positive, CD8-intermediate double-positive thymocyte"", ""score"": 9, ""matched"": [""CD4+"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD4+"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 42, ""rank_best"": 13, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000048/Broad provisional SOULCAP:SC000048 Broad "[""CL:4052055""]" below_top_5 63 39 63 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 14, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 14, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 14, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD4-"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 63, ""rank_best"": 39, ""rank_worst"": 63}]" -provisional/SOULCAP:SC000049/Broad provisional SOULCAP:SC000049 Broad "[""CL:4052055""]" below_top_5 34 2 34 [] "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000570"", ""label"": ""parafollicular cell"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 34, ""rank_best"": 2, ""rank_worst"": 34}]" -provisional/SOULCAP:SC000050/Broad provisional SOULCAP:SC000050 Broad "[""CL:4052055""]" below_top_5 70 42 70 [] "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD4+"", ""CD8-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 70, ""rank_best"": 42, ""rank_worst"": 70}]" -provisional/SOULCAP:SC000051/Broad provisional SOULCAP:SC000051 Broad "[""CL:4052055""]" below_top_5 63 34 63 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD4-"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 63, ""rank_best"": 34, ""rank_worst"": 63}]" -provisional/SOULCAP:SC000052/Broad provisional SOULCAP:SC000052 Broad "[""CL:4052055""]" below_top_5 42 9 42 [] "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD4+"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 42, ""rank_best"": 9, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000053/Broad provisional SOULCAP:SC000053 Broad "[""CL:4052055""]" below_top_5 54 30 54 [] "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD4-"", ""CD8-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 54, ""rank_best"": 30, ""rank_worst"": 54}]" -provisional/SOULCAP:SC000054/Broad provisional SOULCAP:SC000054 Broad "[""CL:4052055""]" below_top_5 34 2 34 [] "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000570"", ""label"": ""parafollicular cell"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 34, ""rank_best"": 2, ""rank_worst"": 34}]" -provisional/SOULCAP:SC000055/Broad provisional SOULCAP:SC000055 Broad "[""CL:4052055""]" below_top_5 70 42 70 [] "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD4+"", ""CD8-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 70, ""rank_best"": 42, ""rank_worst"": 70}]" -provisional/SOULCAP:SC000056/Broad provisional SOULCAP:SC000056 Broad "[""CL:4052055""]" below_top_5 63 34 63 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD4-"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 63, ""rank_best"": 34, ""rank_worst"": 63}]" -provisional/SOULCAP:SC000057/Broad provisional SOULCAP:SC000057 Broad "[""CL:4052055""]" below_top_5 42 9 42 [] "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD4+"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 42, ""rank_best"": 9, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000058/Broad provisional SOULCAP:SC000058 Broad "[""CL:4052055""]" below_top_5 54 30 54 [] "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD4-"", ""CD8-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 54, ""rank_best"": 30, ""rank_worst"": 54}]" -provisional/SOULCAP:SC000059/Exact provisional SOULCAP:SC000059 Exact "[""CL:0000814""]" invalid_profile [] invalid expression in Required phenotypic markers: mixed '|' and space in a group [] [] -provisional/SOULCAP:SC000060/Exact provisional SOULCAP:SC000060 Exact "[""CL:0000789""]" target_not_in_index "[""CL:0000789""]" "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000786"", ""label"": ""plasma cell"", ""score"": 5, ""matched"": [""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000061/Exact provisional SOULCAP:SC000061 Exact "[""CL:0000798""]" target_not_in_index "[""CL:0000798""]" "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000786"", ""label"": ""plasma cell"", ""score"": 5, ""matched"": [""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000062/Broad provisional SOULCAP:SC000062 Broad "[""CL:0000624""]" below_top_5 9 6 36 [] "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000624"", ""label"": ""CD4-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 9, ""rank_best"": 6, ""rank_worst"": 36}]" -provisional/SOULCAP:SC000063/Broad provisional SOULCAP:SC000063 Broad "[""CL:0000625""]" hit_at_5 4 4 27 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 4, ""rank_best"": 4, ""rank_worst"": 27}]" -provisional/SOULCAP:SC000064/Broad provisional SOULCAP:SC000064 Broad "[""CL:0000789""]" target_not_in_index "[""CL:0000789""]" "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000065/Broad provisional SOULCAP:SC000065 Broad "[""CL:0000084""]" target_not_in_index "[""CL:0000084""]" "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000066/Exact provisional SOULCAP:SC000066 Exact "[""CL:0000624""]" below_top_5 9 6 36 [] "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000624"", ""label"": ""CD4-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 9, ""rank_best"": 6, ""rank_worst"": 36}]" -provisional/SOULCAP:SC000067/Exact provisional SOULCAP:SC000067 Exact "[""CL:0000625""]" hit_at_5 4 4 27 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 4, ""rank_best"": 4, ""rank_worst"": 27}]" -provisional/SOULCAP:SC000068/Broad provisional SOULCAP:SC000068 Broad "[""CL:0000789""]" target_not_in_index "[""CL:0000789""]" "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000069/Broad provisional SOULCAP:SC000069 Broad "[""CL:0000789""]" target_not_in_index "[""CL:0000789""]" "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000070/Broad provisional SOULCAP:SC000070 Broad "[""CL:0000798""]" target_not_in_index "[""CL:0000798""]" "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000071/Broad provisional SOULCAP:SC000071 Broad "[""CL:0000798""]" target_not_in_index "[""CL:0000798""]" "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000072/Broad provisional SOULCAP:SC000072 Broad "[""CL:0000798""]" target_not_in_index "[""CL:0000798""]" "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000073/Exact provisional SOULCAP:SC000073 Exact "[""CL:0000803""]" hit_at_5 1 1 6 [] "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 6}]" -provisional/SOULCAP:SC000074/Exact provisional SOULCAP:SC000074 Exact "[""CL:0000940""]" invalid_profile "[""CL:0000940""]" invalid expression in Required phenotypic markers: mixed '|' and space in a group [] [] -provisional/SOULCAP:SC000082/Exact provisional SOULCAP:SC000082 Exact "[""CL:0000904""]" below_top_5 238 238 243 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000904"", ""label"": ""central memory CD4-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 238, ""rank_best"": 238, ""rank_worst"": 243}]" -provisional/SOULCAP:SC000085/Exact provisional SOULCAP:SC000085 Exact "[""CL:0000907""]" below_top_5 239 238 243 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000907"", ""label"": ""central memory CD8-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 239, ""rank_best"": 238, ""rank_worst"": 243}]" -provisional/SOULCAP:SC000087/Exact provisional SOULCAP:SC000087 Exact "[""CL:0000898""]" below_top_5 252 243 261 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000898"", ""label"": ""naive T cell"", ""score"": 2, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 252, ""rank_best"": 243, ""rank_worst"": 261}]" -provisional/SOULCAP:SC000089/Exact provisional SOULCAP:SC000089 Exact "[""CL:0000895""]" below_top_5 238 238 242 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 238, ""rank_best"": 238, ""rank_worst"": 242}]" -provisional/SOULCAP:SC000092/Exact provisional SOULCAP:SC000092 Exact "[""CL:0000900""]" below_top_5 253 242 258 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 2, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 253, ""rank_best"": 242, ""rank_worst"": 258}]" -provisional/SOULCAP:SC000096/Exact provisional SOULCAP:SC000096 Exact "[""CL:0000905""]" below_top_5 238 238 247 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 12, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000905"", ""label"": ""effector memory CD4-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 238, ""rank_best"": 238, ""rank_worst"": 247}]" -provisional/SOULCAP:SC000099/Exact provisional SOULCAP:SC000099 Exact "[""CL:0000913""]" below_top_5 239 238 247 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 12, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000913"", ""label"": ""effector memory CD8-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 239, ""rank_best"": 238, ""rank_worst"": 247}]" -provisional/SOULCAP:SC000103/Exact provisional SOULCAP:SC000103 Exact "[""CL:4030002""]" target_not_in_index "[""CL:4030002""]" "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] diff --git a/reports/regression-triage/regression_triage.json b/reports/regression-triage/regression_triage.json deleted file mode 100644 index 0369b3a..0000000 --- a/reports/regression-triage/regression_triage.json +++ /dev/null @@ -1,216298 +0,0 @@ -{ - "schema_version": 1, - "generated_utc": "2026-09-18T20:51:29.086097+00:00", - "inputs": { - "data/marker_combinations.csv": "29b476e499ac402094b3dbccc410d052010a9b804ca9865e2624dda3ba9bfc44", - "mappings/soulcap_entities.tsv": "b7d312081b5279669599ead19d3d201a1003ff4978eb814302f16c9783b659a8", - "mappings/curated_mappings.tsv": "2ce1d078ed3d374b0c96d04184bb3520d37a1970415ad08584e33bc26e31434e", - "reports/cl_pro_relationships.tsv": "293edb6a7dc435caf9d85a758425be9305eb4eb00c877074fdec4593ef0d1b3c", - "benchmark": "bb1ab9905205a1ab8738b6e9da0a8db382ad3a778eae1103a1279a75335aa706", - "marker_map": "4d1982db77c57a9a9e43b1fc883c5b0b32f0d69184e081764880baacb37992b7", - "marker_policy": "317578b4b7fb1a9837b9a61fa85c2dc1ea6469eab4404b0435476ba4a12a1f84" - }, - "code_hashes": { - "cl_match.py": "4d447e860e8c500196b2859549b91dac9549afeaee236eedd5d63049ca7f7cec", - "phenotype.py": "6d3e7e59b884365fa48596fe1365b8630053b70a6259bb0e8f42413a55a9514a", - "marker_syntax.py": "e40620b1d804eec3c1f05251716092abd7f5a273e11ba91ce61a3345b1872ade", - "registry.py": "a225ca650e0278378566bf7134b3d8daa33dabee0c61c3d479d8affddf7a25fd", - "evaluation.py": "69dd3abd6c1bbf5a5ae453428269179a5cca8b991c1338bb51097dadf06555c5", - "audit.py": "4d2bfeff9583efd80c37d8fef51e06abb887410f4b9d88ce9b68bceace8bc9bb", - "candidate_index.py": "d4c58041cb4c4a4033d1457ae9f04d2e4d814a2d80469dd7aced2e696539e9a6", - "marker_resolution.py": "17feb8779da5a3d429c9d8326d26195cb66bb25cebf9cd005c79410d99efe050", - "regression_triage.py": "699b520311058f0fbd376cf1083e6c1a542608ed176178add35ba21b33d2d361" - }, - "factors": { - "A": "Add alias/allowed-PRO token evidence present in the enhanced index but absent in legacy.", - "P": "Remove legacy token evidence excluded by stricter policies, alias conflicts, synonym scope, or exact-PRO checks.", - "D": "Enable production semantic-clause deduplication using the fixed enhanced canonical alias map." - }, - "mode_order": "APD (0 disabled, 1 enabled)", - "candidate_count": 826, - "endpoint_checks": "passed", - "summary": { - "rank_improvements": 5, - "rank_regressions": 32, - "unchanged_ranks": 43, - "lost_top5": 3, - "gained_top5": 0, - "cases_sensitive_to_factor": { - "A": 0, - "P": 37, - "D": 0 - } - }, - "limitations": [ - "Provisional targets are not biological ground truth; this report does not validate them.", - "A/P separate added and removed index evidence, not independent biological mechanisms. Their identities are fixed by current policy.", - "D uses the same canonical map in every diagnostic run. Intermediate combinations are not supported production settings.", - "Tie bounds describe sensitivity to input order. Factor effects may interact; there is no unique additive causal attribution.", - "All cohort cases remain in denominators. Invalid profiles and targets absent from the fixed index are not silently excluded.", - "No lexical expansion, biological policy edits, scoring-weight changes, or network requests." - ], - "metrics": { - "000": { - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.1524095320342756, - "statuses": { - "below_top_5": 42, - "hit_at_5": 19, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0875, - "hit_at_1_optimistic": 0.125, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.15, - "hit_at_3_optimistic": 0.2, - "hit_at_3_pessimistic": 0.0875, - "hit_at_5": 0.2375, - "hit_at_5_optimistic": 0.275, - "hit_at_5_pessimistic": 0.1 - } - }, - "001": { - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.1524095320342756, - "statuses": { - "below_top_5": 42, - "hit_at_5": 19, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0875, - "hit_at_1_optimistic": 0.125, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.15, - "hit_at_3_optimistic": 0.2, - "hit_at_3_pessimistic": 0.0875, - "hit_at_5": 0.2375, - "hit_at_5_optimistic": 0.275, - "hit_at_5_pessimistic": 0.1 - } - }, - "010": { - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.10812960188222673, - "statuses": { - "below_top_5": 45, - "hit_at_5": 16, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0375, - "hit_at_1_optimistic": 0.075, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.1375, - "hit_at_3_optimistic": 0.15, - "hit_at_3_pessimistic": 0.05, - "hit_at_5": 0.2, - "hit_at_5_optimistic": 0.2, - "hit_at_5_pessimistic": 0.0875 - } - }, - "011": { - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.10812960188222673, - "statuses": { - "below_top_5": 45, - "hit_at_5": 16, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0375, - "hit_at_1_optimistic": 0.075, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.1375, - "hit_at_3_optimistic": 0.15, - "hit_at_3_pessimistic": 0.05, - "hit_at_5": 0.2, - "hit_at_5_optimistic": 0.2, - "hit_at_5_pessimistic": 0.0875 - } - }, - "100": { - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - 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"mrr": 0.1524095320342756, - "statuses": { - "below_top_5": 42, - "hit_at_5": 19, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0875, - "hit_at_1_optimistic": 0.125, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.15, - "hit_at_3_optimistic": 0.2, - "hit_at_3_pessimistic": 0.0875, - "hit_at_5": 0.2375, - "hit_at_5_optimistic": 0.275, - "hit_at_5_pessimistic": 0.1 - } - }, - "110": { - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.10812960188222673, - "statuses": { - "below_top_5": 45, - "hit_at_5": 16, - "invalid_profile": 6, - "target_not_in_index": 13 - 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"label": "myeloid dendritic cell, human", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null - }, - { - "cl_id": "CL:0002000", - "label": "Kit-positive erythroid progenitor cell", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null - }, - { - "cl_id": "CL:0002023", - "label": "CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell", - "score": 10, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 2, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null - }, - { - "cl_id": "CL:0002025", - "label": "CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell", - "score": 10, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 2, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null - }, - { - "cl_id": "CL:0000037", - "label": "hematopoietic stem cell", - "score": 9, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null - } - ], - "target_results": [], - "status": "target_not_in_index", - "note": "" - } - } - } - ] -} diff --git a/reports/resolver-refinement/audit/audit_dashboard.html b/reports/resolver-refinement/audit/audit_dashboard.html deleted file mode 100644 index ca18c10..0000000 --- a/reports/resolver-refinement/audit/audit_dashboard.html +++ /dev/null @@ -1,87 +0,0 @@ - - - - - -SOULCAP · Mapping audit - - - -
SOULCAP × Cell Ontology

Mapping audit

A local review of mapping coverage, phenotype evidence, and source consistency.

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Matcher evaluation

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Marker evidence

Counts refer to proposal records, not distinct cell types.

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Review status

Curator review and marker support are separate evidence sources.

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Select a column heading to sort.
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How to interpret this audit

    Markdown summaryDownload audit JSON
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    Generated by soulcap-audit. Re-run the command to refresh this snapshot. No external scripts, fonts, or services are used.

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    - - - - diff --git a/reports/resolver-refinement/audit/audit_data.json b/reports/resolver-refinement/audit/audit_data.json deleted file mode 100644 index 812e77a..0000000 --- a/reports/resolver-refinement/audit/audit_data.json +++ /dev/null @@ -1,151903 +0,0 @@ -{ - "schema_version": 1, - "resolution_mode": "explicit_marker_policy", - "resolution_inputs": { - "marker_mappings\\marker_protein_gene.csv": "4d1982db77c57a9a9e43b1fc883c5b0b32f0d69184e081764880baacb37992b7", - "marker_mappings\\marker_resolution.tsv": "317578b4b7fb1a9837b9a61fa85c2dc1ea6469eab4404b0435476ba4a12a1f84" - }, - "generated_utc": "2026-09-11T04:13:52.853363+00:00", - "summary": { - "registered_entities": 127, - "source_rows": 127, - "mapping_records": 80, - "source_entities_with_proposals": 80, - "source_entities_without_proposals": 47, - "unresolved_source_rows": 0, - "uncertain_proposals": 8, - "invalid_marker_cells": 26, - "invalid_profile_rows": 23, - "evidence_statuses": { - "partial_support": 54, - "invalid_profile": 6, - "no_marker_support": 20 - }, - "review_statuses": { - "needs_review": 80 - }, - "marker_statuses": { - "mapped": 55, - "no_gene_mapping": 3, - "documented_nonprotein_or_reagent": 3, - "documented_complex_or_family": 10, - "source_artifact_needs_review": 4 - }, - "gap_records": 17, - "finding_severities": { - "error": 23, - "warning": 8, - "info": 81 - } - }, - "sources": [ - { - "subject_id": "SOULCAP:SC000001", - "sheet_row": 2, - "abbreviation": "NK", - "label": "Natural Killer Cell", - "parent": "", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD127", - "CD14", - "CD15", - "CD19", - "CD3", - "CD33", - "CD34", - "CD45", - "CD56", - "CD64", - "CD66b", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "", - "Parent": "", - "Abbreviation": "NK", - "Full Name": "Natural Killer Cell", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "(CD14-|CD33-|CD64-) CD34- CD3- CD19- ", - "Ideal exclusion": "[HLA-DR+ CD11chi]- (CD15-|CD66b-) CD123-", - "Required phenotypic markers": "live/ CD45+ CD56+/hi CD127-", - "Ideal phenotypic markers": "[CD33-|CD64-]", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000001", - "legacy_subject_id": "SOULCAP:NK", - "abbreviation": "NK", - "subject_label": "Natural Killer Cell", - "cl_id": "CL:0000623", - "cl_label": "natural killer cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "CL:0000623 asserts only negative exclusion markers (CD14-/CD19-/CD3-/CD20-); the defining positive CD56 marker is absent — a documented CL gap (cl_term_issues.md), not confirmed here.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001889", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "True" - } - ] - }, - { - "column": "Required exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD34:negative" - }, - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD123:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(CD56:positive OR CD56:high)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD127:negative" - }, - { - "column": "Ideal phenotypic markers", - "clause": "(CD33:negative OR CD64:negative)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD20", - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "77102d43f9abced8b3efd2e11ad6d91a492bf101ebdb061a1fd67aaaa275c58c", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001289", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001889", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD14", - "tokens": [ - "CD14" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001889", - "tokens": [ - "CD14" - ] - } - ] - } - ] - }, - "registry_row": 2, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000002", - "sheet_row": 3, - "abbreviation": "NK2", - "label": "Natural Killer Cell 2", - "parent": "NK", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD127", - "CD14", - "CD15", - "CD16", - "CD19", - "CD3", - "CD33", - "CD34", - "CD45", - "CD56", - "CD57", - "CD64", - "CD66b", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "", - "Parent": "NK", - "Abbreviation": "NK2", - "Full Name": "Natural Killer Cell 2", - "synonym": "", - "Type of Match": "Surface Only (SO)", - "OLS CL identifier": "", - "Required exclusion": "(CD14-|CD33-|CD64-) CD34- CD3- CD19- ", - "Ideal exclusion": "[HLA-DR+ CD11chi]- (CD15-|CD66b-) CD123-", - "Required phenotypic markers": "live/ CD45+ CD56hi CD127- CD16-/lo CD57- ", - "Ideal phenotypic markers": "", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000002", - "legacy_subject_id": "SOULCAP:NK2", - "abbreviation": "NK2", - "subject_label": "Natural Killer Cell 2", - "cl_id": "CL:0000938", - "cl_label": "CD16-negative, CD56-bright natural killer cell, human", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "", - "note": "", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001889", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Required exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD56:high", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001024", - "relation": "RO:0015015", - "sense": "high", - "asserted": "True" - 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"tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000002065", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD117", - "tokens": [ - "CD117" - ] - }, - { - "via": "pro_id", - "pr": "PR:000002065", - "tokens": [ - "CD117" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:P10721", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:P13591", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:P28906", - "asserted": "True", - "paths": [] - } - ] - }, - "registry_row": 7, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000007", - "sheet_row": 8, - "abbreviation": "ILC", - "label": "Innate Lymphoid Cell", - "parent": "", - 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"pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - } - ] - }, - "registry_row": 8, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000008", - "sheet_row": 9, - "abbreviation": "ILC1", - "label": "Innate Lymphoid Cell 1", - "parent": "ILC", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD117", - "CD11c", - "CD123", - "CD127", - "CD14", - "CD15", - "CD19", - "CD294", - "CD3", - "CD33", - "CD34", - "CD45", - "CD56", - "CD64", - "CD66b", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "no", - "WB or PBMC": "", - "Parent": "ILC", - 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"tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001865", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD123", - "tokens": [ - "CD123" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001865", - "tokens": [ - "CD123" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000002027", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD1C", - "tokens": [ - "CD1C" - ] - }, - { - "via": "exact_alias", - "source_token": "CD1C", - "tokens": [ - "CD1C" - ] - }, - { - "via": "pro_id", - "pr": "PR:000002027", - "tokens": [ - "CD1C" - ] - } - ] - } - ] - }, - "registry_row": 14, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000014", - "sheet_row": 15, - "abbreviation": "pDC", - "label": "Peripheral Dendritic Cell", - "parent": "", - "specimen": "PBMC", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD123", - "CD127", - "CD14", - "CD15", - "CD16", - "CD19", - "CD193", - "CD3", - "CD303", - "CD33", - "CD45", - "CD56", - "CD66b", - "FceR1a" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "PBMC", - "Parent": "", - "Abbreviation": "pDC", - "Full Name": "Peripheral Dendritic Cell", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "CD3-", - "Ideal exclusion": "CD56- CD19- CD127- (CD15-|CD66b-) CD14- CD16- ", - "Required phenotypic markers": "live/ CD45+ (CD33lo/+|CD123hi) (CD193-|FceR1a-|CD303+)", - "Ideal phenotypic markers": "", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000014", - "legacy_subject_id": "SOULCAP:pDC", - "abbreviation": "pDC", - "subject_label": "Plasmacytoid Dendritic Cell", - "cl_id": "CL:0001058", - 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Sheet's Full Name reads 'Peripheral Dendritic Cell' (likely a typo for 'Plasmacytoid'); not yet corrected at source.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Ideal exclusion", - "clause": "CD56:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001024", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Ideal exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Ideal exclusion", - "clause": "CD14:negative", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001889", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "True" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD127:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(CD33:low OR CD33:positive OR CD123:high)" - }, - { - "column": "Required phenotypic markers", - "clause": "(CD193:negative OR FCER1A:negative OR CD303:positive)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD11C", - "CD20", - "CD34", - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "90a3916e208c3f3f041f7567896fcd45d341337251da243d921d8127b8562d71", - "sheet_cl_id": "", - 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"pr": "PR:000001865", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD123", - "tokens": [ - "CD123" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001865", - "tokens": [ - "CD123" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000002015", - "asserted": "False", - "paths": [] - } - ] - }, - "registry_row": 15, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000015", - "sheet_row": 16, - "abbreviation": "Basophil", - "label": "Basophil", - "parent": "", - "specimen": "PBMC", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD123", - "CD127", - "CD14", - "CD15", - "CD16", - "CD19", - "CD193", - "CD3", - "CD303", - "CD33", - "CD45", - "CD56", - "CD66b", - "FceR1a", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "PBMC", - "Parent": "", - "Abbreviation": "Basophil", - 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"asserted": "False" - } - ] - }, - { - "column": "Ideal phenotypic markers", - "clause": "FCER1A:positive", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000007431", - "relation": "RO:0015015", - "sense": "high", - "asserted": "False" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD127:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD14:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Ideal phenotypic markers", - "clause": "HLA-DR:negative" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD11B", - "CD154", - "CD203C", - "CD3E", - "CD40", - "CD40LG", - "CD67", - "CD87", - "CD8A" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "6ae772d0622c8988d15f047ef4570ab309a99edce893328ef9c815aec7e0c1b3", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001255", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD193", - "tokens": [ - "CD193" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001255", - "tokens": [ - "CD193" - ] - } - ] - }, - { - "sense": "high", - "pr": "PR:000001865", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD123", - "tokens": [ - "CD123" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001865", - "tokens": [ - "CD123" - ] - } - ] - }, - { - "sense": "high", - "pr": "PR:000007431", - "asserted": "False", - "paths": [ - { - "via": "pro_id", - "pr": "PR:000007431", - 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{ - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001012", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11B", - "tokens": [ - "CD11B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001332", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD66B", - "tokens": [ - "CD66B" - ] - }, - { - "via": "exact_alias", - "source_token": "CD67", - "tokens": [ - "CD67" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001332", - "tokens": [ - "CD66B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001344", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD203C", - "tokens": [ - "CD203C" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001950", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD154", - "tokens": [ - "CD154" - ] - }, - { - "via": "exact_alias", - "source_token": "CD40", - "tokens": [ - "CD40" - ] - }, - { - "via": "exact_alias", - "source_token": "CD40LG", - "tokens": [ - "CD40LG" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001969", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD87", - "tokens": [ - "CD87" - ] - } - ] - } - ] - }, - "registry_row": 16, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000016", - "sheet_row": 17, - "abbreviation": "Basophil", - "label": "Basophil", - "parent": "", - "specimen": "WB", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD123", - "CD127", - "CD15", - "CD19", - "CD193", - "CD3", - "CD45", - "CD56", - "CD66b" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "WB", - 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"assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001024", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Ideal exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD193:positive", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001255", - "relation": "RO:0015015", - "sense": "high", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD123:positive", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001865", - "relation": "RO:0015015", - "sense": "high", - "asserted": "False" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Required exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD127:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD11B", - "CD154", - "CD203C", - "CD3E", - "CD40", - "CD40LG", - "CD67", - "CD87", - "CD8A", - "FCER1A" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "b5e758e040d00ac23abae3ebc35dddae9abe67be32d404eb68c7345159c4132c", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001255", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD193", - "tokens": [ - "CD193" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001255", - "tokens": [ - "CD193" - ] - } - ] - }, - { - "sense": "high", - "pr": "PR:000001865", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD123", - "tokens": [ - "CD123" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001865", - "tokens": [ - "CD123" - ] - } - ] - }, - { - "sense": "high", - "pr": "PR:000007431", - "asserted": "False", - "paths": [ - { - "via": "pro_id", - "pr": "PR:000007431", - "tokens": [ - "FCER1A" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001084", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - }, - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001012", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11B", - "tokens": [ - "CD11B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001332", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD66B", - "tokens": [ - "CD66B" - ] - }, - { - "via": "exact_alias", - "source_token": "CD67", - "tokens": [ - "CD67" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001332", - "tokens": [ - "CD66B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001344", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD203C", - "tokens": [ - "CD203C" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001950", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD154", - "tokens": [ - "CD154" - ] - }, - { - "via": "exact_alias", - "source_token": "CD40", - "tokens": [ - "CD40" - ] - }, - { - "via": "exact_alias", - "source_token": "CD40LG", - "tokens": [ - "CD40LG" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001969", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD87", - "tokens": [ - "CD87" - ] - } - ] - } - ] - }, - "registry_row": 17, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000017", - "sheet_row": 18, - "abbreviation": "Mono", - "label": "Monocyte", - "parent": "", - "specimen": "WB and PBMC", - "errors": [ - { - "column": "Required exclusion", - "expression": "CD56- CD19- ([CD123hi]- CD303-) ([CD123hi|CD193-)", - "error": "unexpected ')' in group" - } - ], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD14", - "CD15", - "CD3", - "CD33", - "CD45", - "CD64", - "CD66b" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "WB and PBMC", - "Parent": "", - "Abbreviation": "Mono", - "Full Name": "Monocyte", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "CL:0000576", - "Required exclusion": "CD56- CD19- ([CD123hi]- CD303-) ([CD123hi|CD193-)", - "Ideal exclusion": "[CD15hi|CD66b+]- CD3-", - "Required phenotypic markers": "live/ CD45+ CD14+/- CD11c+/-", - "Ideal phenotypic markers": "(CD64+/-|CD33+)", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000017", - "legacy_subject_id": "SOULCAP:Mono", - "abbreviation": "Mono", - "subject_label": "Monocyte", - "cl_id": "CL:0000576", - "cl_label": "monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match (OLS4 was timing out); CL:0000576 has no marker axioms recorded at all. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "84c375696035c6d7c9de16751255259e8e834ac9287f201f13ed821a7bfdda5d", - "sheet_cl_id": "CL:0000576", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 18, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000018", - "sheet_row": 19, - "abbreviation": "CMo", - "label": "Classical Monocyte", - "parent": "Mono", - "specimen": "WB and PBMC", - "errors": [ - { - "column": "Required exclusion", - "expression": "CD56- CD19- ([CD123hi]- CD303-) ([CD123hi|CD193-)", - "error": "unexpected ')' in group" - } - ], - "profile_changed": false, - "tokens": [ - "CD14", - "CD15", - "CD16", - "CD3", - "CD33", - "CD45", - "CD64", - "CD66b" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "WB and PBMC", - "Parent": "Mono", - "Abbreviation": "CMo", - "Full Name": "Classical Monocyte", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "CL:0000860", - "Required exclusion": "CD56- CD19- ([CD123hi]- CD303-) ([CD123hi|CD193-)", - "Ideal exclusion": "[CD15hi|CD66b+]- CD3- ", - "Required phenotypic markers": "live/ CD45+ CD14+ CD16-", - "Ideal phenotypic markers": "(CD64+|CD33+)", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000018", - "legacy_subject_id": "SOULCAP:CMo", - "abbreviation": "CMo", - "subject_label": "Classical Monocyte", - "cl_id": "CL:0000860", - "cl_label": "classical monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match. CL:0000860 asserts only CCR2 (CD192) and lineage negatives, not the CD14/CD16 axioms that actually define this subset — already tracked by repo issue #12. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "4c9436c977492d1ccea66ec05a22925897e6235162061f41dbf8e4e09ac940e3", - "sheet_cl_id": "CL:0000860", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 19, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000019", - "sheet_row": 20, - "abbreviation": "NCMo", - "label": "Non-classical Monocyte", - "parent": "Mono", - "specimen": "WB and PBMC", - "errors": [ - { - "column": "Required exclusion", - "expression": "CD56- CD19- ([CD123hi]- CD303-) ([CD123hi|CD193-)", - "error": "unexpected ')' in group" - } - ], - "profile_changed": false, - "tokens": [ - "CD14", - "CD15", - "CD16", - "CD3", - "CD33", - "CD45", - "CD64", - "CD66b" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "WB and PBMC", - "Parent": "Mono", - "Abbreviation": "NCMo", - "Full Name": "Non-classical Monocyte", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "CL:0000875", - "Required exclusion": "CD56- CD19- ([CD123hi]- CD303-) ([CD123hi|CD193-)", - "Ideal exclusion": "[CD15hi|CD66b+]- CD3- ", - "Required phenotypic markers": "live/ CD45+ CD14lo/- CD16+ ", - "Ideal phenotypic markers": "(CD64+/-|CD33+)", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000019", - "legacy_subject_id": "SOULCAP:NCMo", - "abbreviation": "NCMo", - "subject_label": "Non-classical Monocyte", - "cl_id": "CL:0000875", - "cl_label": "non-classical monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match. CL:0000875 asserts only CX3CR1 and lineage negatives, not the CD14/CD16 axioms that actually define this subset — already tracked by repo issue #12. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "2ccb34f2fc50e1126131986d487fe42c67bdcacc16330874b67750b017cbeab0", - "sheet_cl_id": "CL:0000875", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 20, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000020", - "sheet_row": 21, - "abbreviation": "IntMo", - "label": "Intermediate Monocyte", - "parent": "Mono", - "specimen": "WB and PBMC", - "errors": [ - { - "column": "Required exclusion", - "expression": "CD56- CD19- ([CD123hi]- CD303-) ([CD123hi|CD193-)", - "error": "unexpected ')' in group" - } - ], - "profile_changed": false, - "tokens": [ - "CD14", - "CD15", - "CD16", - "CD3", - "CD33", - "CD45", - "CD64", - "CD66b" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "WB and PBMC", - "Parent": "Mono", - "Abbreviation": "IntMo", - "Full Name": "Intermediate Monocyte", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "CL:0002393", - "Required exclusion": "CD56- CD19- ([CD123hi]- CD303-) ([CD123hi|CD193-)", - "Ideal exclusion": "[CD15hi|CD66b+]- CD3- ", - "Required phenotypic markers": "live/ CD45+ CD14+ CD16hi ", - "Ideal phenotypic markers": "(CD64+|CD33+)", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000020", - "legacy_subject_id": "SOULCAP:IntMo", - "abbreviation": "IntMo", - "subject_label": "Intermediate Monocyte", - "cl_id": "CL:0002393", - "cl_label": "intermediate monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match. CL:0002393 asserts only CCR2 (CD192, negative) and lineage negatives, not the CD14/CD16 axioms that actually define this subset — already tracked by repo issue #12. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "aa79f8b8798d9b79b35cd87edef7133ca5b824636f3f05d0dfe1b990d87d97c3", - "sheet_cl_id": "CL:0002393", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 21, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000021", - "sheet_row": 22, - "abbreviation": "Neut", - "label": "Neutrophil", - "parent": "", - "specimen": "WB and PBMC", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD14", - "CD15", - "CD16", - "CD19", - "CD193", - "CD3", - "CD33", - "CD45", - "CD56", - "CD64", - "CD66b", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "WB and PBMC", - "Parent": "", - "Abbreviation": "Neut", - "Full Name": "Neutrophil", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "CD3- CD56- CD14lo/- CD123-", - "Ideal exclusion": "CD19- [HLA-DR+ CD11chi]-", - "Required phenotypic markers": "live/ CD45+ (CD15hi|CD66b+) CD193- CD16hi", - "Ideal phenotypic markers": "(CD64-|CD33+)", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000021", - "legacy_subject_id": "SOULCAP:Neutrophil", - "abbreviation": "Neutrophil", - "subject_label": "Neutrophil", - "cl_id": "CL:0000775", - "cl_label": "neutrophil", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "", - "note": "", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required exclusion", - "clause": "CD56:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001024", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Ideal exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "(CD15:high OR CD66B:positive)", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001332", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "False" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Required exclusion", - "clause": "(CD14:low OR CD14:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD193:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD16:high" - }, - { - "column": "Ideal phenotypic markers", - "clause": "(CD64:negative OR CD33:positive)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD11B", - "CD3E", - "CD67", - "CD87", - "CD8A" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "6a7f385e7dd5e22ba96aeedb4aa46fb2e6ab411bc046567fac5d0aeb3ea7f587", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001084", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - }, - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001012", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11B", - "tokens": [ - "CD11B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001332", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD66B", - "tokens": [ - "CD66B" - ] - }, - { - "via": "exact_alias", - "source_token": "CD67", - "tokens": [ - "CD67" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001332", - "tokens": [ - "CD66B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001479", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:000001879", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:000001969", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD87", - "tokens": [ - "CD87" - ] - } - ] - } - ] - }, - "registry_row": 22, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000022", - "sheet_row": 23, - "abbreviation": "Eos", - "label": "Eosinophil", - "parent": "", - "specimen": "WB", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD14", - "CD15", - "CD16", - "CD19", - "CD193", - "CD3", - "CD33", - "CD45", - "CD56", - "CD64", - "CD66b", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "WB", - "Parent": "", - "Abbreviation": "Eos", - "Full Name": "Eosinophil", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "CD3- CD56- CD14lo/- CD123-", - "Ideal exclusion": "CD19- [HLA-DR+ CD11chi]-", - "Required phenotypic markers": "live/ CD45+ (CD15hi|CD66b+) CD193+ CD16- ", - "Ideal phenotypic markers": "(CD64-|CD33+)", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000022", - "legacy_subject_id": "SOULCAP:Eosinophil", - "abbreviation": "Eosinophil", - "subject_label": "Eosinophil", - "cl_id": "CL:0000771", - "cl_label": "eosinophil", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "", - "note": "CD193 (CCR3) positive is directly asserted (not inferred) on CL:0000771, precisely matching SOULCAP's defining CD193+ requirement — one of the stronger marker-confirmed matches in this set.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required exclusion", - "clause": "CD56:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001024", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Ideal exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "(CD15:high OR CD66B:positive)", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001332", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD193:positive", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001255", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "True" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Required exclusion", - "clause": "(CD14:low OR CD14:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD16:negative" - }, - { - "column": "Ideal phenotypic markers", - "clause": "(CD64:negative OR CD33:positive)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD11B", - "CD191", - "CD3E", - "CD44", - "CD67", - "CD69", - "CD87", - "CD8A", - "CD9", - "CDW44" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "874205816800964db5c591f96652bdac9d28acef6907b20275b346c4e2cc3524", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001084", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - }, - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001012", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11B", - "tokens": [ - "CD11B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001254", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD191", - "tokens": [ - "CD191" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001255", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD193", - "tokens": [ - "CD193" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001255", - "tokens": [ - "CD193" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001307", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD44", - "tokens": [ - "CD44" - ] - }, - { - "via": "exact_alias", - "source_token": "CDW44", - "tokens": [ - "CDW44" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001332", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD66B", - "tokens": [ - "CD66B" - ] - }, - { - "via": "exact_alias", - "source_token": "CD67", - "tokens": [ - "CD67" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001332", - "tokens": [ - "CD66B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001343", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD69", - "tokens": [ - "CD69" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001969", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD87", - "tokens": [ - "CD87" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000005178", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD9", - "tokens": [ - "CD9" - ] - } - ] - } - ] - }, - "registry_row": 23, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000023", - "sheet_row": 24, - "abbreviation": "B cell", - "label": "B cell", - "parent": "", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD127", - "CD14", - "CD15", - "CD16", - "CD19", - "CD20", - "CD3", - "CD33", - "CD45", - "CD56", - "CD64", - "CD66b", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "", - "Parent": "", - "Abbreviation": "B cell", - "Full Name": "B cell", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "(CD14-|CD33-|CD64-) CD3- CD56-", - "Ideal exclusion": "CD127- CD16- (CD15-|CD66b-) [HLA-DR+ CD11chi]- CD123-", - "Required phenotypic markers": "live/ CD45+ (CD20+|CD19+)", - "Ideal phenotypic markers": "CD20+", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000023", - "legacy_subject_id": "SOULCAP:B_cell", - "abbreviation": "B cell", - "subject_label": "B cell", - "cl_id": "CL:0000236", - "cl_label": "B cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OLS4 REST search returned zero hits for this exact query; found instead via OAK. CL:0000236 has no marker axioms recorded.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "no_marker_support", - "matched": [], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Required exclusion", - "clause": "CD56:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD127:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "CD123:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(CD20:positive OR CD19:positive)" - }, - { - "column": "Ideal phenotypic markers", - "clause": "CD20:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "a0300906ff3acd98f58b8ebb9443d973b9710447d8ab4736aa111ae172b1df78", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - }, - "registry_row": 24, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000024", - "sheet_row": 25, - "abbreviation": "ASC", - "label": "Antibody Secreting Cell", - "parent": "", - "specimen": "", - "errors": [], - 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}, - { - "column": "Ideal exclusion", - "clause": "CD123:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD19:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(CD27:positive OR CD27:high)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD38:high" - }, - { - "column": "Ideal phenotypic markers", - "clause": "(CD20:low OR CD20:negative)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "a80b760b7494b5ccacbfeb5822368766f2b27665ee08fea9e8e1f9c303a76c79", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - }, - "registry_row": 25, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000025", - "sheet_row": 26, - "abbreviation": "PB", - "label": "Plasmablast", - "parent": "ASC", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD127", - "CD138", - "CD14", - "CD15", - "CD16", - "CD19", - "CD20", - "CD27", - "CD3", - "CD33", - "CD38", - "CD45", - "CD56", - "CD64", - "CD66b", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "", - "Parent": "ASC", - "Abbreviation": "PB", - "Full Name": "Plasmablast", - "synonym": "", - "Type of Match": "Surface Only (SO)", - "OLS CL identifier": "", - "Required exclusion": "(CD14-|CD33-|CD64-) CD3- CD56-", - "Ideal exclusion": "CD127- CD16- (CD15-|CD66b-) [HLA-DR+ CD11chi]- CD123-", - "Required phenotypic markers": "live/ CD45+ CD19+ CD27+/hi CD38hi CD138-", - "Ideal phenotypic markers": "CD20+/-", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000025", - "legacy_subject_id": "SOULCAP:PB", - "abbreviation": "PB", - "subject_label": "Plasmablast", - "cl_id": "CL:0000980", - "cl_label": "plasmablast", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "Lexical match; marker scoring found nothing useful.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required phenotypic markers", - "clause": "CD19:positive", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "(CD27:positive OR CD27:high)", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001963", - "relation": "RO:0015015", - "sense": "high", - "asserted": "True" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD38:high", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001408", - "relation": "RO:0015015", - "sense": "high", - "asserted": "True" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD138:negative", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001935", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "True" - } - ] - }, - { - "column": "Ideal phenotypic markers", - "clause": "(CD20:low OR CD20:negative)", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001289", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "True" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Required exclusion", - "clause": "CD56:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD127:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "CD123:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD27L", - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "9863d8716862be947cf0fcd9d032cfb66cc1eb2aa59415522dc05bae36ac21f0", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001408", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD38", - "tokens": [ - "CD38" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001408", - "tokens": [ - "CD38" - ] - } - ] - }, - { - "sense": "high", - "pr": "PR:000001963", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD27", - "tokens": [ - "CD27" - ] - }, - { - "via": "exact_alias", - "source_token": "CD27L", - "tokens": [ - "CD27L" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001963", - "tokens": [ - "CD27" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001289", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - 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Same term flagged in repo issue #13 for a rename to 'iNKT cell' (filed upstream, awaiting review) — mapping is correct either way.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required phenotypic markers: mixed '|' and space in a group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "60d4418f4342fb333e84d3d92b22dabdede98114b0a29f3c3f48abfab7e76e12", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "" - }, - "registry_row": 47, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000060", - "sheet_row": 61, - "abbreviation": "TCRab", - "label": "alpha/beta T cell", - "parent": "T cell", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD14", - "CD15", - "CD16", - "CD19", - "CD20", - "CD3", - "CD33", - "CD45", - "CD64", - "CD66b", - "HLA-DR", - "TCRab", - "TCRgd" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "", - "Parent": "T cell", - "Abbreviation": "TCRab", - "Full Name": "alpha/beta T cell", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "(CD14-|CD33-|CD64-) (CD19-|CD20-) CD123-", - "Ideal exclusion": "[HLA-DR+ CD11chi]- (CD15-|CD66b-) CD16-", - "Required phenotypic markers": "CD45+ CD3+ (TCRab+|TCRgd-)", - "Ideal phenotypic markers": "", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000060", - "legacy_subject_id": "SOULCAP:TCRab", - "abbreviation": "TCRab", - "subject_label": "alpha/beta T cell", - "cl_id": "CL:0000789", - "cl_label": "alpha-beta T cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OAK-verified; marker scoring returned unrelated myeloid terms.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "no_marker_support", - "matched": [], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "(CD19:negative OR CD20:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD3:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(TCRAB:positive OR TCRGD:negative)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "ba4169b61b018b402de9c4bdf1a7567c89a69d002b6069e3dcd2040bf2174626", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - }, - "registry_row": 45, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000061", - "sheet_row": 62, - "abbreviation": "TCRgd", - "label": "gamma/delta T cell", - "parent": "T cell", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD14", - "CD15", - "CD16", - "CD19", - "CD20", - "CD3", - "CD33", - "CD45", - "CD64", - "CD66b", - "HLA-DR", - "TCRab", - "TCRgd" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "", - "Parent": "T cell", - "Abbreviation": "TCRgd", - "Full Name": "gamma/delta T cell", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "(CD14-|CD33-|CD64-) (CD19-|CD20-) CD123-", - "Ideal exclusion": "[HLA-DR+ CD11chi]- (CD15-|CD66b-) CD16-", - "Required phenotypic markers": "CD45+ CD3+ (TCRab-|TCRgd+)", - "Ideal phenotypic markers": "", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000061", - "legacy_subject_id": "SOULCAP:TCRgd", - "abbreviation": "TCRgd", - "subject_label": "gamma/delta T cell", - "cl_id": "CL:0000798", - "cl_label": "gamma-delta T cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OAK-verified; marker scoring returned unrelated myeloid terms.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "no_marker_support", - "matched": [], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "(CD19:negative OR CD20:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD3:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(TCRAB:negative OR TCRGD:positive)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "d7791919e73dbff413ca7cdf0c8b00616465d67ed2a7b2301cb1a628e972622e", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - }, - "registry_row": 46, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000062", - "sheet_row": 63, - "abbreviation": "CD4+ T cell", - "label": "alpha/beta and gamma/delta CD4+ T cells", - "parent": "T cell", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD14", - "CD15", - "CD16", - "CD19", - "CD20", - "CD3", - "CD33", - "CD4", - "CD45", - "CD64", - "CD66b", - "CD8", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "", - "Parent": "T cell", - "Abbreviation": "CD4+ T cell", - "Full Name": "alpha/beta and gamma/delta CD4+ T cells", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "(CD14-|CD33-|CD64-) (CD19-|CD20-) CD123-", - "Ideal exclusion": "[HLA-DR+ CD11chi]- (CD15-|CD66b-) CD16-", - "Required phenotypic markers": "CD45+ CD3+ CD4+ CD8-", - "Ideal phenotypic markers": "", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000062", - "legacy_subject_id": "SOULCAP:CD4+_T_cell", - "abbreviation": "CD4+ T cell", - "subject_label": "alpha/beta and gamma/delta CD4+ T cells", - "cl_id": "CL:0000624", - "cl_label": "CD4-positive, alpha-beta T cell", - "match_type": "Broad", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "CL has no combined alpha-beta+gamma-delta CD4+ term; alpha-beta dominates the CD4+ compartment.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required phenotypic markers", - "clause": "CD4:positive", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001004", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "True" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "(CD19:negative OR CD20:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD3:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD8:negative" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "13a042caf6eaa90447c12e475dcdeb8c94ab2c34f1847f43c379e4aff9aa0435", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000025402", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:000001004", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD4", - "tokens": [ - "CD4" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001004", - "tokens": [ - "CD4" - ] - } - ] - } - ] - }, - "registry_row": 52, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ], - "mapping_status": "proposed" - }, - { - "subject_id": "SOULCAP:SC000063", - "sheet_row": 64, - "abbreviation": "CD8+ T cell", - "label": "alpha/beta and gamma/delta CD8+ T cells", - "parent": "T cell", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD14", - "CD15", - "CD16", - "CD19", - "CD20", - "CD3", - "CD33", - "CD4", - "CD45", - "CD64", - "CD66b", - "CD8", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "", - "Parent": "T cell", - "Abbreviation": "CD8+ T cell", - "Full Name": "alpha/beta and gamma/delta CD8+ T cells", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "(CD14-|CD33-|CD64-) (CD19-|CD20-) CD123-", - "Ideal exclusion": "[HLA-DR+ CD11chi]- (CD15-|CD66b-) CD16-", - "Required phenotypic markers": "CD45+ CD3+ CD4- CD8+", - "Ideal phenotypic markers": "", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000063", - "legacy_subject_id": "SOULCAP:CD8+_T_cell", - "abbreviation": "CD8+ T cell", - "subject_label": "alpha/beta and gamma/delta CD8+ T cells", - "cl_id": "CL:0000625", - 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"parent": "T cell", - "specimen": "", - "errors": [], - "profile_changed": false, - "tokens": [ - "CD11c", - "CD123", - "CD14", - "CD15", - "CD16", - "CD19", - "CD20", - "CD3", - "CD33", - "CD4", - "CD45", - "CD64", - "CD66b", - "CD8", - "HLA-DR" - ], - "profile": { - "Ready for OLS": "yes", - "WB or PBMC": "", - "Parent": "T cell", - "Abbreviation": "CD4+/CD8+ T cell", - "Full Name": "alpha/beta and gamma/delta CD4+ and CD8+ T cells", - "synonym": "", - "Type of Match": "Exact", - "OLS CL identifier": "", - "Required exclusion": "(CD14-|CD33-|CD64-) (CD19-|CD20-) CD123-", - "Ideal exclusion": "[HLA-DR+ CD11chi]- (CD15-|CD66b-) CD16-", - "Required phenotypic markers": "CD45+ CD3+ CD4+ CD8+ ", - "Ideal phenotypic markers": "", - "Nomenclature Notes": "", - "CL Mapping Notes": "" - }, - "mappings": [ - { - "subject_id": "SOULCAP:SC000064", - "legacy_subject_id": "SOULCAP:CD4+/CD8+_T_cell", - "abbreviation": "CD4+/CD8+ T cell", - "subject_label": "alpha/beta and gamma/delta CD4+ and CD8+ T cells", - 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{ - "sense": "high", - "pr": "PR:000001255", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD193", - "tokens": [ - "CD193" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001255", - "tokens": [ - "CD193" - ] - } - ] - }, - { - "sense": "high", - "pr": "PR:000001865", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD123", - "tokens": [ - "CD123" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001865", - "tokens": [ - "CD123" - ] - } - ] - }, - { - "sense": "high", - "pr": "PR:000007431", - "asserted": "False", - "paths": [ - { - "via": "pro_id", - "pr": "PR:000007431", - "tokens": [ - "FCER1A" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001084", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - }, - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001012", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11B", - "tokens": [ - "CD11B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001332", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD66B", - "tokens": [ - "CD66B" - ] - }, - { - "via": "exact_alias", - "source_token": "CD67", - "tokens": [ - "CD67" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001332", - "tokens": [ - "CD66B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001344", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD203C", - "tokens": [ - "CD203C" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001950", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD154", - "tokens": [ - "CD154" - ] - }, - { - "via": "exact_alias", - "source_token": "CD40", - "tokens": [ - "CD40" - ] - }, - { - "via": "exact_alias", - "source_token": "CD40LG", - "tokens": [ - "CD40LG" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001969", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD87", - "tokens": [ - "CD87" - ] - } - ] - } - ] - }, - "registry_row": 17, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000017", - "legacy_subject_id": "SOULCAP:Mono", - "abbreviation": "Mono", - "subject_label": "Monocyte", - "cl_id": "CL:0000576", - "cl_label": "monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match (OLS4 was timing out); CL:0000576 has no marker axioms recorded at all. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "84c375696035c6d7c9de16751255259e8e834ac9287f201f13ed821a7bfdda5d", - "sheet_cl_id": "CL:0000576", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 18, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000018", - "legacy_subject_id": "SOULCAP:CMo", - "abbreviation": "CMo", - "subject_label": "Classical Monocyte", - "cl_id": "CL:0000860", - "cl_label": "classical monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match. CL:0000860 asserts only CCR2 (CD192) and lineage negatives, not the CD14/CD16 axioms that actually define this subset — already tracked by repo issue #12. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "4c9436c977492d1ccea66ec05a22925897e6235162061f41dbf8e4e09ac940e3", - "sheet_cl_id": "CL:0000860", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 19, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000019", - "legacy_subject_id": "SOULCAP:NCMo", - "abbreviation": "NCMo", - "subject_label": "Non-classical Monocyte", - "cl_id": "CL:0000875", - "cl_label": "non-classical monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match. CL:0000875 asserts only CX3CR1 and lineage negatives, not the CD14/CD16 axioms that actually define this subset — already tracked by repo issue #12. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "2ccb34f2fc50e1126131986d487fe42c67bdcacc16330874b67750b017cbeab0", - "sheet_cl_id": "CL:0000875", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 20, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000020", - "legacy_subject_id": "SOULCAP:IntMo", - "abbreviation": "IntMo", - "subject_label": "Intermediate Monocyte", - "cl_id": "CL:0002393", - "cl_label": "intermediate monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match. CL:0002393 asserts only CCR2 (CD192, negative) and lineage negatives, not the CD14/CD16 axioms that actually define this subset — already tracked by repo issue #12. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "aa79f8b8798d9b79b35cd87edef7133ca5b824636f3f05d0dfe1b990d87d97c3", - "sheet_cl_id": "CL:0002393", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 21, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000021", - "legacy_subject_id": "SOULCAP:Neutrophil", - "abbreviation": "Neutrophil", - "subject_label": "Neutrophil", - "cl_id": "CL:0000775", - "cl_label": "neutrophil", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "", - "note": "", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required exclusion", - "clause": "CD56:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001024", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Ideal exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "(CD15:high OR CD66B:positive)", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001332", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "False" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Required exclusion", - "clause": "(CD14:low OR CD14:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD193:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD16:high" - }, - { - "column": "Ideal phenotypic markers", - "clause": "(CD64:negative OR CD33:positive)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD11B", - "CD3E", - "CD67", - "CD87", - "CD8A" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "6a7f385e7dd5e22ba96aeedb4aa46fb2e6ab411bc046567fac5d0aeb3ea7f587", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001084", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - }, - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001012", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11B", - "tokens": [ - "CD11B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001332", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD66B", - "tokens": [ - "CD66B" - ] - }, - { - "via": "exact_alias", - "source_token": "CD67", - "tokens": [ - "CD67" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001332", - "tokens": [ - "CD66B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001479", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:000001879", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:000001969", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD87", - "tokens": [ - "CD87" - ] - } - ] - } - ] - }, - "registry_row": 22, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000022", - "legacy_subject_id": "SOULCAP:Eosinophil", - "abbreviation": "Eosinophil", - "subject_label": "Eosinophil", - "cl_id": "CL:0000771", - "cl_label": "eosinophil", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "", - "note": "CD193 (CCR3) positive is directly asserted (not inferred) on CL:0000771, precisely matching SOULCAP's defining CD193+ requirement — one of the stronger marker-confirmed matches in this set.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required exclusion", - "clause": "CD56:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001024", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Ideal exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "(CD15:high OR CD66B:positive)", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001332", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD193:positive", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001255", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "True" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Required exclusion", - "clause": "(CD14:low OR CD14:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD16:negative" - }, - { - "column": "Ideal phenotypic markers", - "clause": "(CD64:negative OR CD33:positive)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD11B", - "CD191", - "CD3E", - "CD44", - "CD67", - "CD69", - "CD87", - "CD8A", - "CD9", - "CDW44" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "874205816800964db5c591f96652bdac9d28acef6907b20275b346c4e2cc3524", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001084", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - }, - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001012", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11B", - "tokens": [ - "CD11B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001254", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD191", - "tokens": [ - "CD191" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001255", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD193", - "tokens": [ - "CD193" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001255", - "tokens": [ - "CD193" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001307", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD44", - "tokens": [ - "CD44" - ] - }, - { - "via": "exact_alias", - "source_token": "CDW44", - "tokens": [ - "CDW44" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001332", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD66B", - "tokens": [ - "CD66B" - ] - }, - { - "via": "exact_alias", - "source_token": "CD67", - "tokens": [ - "CD67" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001332", - "tokens": [ - "CD66B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001343", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD69", - "tokens": [ - "CD69" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001969", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD87", - "tokens": [ - "CD87" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000005178", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD9", - "tokens": [ - "CD9" - ] - } - ] - } - ] - }, - "registry_row": 23, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000023", - "legacy_subject_id": "SOULCAP:B_cell", - "abbreviation": "B cell", - "subject_label": "B cell", - "cl_id": "CL:0000236", - "cl_label": "B cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OLS4 REST search returned zero hits for this exact query; found instead via OAK. 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{ - "pr": "PR:000001255", - "relation": "RO:0015015", - "sense": "high", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD123:positive", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001865", - "relation": "RO:0015015", - "sense": "high", - "asserted": "False" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Required exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD127:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD11B", - "CD154", - "CD203C", - "CD3E", - "CD40", - "CD40LG", - "CD67", - "CD87", - "CD8A", - "FCER1A" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - 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"paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11B", - "tokens": [ - "CD11B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001332", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD66B", - "tokens": [ - "CD66B" - ] - }, - { - "via": "exact_alias", - "source_token": "CD67", - "tokens": [ - "CD67" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001332", - "tokens": [ - "CD66B" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001344", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD203C", - "tokens": [ - "CD203C" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001950", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD154", - "tokens": [ - "CD154" - ] - }, - { - "via": "exact_alias", - "source_token": "CD40", - "tokens": [ - "CD40" - ] - }, - { - "via": "exact_alias", - 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"clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD3:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD4:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD8:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "1a94242804d7d285d6e99a84f940c5920cba588e703bc9807bd7066e7a931273", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - }, - "registry_row": 54, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000068", - "legacy_subject_id": "SOULCAP:CD4+/CD8+_TCRab_T_cell", - "abbreviation": "CD4+/CD8+ TCRab T cell", - 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{ - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD3:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(TCRAB:positive OR TCRGD:negative)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD4:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD8:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "03c69fac8ec012810b035a54f82237833b6f4299be38ce9139c761ca28f65d09", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - }, - "registry_row": 56, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000069", - "legacy_subject_id": "SOULCAP:CD4-/CD8-_TCRab_T_cell", - "abbreviation": "CD4-/CD8- TCRab T cell", - "subject_label": "CD4- and CD8- alpha/beta T cell", - "cl_id": "CL:0000789", - "cl_label": "alpha-beta T cell", - "match_type": "Broad", - "uncertain": true, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "Only CL:0002489 'double negative thymocyte' found — wrong tissue/maturity stage for a blood/PBMC panel.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "no_marker_support", - "matched": [], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "(CD19:negative OR CD20:negative)" - 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"sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - }, - "registry_row": 57, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0000798", - "label": "gamma-delta T cell", - "subject_ids": [ - "SOULCAP:SC000061", - "SOULCAP:SC000070", - "SOULCAP:SC000071", - "SOULCAP:SC000072" - ], - "relations": [ - "Broad", - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000061", - "legacy_subject_id": "SOULCAP:TCRgd", - "abbreviation": "TCRgd", - "subject_label": "gamma/delta T cell", - "cl_id": "CL:0000798", - "cl_label": "gamma-delta T cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OAK-verified; marker scoring returned unrelated myeloid terms.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - 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"clause": "CD16:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD3:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(TCRAB:negative OR TCRGD:positive)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD4:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD8:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "4bdfff88d621b6e25864f108e587296403ce0eb3f750a245df9360950cf11c2a", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - }, - "registry_row": 59, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - 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}, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD3:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(TCRAB:negative OR TCRGD:positive)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD4:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD8:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "133eef6f9076e3eb898ce7cacf7933f562be6fbd2f02d633a0eabe79675295e5", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - 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"clause": "CD3:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(TCRAB:negative OR TCRGD:positive)" - }, - { - "column": "Required phenotypic markers", - "clause": "CD8:negative" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD8A" - ], - "errors": [], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "14aa1fa36c44a759182a64cb01ef6287e81a7962a7a4d9e069923f7cbb98e097", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001004", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD4", - "tokens": [ - "CD4" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001004", - "tokens": [ - "CD4" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001084", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - }, - { - "via": "exact_alias", - "source_token": "CD8A", - "tokens": [ - "CD8A" - ] - } - ] - } - ] - }, - "registry_row": 51, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0000814", - "label": "mature NK T cell", - "subject_ids": [ - "SOULCAP:SC000059" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000059", - "legacy_subject_id": "SOULCAP:iNKT", - "abbreviation": "iNKT", - "subject_label": "Invariant Natural Killer T cell", - "cl_id": "CL:0000814", - "cl_label": "mature NK T cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OAK-verified. Same term flagged in repo issue #13 for a rename to 'iNKT cell' (filed upstream, awaiting review) — mapping is correct either way.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required phenotypic markers: mixed '|' and space in a group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "60d4418f4342fb333e84d3d92b22dabdede98114b0a29f3c3f48abfab7e76e12", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "" - }, - "registry_row": 47, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0000818", - "label": "transitional stage B cell", - "subject_ids": [ - "SOULCAP:SC000028" - ], - "relations": [ - "Broad" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000028", - "legacy_subject_id": "SOULCAP:T1/T2_B", - "abbreviation": "T1/T2 B", - "subject_label": "Transitonal B cell 1 and 2", - "cl_id": "CL:0000818", - "cl_label": "transitional stage B cell", - "match_type": "Broad", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "SOULCAP combines T1+T2 into one gate; CL keeps CL:0000958 (T1) and CL:0000959 (T2) separate under this parent term. Sheet's Full Name has a typo ('Transitonal').", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required phenotypic markers", - "clause": "(CD20:positive OR CD19:positive)", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "False" - }, - { - "pr": "PR:000001289", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "True" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "(CD38:high OR CD10:high)", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001408", - "relation": "RO:0015015", - "sense": "high", - "asserted": "True" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD24:high", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001932", - "relation": "RO:0015015", - "sense": "high", - "asserted": "True" - } - ] - }, - { - "column": "Ideal phenotypic markers", - "clause": "CD20:positive", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001289", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "True" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Required exclusion", - "clause": "CD56:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD127:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "CD123:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD27:negative" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "8e6bd76f1ceb75aafb12ce1c9f1f0a727efdb0db0ab1bd88934207cb56b8d23e", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001408", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD38", - "tokens": [ - "CD38" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001408", - "tokens": [ - "CD38" - ] - } - ] - }, - { - "sense": "high", - "pr": "PR:000001932", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD24", - "tokens": [ - "CD24" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001932", - "tokens": [ - "CD24" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001289", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - } - ] - }, - "registry_row": 28, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0000860", - "label": "classical monocyte", - "subject_ids": [ - "SOULCAP:SC000018" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000018", - "legacy_subject_id": "SOULCAP:CMo", - "abbreviation": "CMo", - "subject_label": "Classical Monocyte", - "cl_id": "CL:0000860", - "cl_label": "classical monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match. CL:0000860 asserts only CCR2 (CD192) and lineage negatives, not the CD14/CD16 axioms that actually define this subset — already tracked by repo issue #12. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "4c9436c977492d1ccea66ec05a22925897e6235162061f41dbf8e4e09ac940e3", - "sheet_cl_id": "CL:0000860", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 19, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0000875", - "label": "non-classical monocyte", - "subject_ids": [ - "SOULCAP:SC000019" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000019", - "legacy_subject_id": "SOULCAP:NCMo", - "abbreviation": "NCMo", - "subject_label": "Non-classical Monocyte", - "cl_id": "CL:0000875", - "cl_label": "non-classical monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match. CL:0000875 asserts only CX3CR1 and lineage negatives, not the CD14/CD16 axioms that actually define this subset — already tracked by repo issue #12. 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"profile_sha256": "2ccb34f2fc50e1126131986d487fe42c67bdcacc16330874b67750b017cbeab0", - "sheet_cl_id": "CL:0000875", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 20, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0000895", - "label": "naive thymus-derived CD4-positive, alpha-beta T cell", - "subject_ids": [ - "SOULCAP:SC000089" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000089", - "legacy_subject_id": "SOULCAP:CD4+_TCRab_Tnaive", - "abbreviation": "CD4+ TCRab Tnaive", - "subject_label": "CD4+ naive alpha/beta T cell", - "cl_id": "CL:0000895", - "cl_label": "naive thymus-derived CD4-positive, alpha-beta T cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OAK-verified.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "no_marker_support", - "matched": [], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "(CD19:negative OR CD20:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD127", - "CD197", - "CD25", - "CD4", - "CD44", - "CD45", - "CD45RA", - "CD62", - "CD62L", - "CDW127", - "CDW197", - "CDW44" - ], - "errors": [], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "9222b43d7123805f910fc3866ccc23838742b15d7126d08ee704d417946754d9", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001318", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD62", - "tokens": [ - "CD62" - ] - }, - { - "via": "exact_alias", - "source_token": "CD62L", - "tokens": [ - "CD62L" - ] - } - ] - }, - { - "sense": "low", - "pr": "PR:000001307", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD44", - "tokens": [ - "CD44" - ] - }, - { - "via": "exact_alias", - "source_token": "CDW44", - "tokens": [ - "CDW44" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001380", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD25", - "tokens": [ - "CD25" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001380", - "tokens": [ - "CD25" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000025402", - "asserted": "False", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:000001004", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD4", - "tokens": [ - "CD4" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001004", - "tokens": [ - "CD4" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001006", - "asserted": "False", - "paths": [ - { - "via": "pro_id", - "pr": "PR:000001006", - "tokens": [ - "CD45" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001015", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD45RA", - "tokens": [ - "CD45RA" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001203", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD197", - "tokens": [ - "CD197" - ] - }, - { - "via": "exact_alias", - "source_token": "CDW197", - "tokens": [ - "CDW197" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001869", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD127", - "tokens": [ - "CD127" - ] - }, - { - "via": "exact_alias", - "source_token": "CDW127", - "tokens": [ - "CDW127" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001869", - "tokens": [ - "CD127" - ] - } - ] - } - ] - }, - "registry_row": 75, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0000898", - "label": "naive T cell", - "subject_ids": [ - "SOULCAP:SC000087" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000087", - "legacy_subject_id": "SOULCAP:Tnaive", - "abbreviation": "Tnaive", - "subject_label": "Naive alpha/beta and gamma/delta T cell", - "cl_id": "CL:0000898", - "cl_label": "naive T cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OAK-verified; the one generic (non-CD4/CD8-split) differentiation-state term that does exist in CL.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "no_marker_support", - "matched": [], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "(CD19:negative OR CD20:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD127", - "CD197", - "CD44", - "CD45", - "CD45RA", - "CD62", - "CD62L", - "CDW127", - "CDW197", - "CDW44" - ], - "errors": [], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "9222b43d7123805f910fc3866ccc23838742b15d7126d08ee704d417946754d9", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001318", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD62", - "tokens": [ - "CD62" - ] - }, - { - "via": "exact_alias", - "source_token": "CD62L", - "tokens": [ - "CD62L" - ] - } - ] - }, - { - "sense": "low", - "pr": "PR:000001307", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD44", - "tokens": [ - "CD44" - ] - }, - { - "via": "exact_alias", - "source_token": "CDW44", - "tokens": [ - "CDW44" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001006", - "asserted": "False", - "paths": [ - { - "via": "pro_id", - "pr": "PR:000001006", - "tokens": [ - "CD45" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001015", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD45RA", - "tokens": [ - "CD45RA" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001203", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD197", - "tokens": [ - "CD197" - ] - }, - { - "via": "exact_alias", - "source_token": "CDW197", - "tokens": [ - "CDW197" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001869", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD127", - "tokens": [ - "CD127" - ] - }, - { - "via": "exact_alias", - "source_token": "CDW127", - "tokens": [ - "CDW127" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001869", - "tokens": [ - "CD127" - ] - } - ] - } - ] - }, - "registry_row": 74, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0000900", - "label": "naive thymus-derived CD8-positive, alpha-beta T cell", - "subject_ids": [ - "SOULCAP:SC000092" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000092", - "legacy_subject_id": "SOULCAP:CD8+_TCRab_Tnaive", - "abbreviation": "CD8+ TCRab Tnaive", - "subject_label": "CD8+ naive alpha/beta T cell", - "cl_id": "CL:0000900", - "cl_label": "naive thymus-derived CD8-positive, alpha-beta T cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OAK-verified.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - 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"sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001935", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD138", - "tokens": [ - "CD138" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001935", - "tokens": [ - "CD138" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001963", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD27", - "tokens": [ - "CD27" - ] - }, - { - "via": "exact_alias", - "source_token": "CD27L", - "tokens": [ - "CD27L" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001963", - "tokens": [ - "CD27" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001289", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - } - ] - }, - "registry_row": 35, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - }, - { - "subject_id": "SOULCAP:SC000036", - "legacy_subject_id": "SOULCAP:BDN4", - "abbreviation": "BDN4", - "subject_label": "Double Negative B cell 4", - "cl_id": "CL:0000981", - "cl_label": "double negative memory B cell", - "match_type": "Broad", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - 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"clause": "CD24:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "IGD:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD21:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD11C:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD185:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "IGE:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD138", - "CD27L", - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "826848dc5698b7889f50a91571479d4d8df3b69818c6e35d375cb0cbf9c78ff5", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001935", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD138", - "tokens": [ - "CD138" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001935", - "tokens": [ - "CD138" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001963", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD27", - "tokens": [ - "CD27" - ] - }, - { - "via": "exact_alias", - "source_token": "CD27L", - "tokens": [ - "CD27L" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001963", - "tokens": [ - "CD27" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001289", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - } - ] - }, - "registry_row": 36, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0000990", - "label": "conventional dendritic cell", - "subject_ids": [ - "SOULCAP:SC000011" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000011", - "legacy_subject_id": "SOULCAP:cDC", - "abbreviation": "cDC", - "subject_label": "Conventional Dendritic Cell", - "cl_id": "CL:0000990", - "cl_label": "conventional dendritic cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "Marker-axiom scoring returned unrelated candidates; match is lexical/name-based only.", - 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{ - "column": "Required exclusion", - "clause": "(CD123:not:high OR CD303:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD14:negative" - }, - { - "column": "Required exclusion", - "clause": "CD16:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD3:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD127:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(CD33:high OR CD64:positive)" - }, - { - "column": "Required phenotypic markers", - "clause": "HLA-DR:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD20", - "CD34", - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "334dd74448fec5173d10655dacd2b628cd103b346f3c6a7b37b061edc4ac9fa6", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001013", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11C", - "tokens": [ - "CD11C" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001013", - "tokens": [ - "CD11C" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001003", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD34", - "tokens": [ - "CD34" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001003", - "tokens": [ - "CD34" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001289", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - } - ] - }, - "registry_row": 12, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0001058", - "label": "plasmacytoid dendritic cell, human", - "subject_ids": [ - "SOULCAP:SC000014" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000014", - "legacy_subject_id": "SOULCAP:pDC", - "abbreviation": "pDC", - "subject_label": "Plasmacytoid Dendritic Cell", - "cl_id": "CL:0001058", - "cl_label": "plasmacytoid dendritic cell, human", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "Marker-axiom scoring returned unrelated candidates; match is lexical/name-based only. Sheet's Full Name reads 'Peripheral Dendritic Cell' (likely a typo for 'Plasmacytoid'); not yet corrected at source.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Ideal exclusion", - "clause": "CD56:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001024", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Ideal exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - }, - { - "column": "Ideal exclusion", - "clause": "CD14:negative", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000001889", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "True" - } - ] - } - ], - "contradictions": [], - 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"asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001289", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001889", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD14", - "tokens": [ - "CD14" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001889", - "tokens": [ - "CD14" - ] - } - ] - }, - { - "sense": "positive", - 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}, - { - "column": "Ideal exclusion", - "clause": "CD123:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD127:positive" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "2382ffa8b1693854f19ee2104691b9f0a0c23f6e976b56d1c507692da08d12fc", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - } - ] - }, - "registry_row": 8, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0001067", - "label": "group 1 innate lymphoid cell", - "subject_ids": [ - "SOULCAP:SC000008" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000008", - "legacy_subject_id": "SOULCAP:ILC1", - "abbreviation": "ILC1", - "subject_label": "Innate Lymphoid Cell 1", - "cl_id": "CL:0001067", - "cl_label": "group 1 innate lymphoid cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "Marker-axiom scoring found nothing useful for this lineage; match is lexical/name-based only. No human-specific CL term exists for group 1 (unlike group 2/3); filed as CL gap, repo issue #14.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required exclusion", - "clause": "CD19:negative", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001002", - "relation": "CL:4030046", - "sense": "negative", - "asserted": "False" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD34:negative" - }, - { - "column": "Required exclusion", - "clause": "CD3:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - 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{ - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - } - ] - }, - "registry_row": 9, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0001074", - "label": "CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human", - "subject_ids": [ - "SOULCAP:SC000006" - ], - "relations": [ - "Broad" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000006", - "legacy_subject_id": "SOULCAP:ILCp", - "abbreviation": "ILCp", - "subject_label": "Innate Lymphoid Cell Progenitor", - "cl_id": "CL:0001074", - "cl_label": "CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human", - "match_type": "Broad", - "uncertain": true, - "review_status": "needs_review", - "evidence_override": "", - "note": "SOULCAP profile does not test CD34; CL:0001073 (CD34-negative) and CL:0001082 (immature innate lymphoid cell) are equally marker-consistent alternatives, not ruled out.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "partial_support", - "matched": [ - { - "column": "Required phenotypic markers", - "clause": "CD56:positive", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001024", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD117:positive", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000002065", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "False" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD3:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD127:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD294:negative" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD19", - "CD34", - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "03443463d5f102ae603565b7efde6d5b2de1f1f9c96016ecffdf886dd673995e", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001003", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD34", - "tokens": [ - "CD34" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001003", - "tokens": [ - "CD34" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000002065", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD117", - "tokens": [ - "CD117" - ] - }, - { - "via": "pro_id", - "pr": "PR:000002065", - "tokens": [ - "CD117" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:P10721", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:P13591", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:P28906", - "asserted": "True", - "paths": [] - } - ] - }, - "registry_row": 7, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0001078", - "label": "group 3 innate lymphoid cell, human", - "subject_ids": [ - "SOULCAP:SC000010" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000010", - "legacy_subject_id": "SOULCAP:ILC3", - "abbreviation": "ILC3", - "subject_label": "Innate Lymphoid Cell 3", - "cl_id": "CL:0001078", - 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"lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "60bbd7b2b4b6bd74a25764ca423e651165008b0e6d59552268caf45876ec18f8", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001869", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - 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"clause": "(CD117:low OR CD117:negative)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD161", - "CD25", - "CD3E", - "CDW127" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "735345c450434e1f351231103ee6c81f7e0ba186fb9ce20230642a95b44c7a23", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001380", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD25", - "tokens": [ - "CD25" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001380", - "tokens": [ - "CD25" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001869", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD127", - "tokens": [ - "CD127" - ] - }, - { - "via": "exact_alias", - "source_token": "CDW127", - "tokens": [ - "CDW127" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001869", - "tokens": [ - "CD127" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001874", - "asserted": "False", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:000001941", - "asserted": "False", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:P01589", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:P16871", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CDW127", - "tokens": [ - "CDW127" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:P23771", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:Q12918", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD161", - "tokens": [ - "CD161" - ] - }, - { - "via": "pro_id", - "pr": "PR:Q12918", - "tokens": [ - "CD161" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:Q9Y5Y4", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD294", - "tokens": [ - "CD294" - ] - }, - { - "via": "pro_id", - "pr": "PR:Q9Y5Y4", - "tokens": [ - "CD294" - ] - } - ] - } - ] - }, - "registry_row": 10, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0002393", - "label": "intermediate monocyte", - "subject_ids": [ - "SOULCAP:SC000020" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000020", - "legacy_subject_id": "SOULCAP:IntMo", - "abbreviation": "IntMo", - "subject_label": "Intermediate Monocyte", - "cl_id": "CL:0002393", - "cl_label": "intermediate monocyte", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "sheet_confirmed", - "note": "OAK-verified exact label match. CL:0002393 asserts only CCR2 (CD192, negative) and lineage negatives, not the CD14/CD16 axioms that actually define this subset — already tracked by repo issue #12. Sheet-confirmed 2026-08: the master Google Sheet's 'OLS CL identifier' column was independently populated with this same CL ID.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "evidence": { - "status": "invalid_profile", - "matched": [], - "contradictions": [], - "gaps": [], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [ - "Required exclusion: unexpected ')' in group" - ], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "Sheet confirmation recorded in existing local edits (2026-08); retained without independent re-verification.", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "aa79f8b8798d9b79b35cd87edef7133ca5b824636f3f05d0dfe1b990d87d97c3", - "sheet_cl_id": "CL:0002393", - "sheet_confirmation": "agrees", - "sheet_notes": "" - }, - "registry_row": 21, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0002394", - "label": "CD141-positive myeloid dendritic cell", - "subject_ids": [ - "SOULCAP:SC000012" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000012", - "legacy_subject_id": "SOULCAP:cDC1", - "abbreviation": "cDC1", - "subject_label": "Conventional Dendritic Cell 1", - "cl_id": "CL:0002394", - "cl_label": "CD141-positive myeloid dendritic cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "Marker-axiom scoring returned unrelated candidates; match is lexical/name-based only, confirmed by direct OLS4 lookup after the batch lexical search had wrongly assigned cDC1 the same term as cDC2.", - 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"clause": "(CD33:high OR CD64:positive)" - }, - { - "column": "Required phenotypic markers", - "clause": "HLA-DR:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "CD1C:negative" - }, - { - "column": "Ideal phenotypic markers", - "clause": "CD172A:negative" - }, - { - "column": "Ideal phenotypic markers", - "clause": "FCER1A:negative" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD20", - "CD34", - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "26b00ac7a3eecc08344c5062dce97e2ccfd3a591c8a347be9f155b32e0128b25", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001013", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11C", - "tokens": [ - "CD11C" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001013", - "tokens": [ - "CD11C" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001003", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD34", - "tokens": [ - "CD34" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001003", - "tokens": [ - "CD34" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001289", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001865", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD123", - "tokens": [ - "CD123" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001865", - "tokens": [ - "CD123" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000002105", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD141", - "tokens": [ - "CD141" - ] - }, - { - "via": "pro_id", - "pr": "PR:000002105", - "tokens": [ - "CD141" - ] - } - ] - } - ] - }, - "registry_row": 13, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:0002399", - "label": "CD1c-positive myeloid dendritic cell", - "subject_ids": [ - "SOULCAP:SC000013" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000013", - "legacy_subject_id": "SOULCAP:cDC2", - "abbreviation": "cDC2", - "subject_label": "Conventional Dendritic Cell 2", - "cl_id": "CL:0002399", - "cl_label": "CD1c-positive myeloid dendritic cell", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "Marker-axiom scoring returned unrelated candidates; match is lexical/name-based only, confirmed correct by cross-check against cDC1.", - "lexical_evidence": "", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - 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"clause": "CD11C:high", - "assertion": "inferred", - "axioms": [ - { - "pr": "PR:000001013", - "relation": "RO:0015015", - "sense": "high", - "asserted": "False" - } - ] - }, - { - "column": "Required phenotypic markers", - "clause": "CD1C:positive", - "assertion": "direct", - "axioms": [ - { - "pr": "PR:000002027", - "relation": "RO:0002104", - "sense": "positive", - "asserted": "True" - } - ] - } - ], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "CD14:negative" - }, - { - "column": "Required exclusion", - "clause": "CD16:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD3:negative" - }, - { - "column": "Ideal exclusion", - "clause": "CD127:negative" - }, - { - "column": "Required phenotypic markers", - "clause": "CD45:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(CD33:high OR CD64:positive)" - }, - { - "column": "Required phenotypic markers", - "clause": "HLA-DR:positive" - }, - { - "column": "Required phenotypic markers", - "clause": "(CD141:low OR CD141:negative)" - }, - { - "column": "Ideal phenotypic markers", - "clause": "CD172A:positive" - }, - { - "column": "Ideal phenotypic markers", - "clause": "(FCER1A:low OR FCER1A:negative)" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [ - "CD11", - "CD20", - "CD34", - "CD3E" - ], - "errors": [], - "lexical_evidence": "", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "3e6dc30f6e3ac086a6d06bc8b78c27895cba0f8f343c29a212dd2cb02d6dddee", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [ - { - "sense": "high", - "pr": "PR:000001013", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD11", - "tokens": [ - "CD11" - ] - }, - { - "via": "exact_alias", - "source_token": "CD11C", - "tokens": [ - "CD11C" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001013", - "tokens": [ - "CD11C" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001003", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD34", - "tokens": [ - "CD34" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001003", - "tokens": [ - "CD34" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001024", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001289", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001865", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD123", - "tokens": [ - "CD123" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001865", - "tokens": [ - "CD123" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000002027", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD1C", - "tokens": [ - "CD1C" - ] - }, - { - "via": "exact_alias", - "source_token": "CD1C", - "tokens": [ - "CD1C" - ] - }, - { - "via": "pro_id", - "pr": "PR:000002027", - "tokens": [ - "CD1C" - ] - } - ] - } - ] - }, - "registry_row": 14, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:4030002", - "label": "effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated", - "subject_ids": [ - "SOULCAP:SC000103" - ], - "relations": [ - "Exact" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000103", - "legacy_subject_id": "SOULCAP:CD4+_TCRab_Temra", - "abbreviation": "CD4+ TCRab Temra", - "subject_label": "CD4+ CD45RA+ effector memory alpha/beta T cell", - "cl_id": "CL:4030002", - "cl_label": "effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated", - "match_type": "Exact", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "OAK-verified. No CD8+-specific counterpart with this 'terminally differentiated' qualifier was found — see gaps.tsv.", - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "evidence_source": "reports/candidate_cl_mappings_narrative.md", - "curator_evidence": "", - "evidence": { - "status": "no_marker_support", - "matched": [], - "contradictions": [], - "gaps": [ - { - "column": "Required exclusion", - "clause": "(CD14:negative OR CD33:negative OR CD64:negative)" - }, - { - "column": "Required exclusion", - "clause": "(CD19:negative OR CD20:negative)" - }, - { - "column": "Required exclusion", - "clause": "CD123:negative" - }, - { - "column": "Ideal exclusion", - "clause": "(HLA-DR:not:positive OR CD11C:not:high)" - }, - { - "column": "Ideal exclusion", - "clause": "(CD15:negative OR CD66B:negative)" - }, - { - "column": "Ideal exclusion", - "clause": "CD16:negative" - } - ], - "ideal_conflicts": [], - "untested_cl_markers": [], - "errors": [], - "lexical_evidence": "Legacy note records OAK verification; no query artifact retained.", - "literature_evidence": "", - "curator_evidence": "", - "review_status": "needs_review", - "resolution_mode": "explicit_marker_policy", - "profile_sha256": "9222b43d7123805f910fc3866ccc23838742b15d7126d08ee704d417946754d9", - "sheet_cl_id": "", - "sheet_confirmation": "not_recorded", - "sheet_notes": "", - "resolution_evidence": [] - }, - "registry_row": 81, - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md", - "href": "../../candidate_cl_mappings_narrative.md" - } - ] - } - ] - }, - { - "cl_id": "CL:4052055", - "label": "mature NK T cell, human", - "subject_ids": [ - "SOULCAP:SC000046", - "SOULCAP:SC000047", - "SOULCAP:SC000048", - "SOULCAP:SC000049", - "SOULCAP:SC000050", - "SOULCAP:SC000051", - "SOULCAP:SC000052", - "SOULCAP:SC000053", - "SOULCAP:SC000054", - "SOULCAP:SC000055", - "SOULCAP:SC000056", - "SOULCAP:SC000057", - "SOULCAP:SC000058" - ], - "relations": [ - "Broad" - ], - "mappings": [ - { - "subject_id": "SOULCAP:SC000046", - "legacy_subject_id": "SOULCAP:CD56+_T_cell", - "abbreviation": "CD56+ T cell", - "subject_label": "CD56+ T cell", - "cl_id": "CL:4052055", - "cl_label": "mature NK T cell, human", - "match_type": "Broad", - "uncertain": false, - "review_status": "needs_review", - "evidence_override": "no_marker_axiom", - "note": "Same term flagged in repo issue #13 for a rename to 'CD56-positive T cell, human' (filed upstream, awaiting review). 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this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "CD33", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#CD33", - "registry_sha256": "1de2ca7ac6bfd4daca770841d698b5635586630584ac1a6d8fd8f16537ea3e90" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "CD34", - "affected_subjects": [ - "SOULCAP:SC000001", - "SOULCAP:SC000002", - "SOULCAP:SC000003", - "SOULCAP:SC000004", - "SOULCAP:SC000005", - "SOULCAP:SC000007", - "SOULCAP:SC000008", - "SOULCAP:SC000009", - "SOULCAP:SC000010" - ], - "records": [ - { - "marker_token": "CD34", - "marker_synonyms": "", - "source_columns": "Required exclusion", - "pro_id": "PR:000001003", - "pro_label": "CD34 molecule", - "uniprot_id": "P28906", - "uniprot_label": "CD34 molecule", - "gene_symbol": "CD34", - "hgnc_id": "HGNC:1662", - "ncbi_gene_id": "", - "mapping_method": "cl_pro_tsv", - "confidence": "high", - "evidence": "reports/cl_pro_relationships.tsv", - "notes": "" - } - ], - "pro_ids": [ - "PR:000001003" - ], - "gene_symbols": [ - "CD34" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "CD34", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#CD34", - "registry_sha256": "ee16d3e65d632814251ced067773c95046ec569930b3dc4d22c9da1d9409c640" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "CD38", - "affected_subjects": [ - "SOULCAP:SC000024", - "SOULCAP:SC000025", - "SOULCAP:SC000026", - "SOULCAP:SC000028", - "SOULCAP:SC000029", - "SOULCAP:SC000030", - "SOULCAP:SC000031", - "SOULCAP:SC000032", - "SOULCAP:SC000033", - "SOULCAP:SC000034", - "SOULCAP:SC000035", - "SOULCAP:SC000036", - "SOULCAP:SC000037", - "SOULCAP:SC000038", - "SOULCAP:SC000039", - "SOULCAP:SC000040", - "SOULCAP:SC000041", - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044" - ], - "records": [ - { - "marker_token": "CD38", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:000001408", - "pro_label": "ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1", - "uniprot_id": "P28907", - "uniprot_label": "ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1", - "gene_symbol": "CD38", - "hgnc_id": "HGNC:1667", - "ncbi_gene_id": "", - "mapping_method": "cl_pro_tsv", - "confidence": "high", - "evidence": "reports/cl_pro_relationships.tsv", - "notes": "" - } - ], - "pro_ids": [ - "PR:000001408" - ], - "gene_symbols": [ - "CD38" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "CD38", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#CD38", - "registry_sha256": "a9443ead57bee08f430cd3737fc54621c649a971ee7e05530042406994fbbfb3" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "CD4", - "affected_subjects": [ - "SOULCAP:SC000047", - "SOULCAP:SC000048", - "SOULCAP:SC000050", - "SOULCAP:SC000051", - "SOULCAP:SC000052", - "SOULCAP:SC000053", - "SOULCAP:SC000055", - "SOULCAP:SC000056", - "SOULCAP:SC000057", - "SOULCAP:SC000058", - "SOULCAP:SC000062", - "SOULCAP:SC000063", - "SOULCAP:SC000064", - "SOULCAP:SC000065", - "SOULCAP:SC000066", - "SOULCAP:SC000067", - "SOULCAP:SC000068", - "SOULCAP:SC000069", - "SOULCAP:SC000070", - "SOULCAP:SC000071", - "SOULCAP:SC000072", - "SOULCAP:SC000073", - "SOULCAP:SC000115", - "SOULCAP:SC000116", - "SOULCAP:SC000117", - "SOULCAP:SC000118", - "SOULCAP:SC000119", - "SOULCAP:SC000121" - ], - "records": [ - { - "marker_token": "CD4", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:000001004", - "pro_label": "CD4 molecule", - "uniprot_id": "P01730", - "uniprot_label": "CD4 molecule", - "gene_symbol": "CD4", - "hgnc_id": "HGNC:1678", - "ncbi_gene_id": "", - "mapping_method": "cl_pro_tsv", - "confidence": "high", - "evidence": "reports/cl_pro_relationships.tsv", - "notes": "" - } - ], - "pro_ids": [ - "PR:000001004" - ], - "gene_symbols": [ - "CD4" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "CD4", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#CD4", - "registry_sha256": "0f768b0ba2691f0fdc2c64d396b8f89f5211d05b6773ee5dcfa2bb41bbff319c" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "CD45", - "affected_subjects": [ - "SOULCAP:SC000001", - "SOULCAP:SC000002", - "SOULCAP:SC000003", - "SOULCAP:SC000004", - "SOULCAP:SC000005", - "SOULCAP:SC000006", - "SOULCAP:SC000007", - "SOULCAP:SC000008", - "SOULCAP:SC000009", - "SOULCAP:SC000010", - "SOULCAP:SC000011", - "SOULCAP:SC000012", - "SOULCAP:SC000013", - "SOULCAP:SC000014", - "SOULCAP:SC000015", - "SOULCAP:SC000016", - "SOULCAP:SC000017", - "SOULCAP:SC000018", - "SOULCAP:SC000019", - "SOULCAP:SC000020", - "SOULCAP:SC000021", - "SOULCAP:SC000022", - "SOULCAP:SC000023", - "SOULCAP:SC000024", - "SOULCAP:SC000025", - "SOULCAP:SC000026", - "SOULCAP:SC000028", - "SOULCAP:SC000029", - "SOULCAP:SC000030", - "SOULCAP:SC000031", - "SOULCAP:SC000032", - "SOULCAP:SC000033", - "SOULCAP:SC000034", - "SOULCAP:SC000035", - "SOULCAP:SC000036", - "SOULCAP:SC000037", - "SOULCAP:SC000038", - "SOULCAP:SC000039", - "SOULCAP:SC000040", - "SOULCAP:SC000041", - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044", - "SOULCAP:SC000045", - "SOULCAP:SC000046", - "SOULCAP:SC000047", - "SOULCAP:SC000048", - "SOULCAP:SC000049", - "SOULCAP:SC000050", - "SOULCAP:SC000051", - "SOULCAP:SC000052", - "SOULCAP:SC000053", - "SOULCAP:SC000054", - "SOULCAP:SC000055", - "SOULCAP:SC000056", - "SOULCAP:SC000057", - "SOULCAP:SC000058", - "SOULCAP:SC000060", - "SOULCAP:SC000061", - "SOULCAP:SC000062", - "SOULCAP:SC000063", - "SOULCAP:SC000064", - "SOULCAP:SC000065", - "SOULCAP:SC000066", - "SOULCAP:SC000067", - "SOULCAP:SC000068", - "SOULCAP:SC000069", - "SOULCAP:SC000070", - "SOULCAP:SC000071", - "SOULCAP:SC000072", - "SOULCAP:SC000073", - "SOULCAP:SC000115", - "SOULCAP:SC000116", - "SOULCAP:SC000117", - "SOULCAP:SC000118", - "SOULCAP:SC000119", - "SOULCAP:SC000121", - "SOULCAP:SC000122" - ], - "records": [ - { - "marker_token": "CD45", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:000001006", - "pro_label": "receptor-type tyrosine-protein phosphatase C", - "uniprot_id": "P08575", - "uniprot_label": "receptor-type tyrosine-protein phosphatase C", - "gene_symbol": "PTPRC", - "hgnc_id": "HGNC:9666", - "ncbi_gene_id": "", - "mapping_method": "cl_pro_tsv", - "confidence": "high", - "evidence": "reports/cl_pro_relationships.tsv", - "notes": "" - } - ], - "pro_ids": [ - "PR:000001006" - ], - "gene_symbols": [ - "PTPRC" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "CD45", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#CD45", - "registry_sha256": "c2144181df41b433bc4c8b7710bfda4122607d87ade0ed2d33ff4865a4b3c49d" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "CD56", - "affected_subjects": [ - "SOULCAP:SC000001", - "SOULCAP:SC000002", - "SOULCAP:SC000003", - "SOULCAP:SC000004", - "SOULCAP:SC000005", - "SOULCAP:SC000006", - "SOULCAP:SC000008", - "SOULCAP:SC000009", - "SOULCAP:SC000010", - "SOULCAP:SC000011", - "SOULCAP:SC000012", - "SOULCAP:SC000013", - "SOULCAP:SC000014", - "SOULCAP:SC000015", - "SOULCAP:SC000016", - "SOULCAP:SC000021", - "SOULCAP:SC000022", - "SOULCAP:SC000023", - "SOULCAP:SC000024", - "SOULCAP:SC000025", - "SOULCAP:SC000026", - "SOULCAP:SC000028", - "SOULCAP:SC000029", - "SOULCAP:SC000030", - "SOULCAP:SC000031", - "SOULCAP:SC000032", - "SOULCAP:SC000033", - "SOULCAP:SC000034", - "SOULCAP:SC000035", - "SOULCAP:SC000036", - "SOULCAP:SC000037", - "SOULCAP:SC000038", - "SOULCAP:SC000039", - "SOULCAP:SC000040", - "SOULCAP:SC000041", - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044", - "SOULCAP:SC000046", - "SOULCAP:SC000047", - "SOULCAP:SC000048", - "SOULCAP:SC000049", - "SOULCAP:SC000050", - "SOULCAP:SC000051", - "SOULCAP:SC000052", - "SOULCAP:SC000053", - "SOULCAP:SC000054", - "SOULCAP:SC000055", - "SOULCAP:SC000056", - "SOULCAP:SC000057", - "SOULCAP:SC000058" - ], - "records": [ - { - "marker_token": "CD56", - "marker_synonyms": "", - "source_columns": "Ideal exclusion|Required exclusion|Required phenotypic markers", - "pro_id": "PR:000001024", - "pro_label": "neural cell adhesion molecule 1", - "uniprot_id": "P13591", - "uniprot_label": "neural cell adhesion molecule 1", - "gene_symbol": "NCAM1", - "hgnc_id": "HGNC:7656", - "ncbi_gene_id": "", - "mapping_method": "cl_pro_tsv", - "confidence": "high", - "evidence": "reports/cl_pro_relationships.tsv", - "notes": "" - } - ], - "pro_ids": [ - "PR:000001024" - ], - "gene_symbols": [ - "NCAM1" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "CD56", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#CD56", - "registry_sha256": "b51d188a6fdfada2e42569c7553233a5f7625ae2976ba24724e84a95db6ceff1" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "CD57", - "affected_subjects": [ - "SOULCAP:SC000002", - "SOULCAP:SC000004", - "SOULCAP:SC000005" - ], - "records": [ - { - "marker_token": "CD57", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "ols4", - "confidence": "low", - "evidence": "https://www.ebi.ac.uk/ols4/api/search?q=CD57&ontology=pr", - "notes": "B3GAT1 / HNK-1 epitope; 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this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "CD64", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#CD64", - "registry_sha256": "46571d20d73b5ef77ec5c7be28beda3c94890e33c17faf4904e285b294e2db47" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "CD66b", - "affected_subjects": [ - "SOULCAP:SC000001", - "SOULCAP:SC000002", - "SOULCAP:SC000003", - "SOULCAP:SC000004", - "SOULCAP:SC000005", - "SOULCAP:SC000007", - "SOULCAP:SC000008", - "SOULCAP:SC000009", - "SOULCAP:SC000010", - "SOULCAP:SC000014", - "SOULCAP:SC000015", - "SOULCAP:SC000016", - "SOULCAP:SC000017", - "SOULCAP:SC000018", - "SOULCAP:SC000019", - "SOULCAP:SC000020", - "SOULCAP:SC000021", - "SOULCAP:SC000022", - "SOULCAP:SC000023", - "SOULCAP:SC000024", - "SOULCAP:SC000025", - "SOULCAP:SC000026", - "SOULCAP:SC000028", - "SOULCAP:SC000029", - "SOULCAP:SC000030", - "SOULCAP:SC000031", - "SOULCAP:SC000032", - "SOULCAP:SC000033", - "SOULCAP:SC000034", - "SOULCAP:SC000035", - "SOULCAP:SC000036", - "SOULCAP:SC000037", - "SOULCAP:SC000038", - "SOULCAP:SC000039", - "SOULCAP:SC000040", - "SOULCAP:SC000041", - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044", - "SOULCAP:SC000045", - "SOULCAP:SC000046", - "SOULCAP:SC000047", - "SOULCAP:SC000048", - "SOULCAP:SC000049", - "SOULCAP:SC000050", - "SOULCAP:SC000051", - "SOULCAP:SC000052", - "SOULCAP:SC000053", - "SOULCAP:SC000054", - "SOULCAP:SC000055", - "SOULCAP:SC000056", - "SOULCAP:SC000057", - "SOULCAP:SC000058", - "SOULCAP:SC000059", - "SOULCAP:SC000060", - "SOULCAP:SC000061", - "SOULCAP:SC000062", - "SOULCAP:SC000063", - "SOULCAP:SC000064", - "SOULCAP:SC000065", - "SOULCAP:SC000066", - "SOULCAP:SC000067", - "SOULCAP:SC000068", - "SOULCAP:SC000069", - "SOULCAP:SC000070", - "SOULCAP:SC000071", - "SOULCAP:SC000072", - "SOULCAP:SC000073", - "SOULCAP:SC000074", - "SOULCAP:SC000075", - "SOULCAP:SC000076", - "SOULCAP:SC000077", - "SOULCAP:SC000078", - "SOULCAP:SC000079", - "SOULCAP:SC000080", - "SOULCAP:SC000081", - "SOULCAP:SC000082", - "SOULCAP:SC000083", - "SOULCAP:SC000084", - "SOULCAP:SC000085", - "SOULCAP:SC000086", - "SOULCAP:SC000087", - "SOULCAP:SC000088", - "SOULCAP:SC000089", - "SOULCAP:SC000090", - "SOULCAP:SC000091", - "SOULCAP:SC000092", - "SOULCAP:SC000093", - "SOULCAP:SC000094", - "SOULCAP:SC000095", - "SOULCAP:SC000096", - "SOULCAP:SC000097", - "SOULCAP:SC000098", - "SOULCAP:SC000099", - "SOULCAP:SC000100", - "SOULCAP:SC000101", - "SOULCAP:SC000102", - "SOULCAP:SC000103", - "SOULCAP:SC000104", - "SOULCAP:SC000105", - "SOULCAP:SC000106", - "SOULCAP:SC000107", - "SOULCAP:SC000108", - "SOULCAP:SC000109", - "SOULCAP:SC000110", - "SOULCAP:SC000111", - "SOULCAP:SC000112", - "SOULCAP:SC000113", - "SOULCAP:SC000114", - "SOULCAP:SC000115", - "SOULCAP:SC000116", - "SOULCAP:SC000117", - "SOULCAP:SC000118", - "SOULCAP:SC000119", - "SOULCAP:SC000120", - "SOULCAP:SC000121", - "SOULCAP:SC000122", - "SOULCAP:SC000123", - "SOULCAP:SC000124", - "SOULCAP:SC000125", - "SOULCAP:SC000126", - "SOULCAP:SC000127" - ], - "records": [ - { - "marker_token": "CD66b", - "marker_synonyms": "", - "source_columns": "Ideal exclusion|Required exclusion|Required phenotypic markers", - "pro_id": "PR:000001332", - "pro_label": "cell adhesion molecule CEACAM8", - "uniprot_id": "P31997", - "uniprot_label": "cell adhesion molecule CEACAM8", - "gene_symbol": "CEACAM8", - "hgnc_id": "HGNC:1820", - "ncbi_gene_id": "", - "mapping_method": "cl_pro_tsv", - "confidence": "high", - "evidence": "reports/cl_pro_relationships.tsv", - "notes": "" - } - ], - "pro_ids": [ - "PR:000001332" - ], - "gene_symbols": [ - "CEACAM8" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "CD66B", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#CD66b", - "registry_sha256": "42305fda07fd524b609244d79f171598c6b1b1b879466170789a47c30bc9033a" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "CD8", - "affected_subjects": [ - "SOULCAP:SC000047", - "SOULCAP:SC000048", - "SOULCAP:SC000050", - "SOULCAP:SC000051", - "SOULCAP:SC000052", - "SOULCAP:SC000053", - "SOULCAP:SC000055", - "SOULCAP:SC000056", - "SOULCAP:SC000057", - "SOULCAP:SC000058", - "SOULCAP:SC000062", - "SOULCAP:SC000063", - "SOULCAP:SC000064", - "SOULCAP:SC000065", - "SOULCAP:SC000066", - "SOULCAP:SC000067", - "SOULCAP:SC000068", - "SOULCAP:SC000069", - "SOULCAP:SC000070", - "SOULCAP:SC000071", - "SOULCAP:SC000072", - "SOULCAP:SC000073", - "SOULCAP:SC000115", - "SOULCAP:SC000116", - "SOULCAP:SC000117", - "SOULCAP:SC000118", - "SOULCAP:SC000119", - "SOULCAP:SC000121" - ], - "records": [ - { - "marker_token": "CD8", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:000001084", - "pro_label": "T-cell surface glycoprotein CD8 alpha chain", - "uniprot_id": "P01732", - "uniprot_label": "T-cell surface glycoprotein CD8 alpha chain", - "gene_symbol": "CD8A", - "hgnc_id": "HGNC:1706", - "ncbi_gene_id": "", - "mapping_method": "cl_pro_tsv", - "confidence": "high", - "evidence": "reports/cl_pro_relationships.tsv", - "notes": "" - } - ], - "pro_ids": [ - "PR:000001084" - ], - "gene_symbols": [ - "CD8A" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; 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https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=PR:000007431", - "notes": "high-affinity IgE receptor alpha chain" - } - ], - "pro_ids": [ - "PR:000007431" - ], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_gene_mapping", - "status": "no_gene_mapping", - "status_reason": "PRO identifier recorded, but no gene symbol or documented representation exception; review is needed.", - "resolution_policy": { - "marker_token": "FCER1A", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#FceR1a", - "registry_sha256": "0ffb585d4dc904f1d78456c5f8ae18e3d3c7e53e0a0addf4306a7654eec5884a" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "HLA-DR", - "affected_subjects": [ - "SOULCAP:SC000001", - "SOULCAP:SC000002", - "SOULCAP:SC000003", - "SOULCAP:SC000004", - "SOULCAP:SC000005", - "SOULCAP:SC000007", - "SOULCAP:SC000008", - "SOULCAP:SC000009", - "SOULCAP:SC000010", - "SOULCAP:SC000011", - "SOULCAP:SC000012", - "SOULCAP:SC000013", - "SOULCAP:SC000015", - "SOULCAP:SC000021", - "SOULCAP:SC000022", - "SOULCAP:SC000023", - "SOULCAP:SC000024", - "SOULCAP:SC000025", - "SOULCAP:SC000026", - "SOULCAP:SC000028", - "SOULCAP:SC000029", - "SOULCAP:SC000030", - "SOULCAP:SC000031", - "SOULCAP:SC000032", - "SOULCAP:SC000033", - "SOULCAP:SC000034", - "SOULCAP:SC000035", - "SOULCAP:SC000036", - "SOULCAP:SC000037", - "SOULCAP:SC000038", - "SOULCAP:SC000039", - "SOULCAP:SC000040", - "SOULCAP:SC000041", - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044", - "SOULCAP:SC000045", - "SOULCAP:SC000046", - "SOULCAP:SC000047", - "SOULCAP:SC000048", - "SOULCAP:SC000049", - "SOULCAP:SC000050", - "SOULCAP:SC000051", - "SOULCAP:SC000052", - "SOULCAP:SC000053", - "SOULCAP:SC000054", - "SOULCAP:SC000055", - "SOULCAP:SC000056", - "SOULCAP:SC000057", - "SOULCAP:SC000058", - "SOULCAP:SC000059", - "SOULCAP:SC000060", - "SOULCAP:SC000061", - "SOULCAP:SC000062", - "SOULCAP:SC000063", - "SOULCAP:SC000064", - "SOULCAP:SC000065", - "SOULCAP:SC000066", - "SOULCAP:SC000067", - "SOULCAP:SC000068", - "SOULCAP:SC000069", - "SOULCAP:SC000070", - "SOULCAP:SC000071", - "SOULCAP:SC000072", - "SOULCAP:SC000073", - "SOULCAP:SC000074", - "SOULCAP:SC000075", - "SOULCAP:SC000076", - "SOULCAP:SC000077", - "SOULCAP:SC000078", - "SOULCAP:SC000079", - "SOULCAP:SC000080", - "SOULCAP:SC000081", - "SOULCAP:SC000082", - "SOULCAP:SC000083", - "SOULCAP:SC000084", - "SOULCAP:SC000085", - "SOULCAP:SC000086", - "SOULCAP:SC000087", - "SOULCAP:SC000088", - "SOULCAP:SC000089", - "SOULCAP:SC000090", - "SOULCAP:SC000091", - "SOULCAP:SC000092", - "SOULCAP:SC000093", - "SOULCAP:SC000094", - "SOULCAP:SC000095", - "SOULCAP:SC000096", - "SOULCAP:SC000097", - "SOULCAP:SC000098", - "SOULCAP:SC000099", - "SOULCAP:SC000100", - "SOULCAP:SC000101", - "SOULCAP:SC000102", - "SOULCAP:SC000103", - "SOULCAP:SC000104", - "SOULCAP:SC000105", - "SOULCAP:SC000106", - "SOULCAP:SC000107", - "SOULCAP:SC000108", - "SOULCAP:SC000109", - "SOULCAP:SC000110", - "SOULCAP:SC000111", - "SOULCAP:SC000112", - "SOULCAP:SC000113", - "SOULCAP:SC000114", - "SOULCAP:SC000115", - "SOULCAP:SC000116", - "SOULCAP:SC000117", - "SOULCAP:SC000118", - "SOULCAP:SC000119", - "SOULCAP:SC000120", - "SOULCAP:SC000121", - "SOULCAP:SC000122", - "SOULCAP:SC000123", - "SOULCAP:SC000124", - "SOULCAP:SC000125", - "SOULCAP:SC000126", - "SOULCAP:SC000127" - ], - "records": [ - { - "marker_token": "HLA-DR", - "marker_synonyms": "", - "source_columns": "Ideal exclusion|Ideal phenotypic markers|Required phenotypic markers", - "pro_id": "PR:000002015", - "pro_label": "MHC class II histocompatibility antigen alpha chain DRA", - "uniprot_id": "", - "uniprot_label": "MHC class II histocompatibility antigen alpha chain DRA", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "ols4", - "confidence": "high", - "evidence": "https://www.ebi.ac.uk/ols4/api/search?q=HLA-DRA&ontology=pr; https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=PR:000002015", - "notes": "HLA-DR is a heterodimer of HLA-DRA + HLA-DRB1; mapped to HLA-DRA as primary chain" - } - ], - "pro_ids": [ - "PR:000002015" - ], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_gene_mapping", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "HLA-DR", - "representation": "complex", - "protein_resolution": "withhold", - "rationale": "Registry notes describe an assembled or multi-gene marker; component PRO identity cannot establish whole-marker equivalence.", - "source_ref": "marker_mappings/marker_protein_gene.csv#HLA-DR", - "registry_sha256": "c7b6d01f0a4eaffefce1df3c4a53407d958d2f032e03a9ce22f0354adbdded3c" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IFNg", - "affected_subjects": [ - "SOULCAP:SC000116" - ], - "records": [ - { - "marker_token": "IFNg", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers", - "pro_id": "PR:P01579", - "pro_label": "interferon gamma (human)", - "uniprot_id": "P01579", - "uniprot_label": "interferon gamma", - "gene_symbol": "IFNG", - "hgnc_id": "HGNC:5438", - "ncbi_gene_id": "", - "mapping_method": "monarch", - "confidence": "high", - "evidence": "https://rest.genenames.org/fetch/symbol/IFNG; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_P01579", - "notes": "intracellular marker" - } - ], - "pro_ids": [ - "PR:P01579" - ], - "gene_symbols": [ - "IFNG" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "IFNG", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IFNg", - "registry_sha256": "984c2f8cfe641da02a4d92ac78be3e3595127852ff7b8d67acacc0ae3361b8ba" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IL-13", - "affected_subjects": [ - "SOULCAP:SC000112", - "SOULCAP:SC000116", - "SOULCAP:SC000117" - ], - "records": [ - { - "marker_token": "IL-13", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers", - "pro_id": "PR:P35225", - "pro_label": "interleukin-13 (human)", - "uniprot_id": "P35225", - "uniprot_label": "interleukin 13", - "gene_symbol": "IL13", - "hgnc_id": "HGNC:5973", - "ncbi_gene_id": "", - "mapping_method": "monarch", - "confidence": "high", - "evidence": "https://rest.genenames.org/fetch/symbol/IL13; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_P35225", - "notes": "intracellular marker" - } - ], - "pro_ids": [ - "PR:P35225" - ], - "gene_symbols": [ - "IL13" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "IL-13", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IL-13", - "registry_sha256": "0fea4e3f83d693c4bb37136de36e615363c0203996bd448c7b9c442f33cda6be" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IL-17a", - "affected_subjects": [ - "SOULCAP:SC000114", - "SOULCAP:SC000119" - ], - "records": [ - { - "marker_token": "IL-17a", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers", - "pro_id": "PR:Q16552", - "pro_label": "interleukin-17A (human)", - "uniprot_id": "Q16552", - "uniprot_label": "interleukin 17A", - "gene_symbol": "IL17A", - "hgnc_id": "HGNC:5981", - "ncbi_gene_id": "", - "mapping_method": "monarch", - "confidence": "high", - "evidence": "https://rest.genenames.org/fetch/symbol/IL17A; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_Q16552", - "notes": "intracellular marker" - } - ], - "pro_ids": [ - "PR:Q16552" - ], - "gene_symbols": [ - "IL17A" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "IL-17A", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IL-17a", - "registry_sha256": "92fcb16f42e797476ce20b25717efcfa123fc60b9e8e0f979c01aefecba1fe2e" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IL-4", - "affected_subjects": [ - "SOULCAP:SC000112", - "SOULCAP:SC000116", - "SOULCAP:SC000117" - ], - "records": [ - { - "marker_token": "IL-4", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers", - "pro_id": "PR:P05112", - "pro_label": "interleukin-4 (human)", - "uniprot_id": "P05112", - "uniprot_label": "interleukin 4", - "gene_symbol": "IL4", - "hgnc_id": "HGNC:6014", - "ncbi_gene_id": "", - "mapping_method": "monarch", - "confidence": "high", - "evidence": "https://rest.genenames.org/fetch/symbol/IL4; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_P05112", - "notes": "intracellular marker" - } - ], - "pro_ids": [ - "PR:P05112" - ], - "gene_symbols": [ - "IL4" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "IL-4", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IL-4", - "registry_sha256": "b73d688d701631fa8fe4c1db97221effb5ee895dad8fec7fdf4b77373958ee3c" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IL-5", - "affected_subjects": [ - "SOULCAP:SC000112", - "SOULCAP:SC000116", - "SOULCAP:SC000117" - ], - "records": [ - { - "marker_token": "IL-5", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers", - "pro_id": "PR:P05113", - "pro_label": "interleukin-5 (human)", - "uniprot_id": "P05113", - "uniprot_label": "interleukin 5", - "gene_symbol": "IL5", - "hgnc_id": "HGNC:6016", - "ncbi_gene_id": "", - "mapping_method": "monarch", - "confidence": "high", - "evidence": "https://rest.genenames.org/fetch/symbol/IL5; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_P05113", - "notes": "intracellular marker" - } - ], - "pro_ids": [ - "PR:P05113" - ], - "gene_symbols": [ - "IL5" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "IL-5", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IL-5", - "registry_sha256": "9359347c3979d2efe87eed401c1bab949de52f4c187ebecafa6336c6327a25cd" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IL-9", - "affected_subjects": [ - "SOULCAP:SC000113", - "SOULCAP:SC000118" - ], - "records": [ - { - "marker_token": "IL-9", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers", - "pro_id": "PR:P15248", - "pro_label": "interleukin-9 (human)", - "uniprot_id": "P15248", - "uniprot_label": "interleukin 9", - "gene_symbol": "IL9", - "hgnc_id": "HGNC:6029", - "ncbi_gene_id": "", - "mapping_method": "monarch", - "confidence": "high", - "evidence": "https://rest.genenames.org/fetch/symbol/IL9; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_P15248", - "notes": "intracellular marker" - } - ], - "pro_ids": [ - "PR:P15248" - ], - "gene_symbols": [ - "IL9" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "IL-9", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IL-9", - "registry_sha256": "9894867ba02520d0af6c0bf4858b55237d8a74be1be3dadaf0721b3a768ab686" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IgA", - "affected_subjects": [ - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044" - ], - "records": [ - { - "marker_token": "IgA", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "Immunoglobulin heavy-chain class A; encoded by IGHA1 and IGHA2 gene family. No single PR ID or UniProt accession covers all isotypes." - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "IGA", - "representation": "protein_family", - "protein_resolution": "withhold", - "rationale": "Registry notes document a non-single-protein or pan-marker representation.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IgA", - "registry_sha256": "61ac45fc138bab46fc31d71e42363d20de18a9585ff4717fb02702cbb03c6685" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IgD", - "affected_subjects": [ - "SOULCAP:SC000030", - "SOULCAP:SC000031", - "SOULCAP:SC000032", - "SOULCAP:SC000033", - "SOULCAP:SC000034", - "SOULCAP:SC000035", - "SOULCAP:SC000036", - "SOULCAP:SC000038", - "SOULCAP:SC000039", - "SOULCAP:SC000040", - "SOULCAP:SC000041", - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044" - ], - "records": [ - { - "marker_token": "IgD", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "Immunoglobulin heavy-chain class D; encoded by IGHD. No single PR ID or UniProt accession." - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "IGD", - "representation": "protein_family", - "protein_resolution": "withhold", - "rationale": "Registry notes document a non-single-protein or pan-marker representation.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IgD", - "registry_sha256": "e4a5f79157c47b9a0e3fccb6d6eb144d50c93d7fb5f71224bd825f3e09adfb52" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IgE", - "affected_subjects": [ - "SOULCAP:SC000033", - "SOULCAP:SC000036", - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044" - ], - "records": [ - { - "marker_token": "IgE", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "Immunoglobulin heavy-chain class E; encoded by IGHE. No single PR ID or UniProt accession." - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "IGE", - "representation": "protein_family", - "protein_resolution": "withhold", - "rationale": "Registry notes document a non-single-protein or pan-marker representation.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IgE", - "registry_sha256": "67b95e398fb1095e4c4a380091f0dae23dec9025456defdd9d0f5f254740da2e" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IgG", - "affected_subjects": [ - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044" - ], - "records": [ - { - "marker_token": "IgG", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "Immunoglobulin heavy-chain class G; encoded by IGHG1/IGHG2/IGHG3/IGHG4 gene family. No single PR ID or UniProt accession covers all subclasses." - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "IGG", - "representation": "protein_family", - "protein_resolution": "withhold", - "rationale": "Registry notes document a non-single-protein or pan-marker representation.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IgG", - "registry_sha256": "c51e1dd6ae671fd9db387be6d0a26fdce6645e0f6a00d14891c0922708a941e7" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "IgM", - "affected_subjects": [ - "SOULCAP:SC000038", - "SOULCAP:SC000039", - "SOULCAP:SC000040", - "SOULCAP:SC000041", - "SOULCAP:SC000042", - "SOULCAP:SC000043", - "SOULCAP:SC000044" - ], - "records": [ - { - "marker_token": "IgM", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "Immunoglobulin heavy-chain class M; encoded by IGHM. No single PR ID or UniProt accession." - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "IGM", - "representation": "protein_family", - "protein_resolution": "withhold", - "rationale": "Registry notes document a non-single-protein or pan-marker representation.", - "source_ref": "marker_mappings/marker_protein_gene.csv#IgM", - "registry_sha256": "fc17667826dd44b6b08bd4cb257f3d4fa23fdbf477c3da79386cb427b0d2f88d" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "MR1", - "affected_subjects": [], - "records": [ - { - "marker_token": "MR1", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:Q95460", - "pro_label": "major histocompatibility complex class I-related protein 1 (human)", - "uniprot_id": "Q95460", - "uniprot_label": "major histocompatibility complex, class I-related", - "gene_symbol": "MR1", - "hgnc_id": "HGNC:4975", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "high", - "evidence": "https://rest.genenames.org/fetch/symbol/MR1; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_Q95460", - "notes": "MHC-related protein 1; also used as 'MR1 tetramer' reagent for MAIT cell detection" - } - ], - "pro_ids": [ - "PR:Q95460" - ], - "gene_symbols": [ - "MR1" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "MR1", - "representation": "unresolved", - "protein_resolution": "withhold", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required.", - "source_ref": "marker_mappings/marker_protein_gene.csv#MR1", - "registry_sha256": "96c5bf22b0be1d144cf60f175968b19c1485c64c4866d4a109f636a9c9af703d" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCR", - "affected_subjects": [ - "SOULCAP:SC000122", - "SOULCAP:SC000123" - ], - "records": [ - { - "marker_token": "TCR", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers|Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "", - "notes": "pan-TCR marker; not specific to a single gene" - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "TCR", - "representation": "protein_family", - "protein_resolution": "withhold", - "rationale": "Registry notes document a non-single-protein or pan-marker representation.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCR", - "registry_sha256": "9a617aa9a766194134020d7afa5feca696fc92cb187377eb72b2bb326d40cae7" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCRVa24", - "affected_subjects": [], - "records": [ - { - "marker_token": "TCRVa24", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:A0A0B4J240", - "pro_label": "T cell receptor alpha variable 10 (human)", - "uniprot_id": "A0A0B4J240", - "uniprot_label": "T cell receptor alpha variable 10 (human)", - "gene_symbol": "TRAV10", - "hgnc_id": "HGNC:12103", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRAV10; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_A0A0B4J240", - "notes": "IMGT nomenclature: TRAV10" - } - ], - "pro_ids": [ - "PR:A0A0B4J240" - ], - "gene_symbols": [ - "TRAV10" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "TCRVA24", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCRVa24", - "registry_sha256": "f81c80eeaa4d2de919813822e062fe2e4210b8a025bd76ebbad546bdd0936315" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCRVa24-Ja18", - "affected_subjects": [], - "records": [ - { - "marker_token": "TCRVa24-Ja18", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:A0A0B4J240", - "pro_label": "T cell receptor alpha variable 10 (human)", - "uniprot_id": "A0A0B4J240", - "uniprot_label": "T cell receptor alpha variable 10 (human)", - "gene_symbol": "TRAV10", - "hgnc_id": "HGNC:12103", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRAV10; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_A0A0B4J240", - "notes": "Invariant iNKT TCR chain; two-gene marker TRAV10+TRAJ18; gene_symbol populated with TRAV10 as primary TRAV gene" - } - ], - "pro_ids": [ - "PR:A0A0B4J240" - ], - "gene_symbols": [ - "TRAV10" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "TCRVA24-JA18", - "representation": "complex", - "protein_resolution": "withhold", - "rationale": "Registry notes describe an assembled or multi-gene marker; component PRO identity cannot establish whole-marker equivalence.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCRVa24-Ja18", - "registry_sha256": "aad1afeeb19ea59d1c85741576656d0bf629f1500ac86d389d008e5adc327020" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCRVa7.2", - "affected_subjects": [], - "records": [ - { - "marker_token": "TCRVa7.2", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:A0A0B4J238", - "pro_label": "T cell receptor alpha variable 1-2 (human)", - "uniprot_id": "A0A0B4J238", - "uniprot_label": "T cell receptor alpha variable 1-2 (human)", - "gene_symbol": "TRAV1-2", - "hgnc_id": "HGNC:12102", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRAV1-2; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_A0A0B4J238", - "notes": "IMGT nomenclature: TRAV1-2" - } - ], - "pro_ids": [ - "PR:A0A0B4J238" - ], - "gene_symbols": [ - "TRAV1-2" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "TCRVA7.2", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCRVa7.2", - "registry_sha256": "1917c912d25db47ddf31fdee753f0093f18dfb1fcf080f5a2dcc9a53cdd490a5" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCRVb11", - "affected_subjects": [], - "records": [ - { - "marker_token": "TCRVb11", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:A0A075B6N4", - "pro_label": "T cell receptor beta variable 25-1 (human)", - "uniprot_id": "A0A075B6N4", - "uniprot_label": "T cell receptor beta variable 25-1 (human)", - "gene_symbol": "TRBV25-1", - "hgnc_id": "HGNC:12205", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRBV25-1; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_A0A075B6N4", - "notes": "IMGT nomenclature: TRBV25-1" - } - ], - "pro_ids": [ - "PR:A0A075B6N4" - ], - "gene_symbols": [ - "TRBV25-1" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "TCRVB11", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCRVb11", - "registry_sha256": "3b0361d975e31467580067f5d17823f53d425f9d2b5ef44745fee1aba08ca941" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCRVd2", - "affected_subjects": [ - "SOULCAP:SC000122" - ], - "records": [ - { - "marker_token": "TCRVd2", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:A0JD36", - "pro_label": "T cell receptor delta variable 2 (human)", - "uniprot_id": "A0JD36", - "uniprot_label": "T cell receptor delta variable 2 (human)", - "gene_symbol": "TRDV2", - "hgnc_id": "HGNC:12263", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRDV2; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_A0JD36", - "notes": "IMGT nomenclature: TRDV2" - } - ], - "pro_ids": [ - "PR:A0JD36" - ], - "gene_symbols": [ - "TRDV2" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "TCRVD2", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCRVd2", - "registry_sha256": "5fb0b153ecc148621ec7c97ffea4618dcaf12f3f62d1642acfb303c5179ef2ec" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCRVg9", - "affected_subjects": [ - "SOULCAP:SC000122" - ], - "records": [ - { - "marker_token": "TCRVg9", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:Q99603", - "pro_label": "T cell receptor gamma variable 9 (human)", - "uniprot_id": "Q99603", - "uniprot_label": "T cell receptor gamma variable 9 (human)", - "gene_symbol": "TRGV9", - "hgnc_id": "HGNC:12295", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRGV9; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_Q99603", - "notes": "IMGT nomenclature: TRGV9" - } - ], - "pro_ids": [ - "PR:Q99603" - ], - "gene_symbols": [ - "TRGV9" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "TCRVG9", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCRVg9", - "registry_sha256": "9318391135642e811b2781de7a9be4cc58f52c5f21dbfe8a0d316f3619f245f1" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCRab", - "affected_subjects": [ - "SOULCAP:SC000049", - "SOULCAP:SC000050", - "SOULCAP:SC000051", - "SOULCAP:SC000052", - "SOULCAP:SC000053", - "SOULCAP:SC000054", - "SOULCAP:SC000055", - "SOULCAP:SC000056", - "SOULCAP:SC000057", - "SOULCAP:SC000058", - "SOULCAP:SC000060", - "SOULCAP:SC000061", - "SOULCAP:SC000066", - "SOULCAP:SC000067", - "SOULCAP:SC000068", - "SOULCAP:SC000069", - "SOULCAP:SC000070", - "SOULCAP:SC000071", - "SOULCAP:SC000072", - "SOULCAP:SC000073", - "SOULCAP:SC000122" - ], - "records": [ - { - "marker_token": "TCRab", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "", - "notes": "pan-αβ TCR marker; recognises assembled αβ heterodimer" - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "TCRAB", - "representation": "complex", - "protein_resolution": "withhold", - "rationale": "Registry notes describe an assembled or multi-gene marker; component PRO identity cannot establish whole-marker equivalence.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCRab", - "registry_sha256": "db65f2afbe24e19148fe8039a5a7df5983c5e9d0963d9cff9dec278958e33382" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCRgd", - "affected_subjects": [ - "SOULCAP:SC000049", - "SOULCAP:SC000050", - "SOULCAP:SC000051", - "SOULCAP:SC000052", - "SOULCAP:SC000053", - "SOULCAP:SC000054", - "SOULCAP:SC000055", - "SOULCAP:SC000056", - "SOULCAP:SC000057", - "SOULCAP:SC000058", - "SOULCAP:SC000060", - "SOULCAP:SC000061", - "SOULCAP:SC000066", - "SOULCAP:SC000067", - "SOULCAP:SC000068", - "SOULCAP:SC000069", - "SOULCAP:SC000070", - "SOULCAP:SC000071", - "SOULCAP:SC000072", - "SOULCAP:SC000073", - "SOULCAP:SC000122" - ], - "records": [ - { - "marker_token": "TCRgd", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "", - "notes": "pan-γδ TCR marker; recognises assembled γδ heterodimer" - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "documented_complex_or_family", - "status_reason": "Registry notes describe a complex, multi-gene, or non-single-protein marker; inspect the recorded representation.", - "resolution_policy": { - "marker_token": "TCRGD", - "representation": "complex", - "protein_resolution": "withhold", - "rationale": "Registry notes describe an assembled or multi-gene marker; component PRO identity cannot establish whole-marker equivalence.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCRgd", - "registry_sha256": "49ec8f76a1338a63effb3e88e3c748f97f2753861e47ad476c1f4a96384b40ec" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "TCRva24", - "affected_subjects": [], - "records": [ - { - "marker_token": "TCRva24", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:A0A0B4J240", - "pro_label": "T cell receptor alpha variable 10 (human)", - "uniprot_id": "A0A0B4J240", - "uniprot_label": "T cell receptor alpha variable 10 (human)", - "gene_symbol": "TRAV10", - "hgnc_id": "HGNC:12103", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRAV10; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_A0A0B4J240", - "notes": "Likely duplicate of TCRVa24 (different capitalisation) — data quality issue; mapped identically to TCRVa24 / TRAV10" - } - ], - "pro_ids": [ - "PR:A0A0B4J240" - ], - "gene_symbols": [ - "TRAV10" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "TCRVA24", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#TCRVa24", - "registry_sha256": "f81c80eeaa4d2de919813822e062fe2e4210b8a025bd76ebbad546bdd0936315" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "Tetramer", - "affected_subjects": [], - "records": [ - { - "marker_token": "Tetramer", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "generic reagent term; not a specific protein" - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "documented_nonprotein_or_reagent", - "status_reason": "Registry notes document a non-protein gate or reagent; a single gene/PRO mapping may not apply.", - "resolution_policy": { - "marker_token": "TETRAMER", - "representation": "reagent_gate", - "protein_resolution": "withhold", - "rationale": "Registry notes describe a reagent, lipid antigen, or carbohydrate epitope rather than a single protein.", - "source_ref": "marker_mappings/marker_protein_gene.csv#Tetramer", - "registry_sha256": "2f3894386ee2918f58d53b858eebc8e09729f16699a8f9d6faab2d5900495227" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "V", - "affected_subjects": [ - "SOULCAP:SC000122", - "SOULCAP:SC000123" - ], - "records": [ - { - "marker_token": "V", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers|Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "likely parsing artifact from multi-word TCR gene name — data quality issue; see reports/marker_validation.md" - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "source_artifact_needs_review", - "status_reason": "Registry notes describe a possible parsing artifact; source clarification is needed.", - "resolution_policy": { - "marker_token": "V", - "representation": "unresolved", - "protein_resolution": "withhold", - "rationale": "No PRO identity recorded; possible source artifact or unresolved marker requires clarification.", - "source_ref": "marker_mappings/marker_protein_gene.csv#V", - "registry_sha256": "610b267c4ba493d65f1528fb008a91bcab513fe39cd039617f4ba0313b50fa61" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "VB11", - "affected_subjects": [], - "records": [ - { - "marker_token": "VB11", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:A0A075B6N4", - "pro_label": "T cell receptor beta variable 25-1 (human)", - "uniprot_id": "A0A075B6N4", - "uniprot_label": "T cell receptor beta variable 25-1 (human)", - "gene_symbol": "TRBV25-1", - "hgnc_id": "HGNC:12205", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRBV25-1; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_A0A075B6N4", - "notes": "Duplicate of TCRVb11 (uppercase) — data quality issue; same mapping as TCRVb11 / TRBV25-1" - } - ], - "pro_ids": [ - "PR:A0A075B6N4" - ], - "gene_symbols": [ - "TRBV25-1" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "VB11", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#VB11", - "registry_sha256": "6642023972a293e8a24efa26bb504964bc55c6f68d25a2186fd5609b89465e9f" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "Vb11", - "affected_subjects": [], - "records": [ - { - "marker_token": "Vb11", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:A0A075B6N4", - "pro_label": "T cell receptor beta variable 25-1 (human)", - "uniprot_id": "A0A075B6N4", - "uniprot_label": "T cell receptor beta variable 25-1 (human)", - "gene_symbol": "TRBV25-1", - "hgnc_id": "HGNC:12205", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRBV25-1; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_A0A075B6N4", - "notes": "Duplicate of TCRVb11 — data quality issue; same mapping as TCRVb11 / TRBV25-1" - } - ], - "pro_ids": [ - "PR:A0A075B6N4" - ], - "gene_symbols": [ - "TRBV25-1" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "VB11", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#VB11", - "registry_sha256": "6642023972a293e8a24efa26bb504964bc55c6f68d25a2186fd5609b89465e9f" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "Vd1", - "affected_subjects": [], - "records": [ - { - "marker_token": "Vd1", - "marker_synonyms": "", - "source_columns": "Required phenotypic markers", - "pro_id": "PR:A0A1B0GX56", - "pro_label": "T cell receptor delta variable 1 (human)", - "uniprot_id": "A0A1B0GX56", - "uniprot_label": "T cell receptor delta variable 1 (human)", - "gene_symbol": "TRDV1", - "hgnc_id": "HGNC:12262", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "medium", - "evidence": "https://rest.genenames.org/fetch/symbol/TRDV1; https://www.ebi.ac.uk/ols4/api/ontologies/pr/terms?iri=obo:PR_A0A1B0GX56", - "notes": "IMGT nomenclature: TRDV1" - } - ], - "pro_ids": [ - "PR:A0A1B0GX56" - ], - "gene_symbols": [ - "TRDV1" - ], - "ncbi_gene_ids": [], - "identifier_status": "mapped", - "status": "mapped", - "status_reason": "PRO identifier and gene symbol recorded; this is not a biological sign-off.", - "resolution_policy": { - "marker_token": "VD1", - "representation": "single_protein", - "protein_resolution": "allow", - "rationale": "Retains the registry's single PRO representation; computational identity only, not biological sign-off.", - "source_ref": "marker_mappings/marker_protein_gene.csv#Vd1", - "registry_sha256": "adcc38bd179456a5c30cbddcb322a4cec7c64ca04f5c0f5ca79aef2703ee25fc" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "delta", - "affected_subjects": [], - "records": [ - { - "marker_token": "delta", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers|Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "likely parsing artifact from multi-word TCR gene name — data quality issue; see reports/marker_validation.md" - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "source_artifact_needs_review", - "status_reason": "Registry notes describe a possible parsing artifact; source clarification is needed.", - "resolution_policy": { - "marker_token": "DELTA", - "representation": "unresolved", - "protein_resolution": "withhold", - "rationale": "No PRO identity recorded; possible source artifact or unresolved marker requires clarification.", - "source_ref": "marker_mappings/marker_protein_gene.csv#delta", - "registry_sha256": "83aed236bb5fcdc28afafd651c50af0e2bc053b7d9f64f979e47e39e66751b5e" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "delta1", - "affected_subjects": [ - "SOULCAP:SC000122", - "SOULCAP:SC000123" - ], - "records": [ - { - "marker_token": "delta1", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "likely parsing artifact from multi-word TCR gene name — data quality issue; see reports/marker_validation.md" - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "source_artifact_needs_review", - "status_reason": "Registry notes describe a possible parsing artifact; source clarification is needed.", - "resolution_policy": { - "marker_token": "DELTA1", - "representation": "unresolved", - "protein_resolution": "withhold", - "rationale": "No PRO identity recorded; possible source artifact or unresolved marker requires clarification.", - "source_ref": "marker_mappings/marker_protein_gene.csv#delta1", - "registry_sha256": "5b366a2c0a5c2f3a19355bb66e4ad0f88c172aa901c577aa9b16acff92294995" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - }, - { - "marker_token": "gamma", - "affected_subjects": [], - "records": [ - { - "marker_token": "gamma", - "marker_synonyms": "", - "source_columns": "Ideal phenotypic markers|Required phenotypic markers", - "pro_id": "", - "pro_label": "", - "uniprot_id": "", - "uniprot_label": "", - "gene_symbol": "", - "hgnc_id": "", - "ncbi_gene_id": "", - "mapping_method": "manual", - "confidence": "low", - "evidence": "", - "notes": "likely parsing artifact from multi-word TCR gene name — data quality issue; see reports/marker_validation.md" - } - ], - "pro_ids": [], - "gene_symbols": [], - "ncbi_gene_ids": [], - "identifier_status": "no_pro_mapping", - "status": "source_artifact_needs_review", - "status_reason": "Registry notes describe a possible parsing artifact; source clarification is needed.", - "resolution_policy": { - "marker_token": "GAMMA", - "representation": "unresolved", - "protein_resolution": "withhold", - "rationale": "No PRO identity recorded; possible source artifact or unresolved marker requires clarification.", - "source_ref": "marker_mappings/marker_protein_gene.csv#gamma", - "registry_sha256": "dc9b95fd067723b54cfdb2e4fcf8948e571b2dfc83b0fa6dc407a4bcf6f402be" - }, - "classification_basis": "Local registry identifiers and notes; not externally verified." - } - ], - "gaps": [ - { - "soulcap_abbreviation": "NK", - "soulcap_full_name": "Natural Killer Cell", - "gap_type": "cl_axiom_gap", - "description": "CL:0000623 asserts only negative exclusion markers (CD14-/CD19-/CD3-/CD20-); the field-standard defining positive marker CD56 is absent from its own axioms, though present on its child terms.", - "related_cl_ids": "CL:0000623", - "evidence": "reports/cl_pro_relationships.md; reports/literature/nk_cell_markers.md; reports/cl_term_issues.md#natural-killer-cell-missing-cd56-marker-axiom--cl0000623", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-22", - "association": "exact_abbreviation", - "subject_ids": [ - "SOULCAP:SC000001" - ], - "candidate_subject_ids": [ - "SOULCAP:SC000001" - ], - "evidence_links": [ - { - "label": "reports/cl_pro_relationships.md", - "href": "../../cl_pro_relationships.md" - }, - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - }, - { - "label": "reports/cl_term_issues.md#natural-killer-cell-missing-cd56-marker-axiom--cl0000623", - "href": "../../cl_term_issues.md#natural-killer-cell-missing-cd56-marker-axiom--cl0000623" - } - ] - }, - { - "soulcap_abbreviation": "NK1 / NK3", - "soulcap_full_name": "Natural Killer Cell 1 / Natural Killer Cell 3", - "gap_type": "cl_axiom_gap", - "description": "CL:0000939 (CD16-positive, CD56-dim NK cell, human) does not distinguish CD57-negative (NK1) from CD57-positive (NK3) substates; both SOULCAP rows currently map to the same CL term at Broad match type.", - "related_cl_ids": "CL:0000939", - "evidence": "reports/candidate_cl_mappings_narrative.md#ctnk--nk1--nk3--cytotoxic-natural-killer-cell-cd16-positive", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-22", - "association": "family_or_unresolved", - "subject_ids": [], - "candidate_subject_ids": [], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#ctnk--nk1--nk3--cytotoxic-natural-killer-cell-cd16-positive", - "href": "../../candidate_cl_mappings_narrative.md#ctnk--nk1--nk3--cytotoxic-natural-killer-cell-cd16-positive" - } - ] - }, - { - "soulcap_abbreviation": "ILC1", - "soulcap_full_name": "Innate Lymphoid Cell 1", - "gap_type": "cl_axiom_gap", - "description": "No human-specific \"group 1 innate lymphoid cell\" CL term exists, unlike group 2 (CL:0001081) and group 3 (CL:0001078); confirmed by direct OLS4 search returning zero hits for the human-qualified query.", - "related_cl_ids": "CL:0001067", - "evidence": "reports/cl_term_issues.md#missing-human-specific-group-1-innate-lymphoid-cell-term", - "status": "filed_as_issue", - "repo_issue": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/14", - "date_logged": "2026-07-23", - "association": "exact_abbreviation", - "subject_ids": [ - "SOULCAP:SC000008" - ], - "candidate_subject_ids": [ - "SOULCAP:SC000008" - ], - "evidence_links": [ - { - "label": "reports/cl_term_issues.md#missing-human-specific-group-1-innate-lymphoid-cell-term", - "href": "../../cl_term_issues.md#missing-human-specific-group-1-innate-lymphoid-cell-term" - }, - { - "label": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/14", - "href": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/14" - } - ] - }, - { - "soulcap_abbreviation": "Transitional", - "soulcap_full_name": "Transitional B cell", - "gap_type": "no_reasonable_cl_match", - "description": "SOULCAP row has all four marker columns (Required/Ideal exclusion, Required/Ideal phenotypic markers) completely empty in the master sheet — there is no marker definition to match against at all, so no CL candidate can be derived from markers. Distinct from the more specific \"T3\" (Transitional B cell 3) row, which does have marker data.", - "related_cl_ids": "(none)", - "evidence": "reports/candidate_cl_mappings_batch.tsv (note column); data/marker_combinations.csv", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "exact_abbreviation", - "subject_ids": [ - "SOULCAP:SC000027" - ], - "candidate_subject_ids": [ - "SOULCAP:SC000027" - ], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_batch.tsv", - "href": "../../candidate_cl_mappings_batch.tsv" - }, - { - "label": "data/marker_combinations.csv", - "href": "../../../data/marker_combinations.csv" - } - ] - }, - { - "soulcap_abbreviation": "CTNK", - "soulcap_full_name": "Cytotoxic Natural Killer Cell", - "gap_type": "sheet_data_issue", - "description": "Sheet's Full Name reads \"Cytotoxice Natural Killer Cell\" (typo, extra trailing \"e\"); this broke batch lexical search entirely for the row (zero OLS4 hits). Marker-based match was unaffected. Cannot be fixed in this repo — requires a correction in the Google Sheet master.", - "related_cl_ids": "CL:0000939", - "evidence": "reports/candidate_cl_mappings_narrative.md#dc-family--dendritic-cells", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-22", - "association": "exact_abbreviation", - "subject_ids": [ - "SOULCAP:SC000003" - ], - "candidate_subject_ids": [ - "SOULCAP:SC000003" - ], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#dc-family--dendritic-cells", - "href": "../../candidate_cl_mappings_narrative.md#dc-family--dendritic-cells" - } - ] - }, - { - "soulcap_abbreviation": "pDC", - "soulcap_full_name": "Peripheral Dendritic Cell (as written)", - "gap_type": "sheet_data_issue", - "description": "Sheet's Full Name reads \"Peripheral Dendritic Cell,\" but the row's markers (CD123hi, CD303+, low CD33) are the textbook definition of plasmacytoid dendritic cells — likely a wrong word, should probably read \"Plasmacytoid.\" This broke batch lexical search (returned an unrelated \"migratory dendritic cell\" hit). Cannot be fixed in this repo — requires a correction in the Google Sheet master.", - "related_cl_ids": "CL:0001058", - "evidence": "reports/candidate_cl_mappings_narrative.md#dc-family--dendritic-cells", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-22", - "association": "exact_abbreviation", - "subject_ids": [ - "SOULCAP:SC000014" - ], - "candidate_subject_ids": [ - "SOULCAP:SC000014" - ], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#dc-family--dendritic-cells", - "href": "../../candidate_cl_mappings_narrative.md#dc-family--dendritic-cells" - } - ] - }, - { - "soulcap_abbreviation": "Mono", - "soulcap_full_name": "Monocyte", - "gap_type": "cl_axiom_gap", - "description": "CL:0000576 (plain \"monocyte\") has zero marker axiom rows in cl_pro_relationships.tsv — same parent-class axiom-gap pattern as NK/ILC/cDC/B cell. Match is lexical-only (OAK-verified), not marker-confirmed.", - "related_cl_ids": "CL:0000576", - "evidence": "reports/candidate_cl_mappings_narrative.md#monocyte-family; reports/cl_pro_relationships.tsv", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "exact_abbreviation", - "subject_ids": [ - "SOULCAP:SC000017" - ], - "candidate_subject_ids": [ - "SOULCAP:SC000017" - ], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#monocyte-family", - "href": "../../candidate_cl_mappings_narrative.md#monocyte-family" - }, - { - "label": "reports/cl_pro_relationships.tsv", - "href": "../../cl_pro_relationships.tsv" - } - ] - }, - { - "soulcap_abbreviation": "CMo / NCMo / IntMo", - "soulcap_full_name": "Classical / Non-classical / Intermediate Monocyte", - "gap_type": "cl_axiom_gap", - "description": "CL:0000860/CL:0000875/CL:0002393 assert only CCR2 (CD192) and CX3CR1 status plus lineage negatives — none assert the CD14/CD16 axioms that actually define these three subsets per Ziegler-Heitbrock et al. 2010 (PMID:20628149). Already covered by repo issue #12 (filed upstream as CL#3665) — not a new gap, cited here for context on why these rows can only be matched lexically.", - "related_cl_ids": "CL:0000860; CL:0000875; CL:0002393", - "evidence": "reports/candidate_cl_mappings_narrative.md#monocyte-family; https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/12", - "status": "filed_as_issue", - "repo_issue": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/12", - "date_logged": "2026-07-24", - "association": "family_or_unresolved", - "subject_ids": [], - "candidate_subject_ids": [], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#monocyte-family", - "href": "../../candidate_cl_mappings_narrative.md#monocyte-family" - }, - { - "label": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/12", - "href": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/12" - }, - { - "label": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/12", - "href": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/12" - } - ] - }, - { - "soulcap_abbreviation": "Mono / CMo / NCMo / IntMo", - "soulcap_full_name": "Monocyte family", - "gap_type": "sheet_data_issue", - "description": "Required exclusion column reads \"CD56- CD19- ([CD123hi]- CD303-) ([CD123hi|CD193-)\" for all four rows — the second group is missing a \"]\" after CD123hi (likely should read \"([CD123hi]-|CD193-)\", matching the cDC/pDC pattern). Cannot be fixed in this repo — requires a correction in the Google Sheet master.", - "related_cl_ids": "(none)", - "evidence": "reports/candidate_cl_mappings_narrative.md#monocyte-family; data/marker_combinations.csv", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "family_or_unresolved", - "subject_ids": [], - "candidate_subject_ids": [], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#monocyte-family", - "href": "../../candidate_cl_mappings_narrative.md#monocyte-family" - }, - { - "label": "data/marker_combinations.csv", - "href": "../../../data/marker_combinations.csv" - } - ] - }, - { - "soulcap_abbreviation": "B cell", - "soulcap_full_name": "B cell", - "gap_type": "cl_axiom_gap", - "description": "CL:0000236 (plain \"B cell\") has zero marker axiom rows in cl_pro_relationships.tsv — same parent-class axiom-gap pattern as NK/ILC/cDC/monocyte. Match is lexical-only (OAK-verified after OLS4 REST search returned zero hits for this exact query), not marker-confirmed.", - "related_cl_ids": "CL:0000236", - "evidence": "reports/candidate_cl_mappings_narrative.md#b-cell-parent; reports/cl_pro_relationships.tsv", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "exact_abbreviation", - "subject_ids": [ - "SOULCAP:SC000023" - ], - "candidate_subject_ids": [ - "SOULCAP:SC000023" - ], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#b-cell-parent", - "href": "../../candidate_cl_mappings_narrative.md#b-cell-parent" - }, - { - "label": "reports/cl_pro_relationships.tsv", - "href": "../../cl_pro_relationships.tsv" - } - ] - }, - { - "soulcap_abbreviation": "BDN1 / BDN2 / BDN3 / BDN4", - "soulcap_full_name": "Double Negative B cell 1-4", - "gap_type": "cl_axiom_gap", - "description": "SOULCAP defines four \"double negative\" B cell subsets (DN1-4, the atypical/age-associated B cell scheme from the autoimmunity/aging literature) via CD21/CD11c/CD185/IgE combinations. CL has only the general parent CL:0000981 \"double negative memory B cell\" with no DN1-4 subtyping; direct searches for \"DN1 B cell\" through \"DN4 B cell\" and \"atypical memory B cell\" returned zero CL hits. All four SOULCAP rows currently collapse to the same Broad match.", - "related_cl_ids": "CL:0000981", - "evidence": "reports/candidate_cl_mappings_narrative.md#b-cell-maturation-tree--transitional--mature--naive--double-negative", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "family_or_unresolved", - "subject_ids": [], - "candidate_subject_ids": [], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#b-cell-maturation-tree--transitional--mature--naive--double-negative", - "href": "../../candidate_cl_mappings_narrative.md#b-cell-maturation-tree--transitional--mature--naive--double-negative" - } - ] - }, - { - "soulcap_abbreviation": "IgD only", - "soulcap_full_name": "IgD only Memory B cell", - "gap_type": "cl_axiom_gap", - "description": "SOULCAP distinguishes IgD+IgM- (\"IgD only\") from IgD+IgM+ (\"Unswitched\") memory B cells as two separate populations. No CL term exists for the IgD+IgM- subset — direct searches for \"IgD-positive memory B cell\" and \"IgD only memory B cell\" returned zero hits; the only IgD-related term found, CL:0001053 \"IgD-negative memory B cell,\" is the opposite polarity. Left unmapped rather than forced onto a wrong-polarity term.", - "related_cl_ids": "CL:0001053 (wrong polarity, not used)", - "evidence": "reports/candidate_cl_mappings_narrative.md#memory-b-cell-tree", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "exact_abbreviation", - "subject_ids": [ - "SOULCAP:SC000038" - ], - "candidate_subject_ids": [ - "SOULCAP:SC000038" - ], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#memory-b-cell-tree", - "href": "../../candidate_cl_mappings_narrative.md#memory-b-cell-tree" - } - ] - }, - { - "soulcap_abbreviation": "CD4+ T cell / CD8+ T cell / CD4+/CD8+ T cell / CD4-/CD8- T cell / CD4+/CD8+ TCRab T cell / CD4-/CD8- TCRab T cell / CD4+ TCRgd T cell / CD8+ TCRgd T cell / CD4+/CD8+ TCRgd", - "soulcap_full_name": "various", - "gap_type": "cl_axiom_gap", - "description": "CL organizes CD4/CD8 status primarily under the alpha-beta T cell lineage: no combined alpha-beta+gamma-delta CD4/CD8 terms exist, no clean double-positive alpha-beta term exists, and the only double-negative term found (CL:0002489) is a thymocyte-stage term (wrong tissue for a blood/PBMC panel). All 9 rows Broad-matched to the nearest alpha-beta or gamma-delta parent with this gap noted.", - "related_cl_ids": "CL:0000624; CL:0000625; CL:0000789; CL:0000084; CL:0000798", - "evidence": "reports/candidate_cl_mappings_narrative.md#combined-lineage-b-and-double-positivedouble-negative-gaps", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "family_or_unresolved", - "subject_ids": [], - "candidate_subject_ids": [], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#combined-lineage-b-and-double-positivedouble-negative-gaps", - "href": "../../candidate_cl_mappings_narrative.md#combined-lineage-b-and-double-positivedouble-negative-gaps" - } - ] - }, - { - "soulcap_abbreviation": "CD56+ T cell family (13 rows)", - "soulcap_full_name": "various CD56+ T cell subsets", - "gap_type": "cl_axiom_gap", - "description": "SOULCAP crosses CD56 positivity with CD4/CD8/DP/DN status and TCRab/TCRgd lineage (13 variants); CL has only one term at this level (CL:4052055, pending rename to \"CD56-positive T cell, human\" per issue #13) with no further subdivision. All 13 rows Broad-match to CL:4052055.", - "related_cl_ids": "CL:4052055", - "evidence": "reports/candidate_cl_mappings_narrative.md#cd56-t-cell-family; https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/13", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "family_or_unresolved", - "subject_ids": [], - "candidate_subject_ids": [], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#cd56-t-cell-family", - "href": "../../candidate_cl_mappings_narrative.md#cd56-t-cell-family" - }, - { - "label": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/13", - "href": "https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/13" - } - ] - }, - { - "soulcap_abbreviation": "Tcm / Tem / Temra (general, no CD4/CD8 split) and all TCRgd-specific Tnaive/Tcm/Tem/Temra rows", - "soulcap_full_name": "various", - "gap_type": "cl_axiom_gap", - "description": "CL has no generic central/effector memory T cell term spanning both CD4 and CD8 (only CD4-specific and CD8-specific versions exist), and no gamma-delta-specific differentiation-state terms at all. ~13 rows Broad-matched to the nearest available parent (CL:0000084 T cell, or CL:0000798 gamma-delta T cell) with this gap noted.", - "related_cl_ids": "CL:0000084; CL:0000798", - "evidence": "reports/candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "family_or_unresolved", - "subject_ids": [], - "candidate_subject_ids": [], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree", - "href": "../../candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree" - } - ] - }, - { - "soulcap_abbreviation": "CD8+ Temra / CD8+ TCRab Temra", - "soulcap_full_name": "CD8+ CD45RA+ effector memory T cell", - "gap_type": "cl_axiom_gap", - "description": "CL:4030002 (effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated) appears to be CD4-specific only; no CD8+ counterpart with the same \"terminally differentiated\" qualifier was found — only the non-TEMRA-specific CL:0000913 (effector memory CD8-positive, alpha-beta T cell). Possible asymmetry in CL's own hierarchy; needs a second look before concluding it's a genuine omission rather than differently-named.", - "related_cl_ids": "CL:4030002; CL:0000913", - "evidence": "reports/candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "family_or_unresolved", - "subject_ids": [], - "candidate_subject_ids": [], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree", - "href": "../../candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree" - } - ] - }, - { - "soulcap_abbreviation": "(26 rows, various abbreviations)", - "soulcap_full_name": "(no Full Name in sheet)", - "gap_type": "sheet_data_issue", - "description": "26 rows in the T cell branch have a completely empty Full Name field, so no name-based match can be attempted (Conv TCRab family, T helper, T cytotoxic, Tfh, CD4 PanT helper/Treg, ConT Treg-like/Tfh-like, Th1/2/9/17-like, Vg9/Vd1/Vd2/Vd3 subsets). Additionally, Th1-like/Th2-like/Th9-like/Th17-like each appear TWICE in the sheet: one copy (parented under \"CD4 ConT\") has iNKT-style TCRVa24-Ja18/CD1d-a-GalCer markers that look copy-pasted from an unrelated row; the other (no parent) has the correct Th-subset chemokine receptor panel (CD183/CD185/CD194/CD196). Likely a genuine sheet data bug, not two intentional variants. Cannot be fixed here — requires correction in the Google Sheet master.", - "related_cl_ids": "CL:0000912 (T helper, once named); CL:0000910 (T cytotoxic, once named)", - "evidence": "reports/candidate_cl_mappings_narrative.md#rows-with-no-full-name-in-the-sheet--not-mapped", - "status": "open", - "repo_issue": "(not yet filed)", - "date_logged": "2026-07-24", - "association": "family_or_unresolved", - "subject_ids": [], - "candidate_subject_ids": [], - "evidence_links": [ - { - "label": "reports/candidate_cl_mappings_narrative.md#rows-with-no-full-name-in-the-sheet--not-mapped", - "href": "../../candidate_cl_mappings_narrative.md#rows-with-no-full-name-in-the-sheet--not-mapped" - } - ] - } - ], - "findings": [ - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000017", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000018", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000019", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000020", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000059", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000074", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000075", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000076", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000077", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000078", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000079", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000107", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000109", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000110", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000111", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000112", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000113", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000114", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000123", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000124", - "message": "2 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000125", - "message": "1 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000126", - "message": "2 marker cell(s) cannot be scored." - }, - { - "severity": "error", - "code": "invalid_profile", - "subject": "SOULCAP:SC000127", - "message": "2 marker cell(s) cannot be scored." - }, - { - "severity": "warning", - "code": "uncertain_proposal", - "subject": "SOULCAP:SC000006", - "message": "Proposal for CL:0001074 is explicitly uncertain." - }, - { - "severity": "warning", - "code": "uncertain_proposal", - "subject": "SOULCAP:SC000064", - "message": "Proposal for CL:0000789 is explicitly uncertain." - }, - { - "severity": "warning", - "code": "uncertain_proposal", - "subject": "SOULCAP:SC000065", - "message": "Proposal for CL:0000084 is explicitly uncertain." - }, - { - "severity": "warning", - "code": "uncertain_proposal", - "subject": "SOULCAP:SC000068", - "message": "Proposal for CL:0000789 is explicitly uncertain." - }, - { - "severity": "warning", - "code": "uncertain_proposal", - "subject": "SOULCAP:SC000069", - "message": "Proposal for CL:0000789 is explicitly uncertain." - }, - { - "severity": "warning", - "code": "uncertain_proposal", - "subject": "SOULCAP:SC000070", - "message": "Proposal for CL:0000798 is explicitly uncertain." - }, - { - "severity": "warning", - "code": "uncertain_proposal", - "subject": "SOULCAP:SC000071", - "message": "Proposal for CL:0000798 is explicitly uncertain." - }, - { - "severity": "warning", - "code": "uncertain_proposal", - "subject": "SOULCAP:SC000072", - "message": "Proposal for CL:0000798 is explicitly uncertain." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000001", - "message": "CL:0000623: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000002", - "message": "CL:0000938: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000003", - "message": "CL:0000939: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000004", - "message": "CL:0000939: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000005", - "message": "CL:0000939: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000006", - "message": "CL:0001074: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000007", - "message": "CL:0001065: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000008", - "message": "CL:0001067: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000009", - "message": "CL:0001081: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000010", - "message": "CL:0001078: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000011", - "message": "CL:0000990: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000012", - "message": "CL:0002394: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000013", - "message": "CL:0002399: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000014", - "message": "CL:0001058: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000015", - "message": "CL:0000043: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000016", - "message": "CL:0000043: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000017", - "message": "CL:0000576: structured fields empty: literature_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000018", - "message": "CL:0000860: structured fields empty: literature_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000019", - "message": "CL:0000875: structured fields empty: literature_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000020", - "message": "CL:0002393: structured fields empty: literature_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000021", - "message": "CL:0000775: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000022", - "message": "CL:0000771: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000023", - "message": "CL:0000236: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000024", - "message": "CL:0000946: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000025", - "message": "CL:0000980: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000026", - "message": "CL:0000786: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000028", - "message": "CL:0000818: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000029", - "message": "CL:0000785: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000030", - "message": "CL:0000960: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000031", - "message": "CL:0000788: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000032", - "message": "CL:0000981: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000033", - "message": "CL:0000981: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000034", - "message": "CL:0000981: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000035", - "message": "CL:0000981: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000036", - "message": "CL:0000981: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000037", - "message": "CL:0000787: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000039", - "message": "CL:0000970: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000040", - "message": "CL:0000971: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000041", - "message": "CL:0000972: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000042", - "message": "CL:0000973: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000043", - "message": "CL:0000979: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000044", - "message": "CL:0000948: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000045", - "message": "CL:0000084: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000046", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000047", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000048", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000049", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000050", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000051", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000052", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000053", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000054", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000055", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000056", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000057", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000058", - "message": "CL:4052055: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000059", - "message": "CL:0000814: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000060", - "message": "CL:0000789: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000061", - "message": "CL:0000798: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000062", - "message": "CL:0000624: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000063", - "message": "CL:0000625: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000064", - "message": "CL:0000789: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000065", - "message": "CL:0000084: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000066", - "message": "CL:0000624: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000067", - "message": "CL:0000625: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000068", - "message": "CL:0000789: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000069", - "message": "CL:0000789: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000070", - "message": "CL:0000798: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000071", - "message": "CL:0000798: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000072", - "message": "CL:0000798: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000073", - "message": "CL:0000803: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000074", - "message": "CL:0000940: structured fields empty: lexical_evidence, literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000082", - "message": "CL:0000904: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000085", - "message": "CL:0000907: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000087", - "message": "CL:0000898: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000089", - "message": "CL:0000895: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000092", - "message": "CL:0000900: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000096", - "message": "CL:0000905: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000099", - "message": "CL:0000913: structured fields empty: literature_evidence, curator_evidence. Legacy narrative may contain evidence." - }, - { - "severity": "info", - "code": "evidence_not_recorded", - "subject": "SOULCAP:SC000103", - "message": "CL:4030002: structured fields empty: literature_evidence, curator_evidence. 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DOI:10.3389/fimmu.2017.00360)", - "quote": "ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303).", - "source_ref": "reports/literature/nk_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000623", - "cl_label": "natural killer cell", - "pr_id": "PR:000001889", - "pr_label": "CD14 molecule", - "cd_synonym": "CD14 (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892)", - "quote": "there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes", - "source_ref": "reports/literature/nk_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000624", - "cl_label": "CD4-positive, alpha-beta T cell", - "pr_id": "PR:000025402", - "pr_label": "T cell receptor co-receptor CD8", - "cd_synonym": "CD8 (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8−/CD4+/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000624", - "cl_label": "CD4-positive, alpha-beta T cell", - "pr_id": "PR:000001004", - "pr_label": "CD4 molecule", - "cd_synonym": "CD4 (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8−/CD4+/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000625", - "cl_label": "CD8-positive, alpha-beta T cell", - "pr_id": "PR:000001004", - "pr_label": "CD4 molecule", - "cd_synonym": "CD4 (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8+/CD4−/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000625", - "cl_label": "CD8-positive, alpha-beta T cell", - "pr_id": "PR:000025402", - "pr_label": "T cell receptor co-receptor CD8", - "cd_synonym": "CD8 (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8+/CD4−/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000771", - "cl_label": "eosinophil", - "pr_id": "PR:000001254", - "pr_label": "C-C chemokine receptor type 1", - "cd_synonym": "CD191 (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "CD191/CCR1 not among the markers studied in PMID:38666394 (CCR3/CD193 is, but not CCR1); no other eosinophil-specific CD191 evidence found via targeted EuropePMC search.", - "evidence_links": [] - }, - { - "cl_id": "CL:0000771", - "cl_label": "eosinophil", - "pr_id": "PR:000001255", - "pr_label": "C-C chemokine receptor type 3", - "cd_synonym": "CD193 (exact)", - "species_support": "human", - "evidence_source": "europepmc_search", - "citation": "(Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow", - "quote": "candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry", - "source_ref": "https://europepmc.org/article/MED/38666394", - "evidence_links": [ - { - "label": "https://europepmc.org/article/MED/38666394", - "href": "https://europepmc.org/article/MED/38666394" - } - ] - }, - { - "cl_id": "CL:0000771", - "cl_label": "eosinophil", - "pr_id": "PR:000001307", - "pr_label": "CD44 molecule", - "cd_synonym": "CD44 (label); CDw44 (exact)", - "species_support": "human", - "evidence_source": "europepmc_search", - "citation": "(Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow", - "quote": "candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry", - "source_ref": "https://europepmc.org/article/MED/38666394", - "evidence_links": [ - { - "label": "https://europepmc.org/article/MED/38666394", - "href": "https://europepmc.org/article/MED/38666394" - } - ] - }, - { - "cl_id": "CL:0000771", - "cl_label": "eosinophil", - "pr_id": "PR:000001343", - "pr_label": "CD69 molecule", - "cd_synonym": "CD69 (label)", - "species_support": "human", - "evidence_source": "europepmc_search", - "citation": "(Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow", - "quote": "candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry", - "source_ref": "https://europepmc.org/article/MED/38666394", - "evidence_links": [ - { - "label": "https://europepmc.org/article/MED/38666394", - "href": "https://europepmc.org/article/MED/38666394" - } - ] - }, - { - "cl_id": "CL:0000771", - "cl_label": "eosinophil", - "pr_id": "PR:000005178", - "pr_label": "CD9 molecule", - "cd_synonym": "CD9 (label)", - "species_support": "human", - "evidence_source": "europepmc_search", - "citation": "(Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow", - "quote": "candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry", - "source_ref": "https://europepmc.org/article/MED/38666394", - "evidence_links": [ - { - "label": "https://europepmc.org/article/MED/38666394", - "href": "https://europepmc.org/article/MED/38666394" - } - ] - }, - { - "cl_id": "CL:0000775", - "cl_label": "neutrophil", - "pr_id": "PR:000001479", - "pr_label": "low affinity immunoglobulin gamma Fc region receptor II", - "cd_synonym": "CD32 (broad)", - "species_support": "human", - "evidence_source": "europepmc_search", - "citation": "Su K et al. 2007 (PMID:17312177; DOI:10.4049/jimmunol.178.5.3272) -- FcγRIIb (CD32B) expression profiling in human circulating leukocytes", - "quote": "we found that FcgammaRIIb is expressed on the cell surface of circulating B lymphocytes, monocytes, neutrophils, myeloid dendritic cells (DCs), and at very low levels on plasmacytoid DCs from some donors", - "source_ref": "https://europepmc.org/article/MED/17312177", - "evidence_links": [ - { - "label": "https://europepmc.org/article/MED/17312177", - "href": "https://europepmc.org/article/MED/17312177" - } - ] - }, - { - "cl_id": "CL:0000775", - "cl_label": "neutrophil", - "pr_id": "PR:000001879", - "pr_label": "leukosialin", - "cd_synonym": "CD43 (related)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "CD43 not found in any targeted EuropePMC search in a human-neutrophil-specific context ('CD43 leukosialin human neutrophil' returned unrelated papers).", - "evidence_links": [] - }, - { - "cl_id": "CL:0000786", - "cl_label": "plasma cell", - "pr_id": "PR:000001289", - "pr_label": "membrane-spanning 4-domains subfamily A member 1", - "cd_synonym": "CD20 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122)", - "quote": "as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000786", - "cl_label": "plasma cell", - "pr_id": "PR:000001935", - "pr_label": "syndecan-1", - "cd_synonym": "CD138 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122)", - "quote": "as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000787", - "cl_label": "memory B cell", - "pr_id": "PR:000001935", - "pr_label": "syndecan-1", - "cd_synonym": "CD138 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) -- describes the plasmablast/plasma-cell transition boundary, not memory B cells directly, but confirms CD138 as a human B-lineage differentiation marker", - "quote": "as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000787", - "cl_label": "memory B cell", - "pr_id": "PR:000001289", - "pr_label": "membrane-spanning 4-domains subfamily A member 1", - "cd_synonym": "CD20 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122)", - "quote": "Mature B cells typically express both CD19 and CD20.", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000788", - "cl_label": "naive B cell", - "pr_id": "PR:000001963", - "pr_label": "CD27 molecule", - "cd_synonym": "CD27 (label); CD27L (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z)", - "quote": "\"**N**: CD19+ CD27− CD38− CD24− IgD+\" [naive B cell gating entry, Table 1]", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000788", - "cl_label": "naive B cell", - "pr_id": "PR:000001289", - "pr_label": "membrane-spanning 4-domains subfamily A member 1", - "cd_synonym": "CD20 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122)", - "quote": "Mature B cells typically express both CD19 and CD20.", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000803", - "cl_label": "CD4-negative CD8-negative gamma-delta intraepithelial T cell", - "pr_id": "PR:000001004", - "pr_label": "CD4 molecule", - "cd_synonym": "CD4 (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462)", - "quote": "Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies.", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000803", - "cl_label": "CD4-negative CD8-negative gamma-delta intraepithelial T cell", - "pr_id": "PR:000001084", - "pr_label": "T-cell surface glycoprotein CD8 alpha chain", - "cd_synonym": "CD8 (label); CD8A (exact); CD8a (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462)", - "quote": "Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies.", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000814", - "cl_label": "mature NK T cell", - "pr_id": "PR:000001874", - "pr_label": "KLRB1-like protein", - "cd_synonym": "", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Lal KG et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357)", - "quote": "we defined iNKT cell subsets by the co-expression of TCR Vα24 and Vβ11 among CD3+ cells, and further through their expression of CD4 and CD161", - "source_ref": "reports/literature/inkt_markers.md", - "evidence_links": [ - { - "label": "reports/literature/inkt_markers.md", - "href": "../../literature/inkt_markers.md" - } - ] - }, - { - "cl_id": "CL:0000818", - "cl_label": "transitional stage B cell", - "pr_id": "PR:000001408", - "pr_label": "ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1", - "cd_synonym": "CD38 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546)", - "quote": "T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−)", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000818", - "cl_label": "transitional stage B cell", - "pr_id": "PR:000001932", - "pr_label": "signal transducer CD24", - "cd_synonym": "CD24 (label); CD24A (related)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546)", - "quote": "T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−)", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000818", - "cl_label": "transitional stage B cell", - "pr_id": "PR:000001289", - "pr_label": "membrane-spanning 4-domains subfamily A member 1", - "cd_synonym": "CD20 (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "CD20 positivity on transitional B cells is not stated verbatim in reports/literature/b_cell_markers.md -- the report only confirms CD20 on 'mature B cells' generally (Griffin & Rothstein 2012), not the transitional stage specifically.", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000860", - "cl_label": "classical monocyte", - "pr_id": "PR:000001199", - "pr_label": "C-C chemokine receptor type 2", - "cd_synonym": "CD192 (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0000860", - "cl_label": "classical monocyte", - "pr_id": "PR:000001002", - "pr_label": "CD19 molecule", - "cd_synonym": "CD19 (label)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0000860", - "cl_label": "classical monocyte", - "pr_id": "PR:000001020", - "pr_label": "CD3 epsilon", - "cd_synonym": "CD3 (label); CD3E (exact); CD3e (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0000860", - "cl_label": "classical monocyte", - "pr_id": "PR:000001289", - "pr_label": "membrane-spanning 4-domains subfamily A member 1", - "cd_synonym": "CD20 (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0000875", - "cl_label": "non-classical monocyte", - "pr_id": "PR:000001206", - "pr_label": "CX3C chemokine receptor 1", - "cd_synonym": "", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0000875", - "cl_label": "non-classical monocyte", - "pr_id": "PR:000001002", - "pr_label": "CD19 molecule", - "cd_synonym": "CD19 (label)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0000875", - "cl_label": "non-classical monocyte", - "pr_id": "PR:000001020", - "pr_label": "CD3 epsilon", - "cd_synonym": "CD3 (label); CD3E (exact); CD3e (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0000875", - "cl_label": "non-classical monocyte", - "pr_id": "PR:000001289", - "pr_label": "membrane-spanning 4-domains subfamily A member 1", - "cd_synonym": "CD20 (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0000895", - "cl_label": "naive thymus-derived CD4-positive, alpha-beta T cell", - "pr_id": "PR:000001380", - "pr_label": "interleukin-2 receptor subunit alpha", - "cd_synonym": "CD25 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg", - "quote": "In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000898", - "cl_label": "naive T cell", - "pr_id": "PR:000001318", - "pr_label": "L-selectin", - "cd_synonym": "CD62 (exact); CD62L (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Kamigaichi A et al. 2026 (PMID: 42047825; DOI: 10.1007/s00262-026-04357-4; PMC: PMC13125411) -- confirms CD62L used on human CD4+ T cells, though in a Th1 (not naive-T) context", - "quote": "Th1 (CXCR3+CCR4−CCR6− CD62LlowCD4+ T cells)", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000898", - "cl_label": "naive T cell", - "pr_id": "PR:000001307", - "pr_label": "CD44 molecule", - "cd_synonym": "CD44 (label); CDw44 (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "CD44 not mentioned anywhere in reports/literature/t_cell_markers.md; not found via a targeted EuropePMC search either ('CD44 human naive T cell surface marker' returned unrelated tissue-resident-memory/B-cell papers).", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000898", - "cl_label": "naive T cell", - "pr_id": "PR:000001015", - "pr_label": "receptor-type tyrosine-protein phosphatase C isoform CD45RA", - "cd_synonym": "CD45RA (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8−/CD4+/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000898", - "cl_label": "naive T cell", - "pr_id": "PR:000001203", - "pr_label": "C-C chemokine receptor type 7", - "cd_synonym": "CD197 (exact); CDw197 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8−/CD4+/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000898", - "cl_label": "naive T cell", - "pr_id": "PR:000001869", - "pr_label": "interleukin-7 receptor subunit alpha", - "cd_synonym": "CD127 (exact); CDw127 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg", - "quote": "In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000900", - "cl_label": "naive thymus-derived CD8-positive, alpha-beta T cell", - "pr_id": "PR:000001380", - "pr_label": "interleukin-2 receptor subunit alpha", - "cd_synonym": "CD25 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg", - "quote": "In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000904", - "cl_label": "central memory CD4-positive, alpha-beta T cell", - "pr_id": "PR:000001015", - "pr_label": "receptor-type tyrosine-protein phosphatase C isoform CD45RA", - "cd_synonym": "CD45RA (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8−/CD4+/CCR7+/CD45RA−", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000904", - "cl_label": "central memory CD4-positive, alpha-beta T cell", - "pr_id": "PR:000001203", - "pr_label": "C-C chemokine receptor type 7", - "cd_synonym": "CD197 (exact); CDw197 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8−/CD4+/CCR7+/CD45RA−", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000905", - "cl_label": "effector memory CD4-positive, alpha-beta T cell", - "pr_id": "PR:000001015", - "pr_label": "receptor-type tyrosine-protein phosphatase C isoform CD45RA", - "cd_synonym": "CD45RA (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8−/CD4+/CCR7−/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000905", - "cl_label": "effector memory CD4-positive, alpha-beta T cell", - "pr_id": "PR:000001203", - "pr_label": "C-C chemokine receptor type 7", - "cd_synonym": "CD197 (exact); CDw197 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244)", - "quote": "CD3+/CD8−/CD4+/CCR7−/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000907", - "cl_label": "central memory CD8-positive, alpha-beta T cell", - "pr_id": "PR:000001015", - "pr_label": "receptor-type tyrosine-protein phosphatase C isoform CD45RA", - "cd_synonym": "CD45RA (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design", - "quote": "CD3+/CD8+/CD4−/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000907", - "cl_label": "central memory CD8-positive, alpha-beta T cell", - "pr_id": "PR:000001203", - "pr_label": "C-C chemokine receptor type 7", - "cd_synonym": "CD197 (exact); CDw197 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design", - "quote": "CD3+/CD8+/CD4−/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000913", - "cl_label": "effector memory CD8-positive, alpha-beta T cell", - "pr_id": "PR:000001015", - "pr_label": "receptor-type tyrosine-protein phosphatase C isoform CD45RA", - "cd_synonym": "CD45RA (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design", - "quote": "CD3+/CD8+/CD4−/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000913", - "cl_label": "effector memory CD8-positive, alpha-beta T cell", - "pr_id": "PR:000001203", - "pr_label": "C-C chemokine receptor type 7", - "cd_synonym": "CD197 (exact); CDw197 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design", - "quote": "CD3+/CD8+/CD4−/CCR7+/CD45RA+", - "source_ref": "reports/literature/t_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/t_cell_markers.md", - "href": "../../literature/t_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000938", - "cl_label": "CD16-negative, CD56-bright natural killer cell, human", - "pr_id": "PR:000001024", - "pr_label": "neural cell adhesion molecule 1", - "cd_synonym": "CD56 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0)", - "quote": "human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells.", - "source_ref": "reports/literature/nk_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000938", - "cl_label": "CD16-negative, CD56-bright natural killer cell, human", - "pr_id": "PR:000001483", - "pr_label": "low affinity immunoglobulin gamma Fc region receptor III", - "cd_synonym": "CD16 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360)", - "quote": "CD56bright human NK cells express high levels of CD62L (l-selectin) and CD94 but absent or low levels of CD16 and KIRs", - "source_ref": "reports/literature/nk_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000938", - "cl_label": "CD16-negative, CD56-bright natural killer cell, human", - "pr_id": "PR:000002015", - "pr_label": "MHC class II histocompatibility antigen alpha chain DRA", - "cd_synonym": "", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim", - "quote": "Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1)", - "source_ref": "reports/literature/nk_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000938", - "cl_label": "CD16-negative, CD56-bright natural killer cell, human", - "pr_id": "PR:000001319", - "pr_label": "SLAM family member 5", - "cd_synonym": "CD84 (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No CD84-on-NK-cell evidence found in reports/literature/nk_cell_markers.md or a targeted EuropePMC search ('CD84 human natural killer cell surface marker' -- top hits were CD84 in MDSCs/breast cancer/CLL, none NK-specific).", - "evidence_links": [ - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000939", - "cl_label": "CD16-positive, CD56-dim natural killer cell, human", - "pr_id": "PR:000001024", - "pr_label": "neural cell adhesion molecule 1", - "cd_synonym": "CD56 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0)", - "quote": "human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells.", - "source_ref": "reports/literature/nk_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000939", - "cl_label": "CD16-positive, CD56-dim natural killer cell, human", - "pr_id": "PR:000002015", - "pr_label": "MHC class II histocompatibility antigen alpha chain DRA", - "cd_synonym": "", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim", - "quote": "Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1)", - "source_ref": "reports/literature/nk_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000939", - "cl_label": "CD16-positive, CD56-dim natural killer cell, human", - "pr_id": "PR:000001483", - "pr_label": "low affinity immunoglobulin gamma Fc region receptor III", - "cd_synonym": "CD16 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360)", - "quote": "In contrast, CD56dim NK cells are CD16hi and express more KIRs but less CD94 and CD62L; they predominate in PB", - "source_ref": "reports/literature/nk_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/nk_cell_markers.md", - "href": "../../literature/nk_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000960", - "cl_label": "T3 B cell", - "pr_id": "PR:000001318", - "pr_label": "L-selectin", - "cd_synonym": "CD62 (exact); CD62L (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "CD62L not mentioned in the T3-transitional context in reports/literature/b_cell_markers.md (only mentioned for DN2 B cells: 'lack of CXCR5 and CD62L expression', Sachinidis 2021, a different B cell subset).", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000960", - "cl_label": "T3 B cell", - "pr_id": "PR:000001338", - "pr_label": "complement receptor type 2", - "cd_synonym": "CD21 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546)", - "quote": "The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000960", - "cl_label": "T3 B cell", - "pr_id": "PR:000001880", - "pr_label": "low affinity immunoglobulin epsilon Fc receptor", - "cd_synonym": "CD23 (exact); CD23A (related)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546)", - "quote": "The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000970", - "cl_label": "unswitched memory B cell", - "pr_id": "PR:000001963", - "pr_label": "CD27 molecule", - "cd_synonym": "CD27 (label); CD27L (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z)", - "quote": "\"**M**: CD19+ CD27+ CD38−/lo\" [memory B cell gating entry]", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000972", - "cl_label": "class switched memory B cell", - "pr_id": "PR:000001963", - "pr_label": "CD27 molecule", - "cd_synonym": "CD27 (label); CD27L (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z)", - "quote": "\"**M**: CD19+ CD27+ CD38−/lo\" [memory B cell gating entry]", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000980", - "cl_label": "plasmablast", - "pr_id": "PR:000001408", - "pr_label": "ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1", - "cd_synonym": "CD38 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z)", - "quote": "\"**ASC**: CD19+ CD27+ CD38hi\" and \"**M**: CD19+ CD27+ CD38−/lo\" and", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000980", - "cl_label": "plasmablast", - "pr_id": "PR:000001963", - "pr_label": "CD27 molecule", - "cd_synonym": "CD27 (label); CD27L (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z)", - "quote": "\"**ASC**: CD19+ CD27+ CD38hi\" and \"**M**: CD19+ CD27+ CD38−/lo\" and", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000980", - "cl_label": "plasmablast", - "pr_id": "PR:000001289", - "pr_label": "membrane-spanning 4-domains subfamily A member 1", - "cd_synonym": "CD20 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122)", - "quote": "as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000980", - "cl_label": "plasmablast", - "pr_id": "PR:000001935", - "pr_label": "syndecan-1", - "cd_synonym": "CD138 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z)", - "quote": "\"**CD138neg ASC**: CD138−\" and \"**CD138pos ASC**: CD138+\" [gating labels distinguishing", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000981", - "cl_label": "double negative memory B cell", - "pr_id": "PR:000001963", - "pr_label": "CD27 molecule", - "cd_synonym": "CD27 (label); CD27L (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Sachinidis A & Garyfallos A 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192)", - "quote": "Double negative (DN) B cells, also known as atypical memory B cells, constitute a B cell population that lacks expression of immunoglobulin D and CD27 memory marker.", - "source_ref": "reports/literature/b_cell_markers.md", - "evidence_links": [ - { - "label": "reports/literature/b_cell_markers.md", - "href": "../../literature/b_cell_markers.md" - } - ] - }, - { - "cl_id": "CL:0000990", - "cl_label": "conventional dendritic cell", - "pr_id": "PR:000001013", - "pr_label": "integrin alpha-X", - "cd_synonym": "CD11 (exact); CD11C (related); CD11c (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088)", - "quote": "Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123−", - "source_ref": "reports/literature/dc_markers.md", - "evidence_links": [ - { - "label": "reports/literature/dc_markers.md", - "href": "../../literature/dc_markers.md" - } - ] - }, - { - "cl_id": "CL:0001058", - "cl_label": "plasmacytoid dendritic cell, human", - "pr_id": "PR:000001013", - "pr_label": "integrin alpha-X", - "cd_synonym": "CD11 (exact); CD11C (related); CD11c (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088)", - "quote": "Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123−", - "source_ref": "reports/literature/dc_markers.md", - "evidence_links": [ - { - "label": "reports/literature/dc_markers.md", - "href": "../../literature/dc_markers.md" - } - ] - }, - { - "cl_id": "CL:0001058", - "cl_label": "plasmacytoid dendritic cell, human", - "pr_id": "PR:000001889", - "pr_label": "CD14 molecule", - "cd_synonym": "CD14 (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573)", - "quote": "DCs were defined as live, LIN(CD3, CD19, CD56)−CD14−HLA-DR+ cells.", - "source_ref": "reports/literature/dc_markers.md", - "evidence_links": [ - { - "label": "reports/literature/dc_markers.md", - "href": "../../literature/dc_markers.md" - } - ] - }, - { - "cl_id": "CL:0001058", - "cl_label": "plasmacytoid dendritic cell, human", - "pr_id": "PR:000001865", - "pr_label": "interleukin-3 receptor class 2 alpha chain", - "cd_synonym": "CD123 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088)", - "quote": "pDCs are CD11c− CD123+ cells best characterized for their type I interferon", - "source_ref": "reports/literature/dc_markers.md", - "evidence_links": [ - { - "label": "reports/literature/dc_markers.md", - "href": "../../literature/dc_markers.md" - } - ] - }, - { - "cl_id": "CL:0001065", - "cl_label": "innate lymphoid cell", - "pr_id": "PR:000001002", - "pr_label": "CD19 molecule", - "cd_synonym": "CD19 (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696)", - "quote": "Subsequently we gated out non‐relevant lineages using antibodies against CD3, CD4, TCRαβ, and TCRγδ (T cells), CD19 (B cells) CD14 (monocytes) FcRεR1a (mast cells), BDCA2 (pDCs), CD123 (pDCs, basophils), and CD34 (hematopoietic progenitors).", - "source_ref": "reports/literature/ilc_markers.md", - "evidence_links": [ - { - "label": "reports/literature/ilc_markers.md", - "href": "../../literature/ilc_markers.md" - } - ] - }, - { - "cl_id": "CL:0001065", - "cl_label": "innate lymphoid cell", - "pr_id": "PR:000001020", - "pr_label": "CD3 epsilon", - "cd_synonym": "CD3 (label); CD3E (exact); CD3e (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696)", - "quote": "We gated for lymphocytes, excluded doublets and dead cells and selected CD45+CD3− cells", - "source_ref": "reports/literature/ilc_markers.md", - "evidence_links": [ - { - "label": "reports/literature/ilc_markers.md", - "href": "../../literature/ilc_markers.md" - } - ] - }, - { - "cl_id": "CL:0002393", - "cl_label": "intermediate monocyte", - "pr_id": "PR:000001002", - "pr_label": "CD19 molecule", - "cd_synonym": "CD19 (label)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0002393", - "cl_label": "intermediate monocyte", - "pr_id": "PR:000001020", - "pr_label": "CD3 epsilon", - "cd_synonym": "CD3 (label); CD3E (exact); CD3e (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0002393", - "cl_label": "intermediate monocyte", - "pr_id": "PR:000001199", - "pr_label": "C-C chemokine receptor type 2", - "cd_synonym": "CD192 (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0002393", - "cl_label": "intermediate monocyte", - "pr_id": "PR:000001289", - "pr_label": "membrane-spanning 4-domains subfamily A member 1", - "cd_synonym": "CD20 (exact)", - "species_support": "insufficient_evidence", - "evidence_source": "none", - "citation": "", - "quote": "", - "source_ref": "No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements.", - "evidence_links": [] - }, - { - "cl_id": "CL:0002394", - "cl_label": "CD141-positive myeloid dendritic cell", - "pr_id": "PR:000002105", - "pr_label": "thrombomodulin", - "cd_synonym": "CD141 (exact)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573)", - "quote": "DC1 corresponds to the cross-presenting CD141/BDCA-3+ cDC1, which is best marked by CLEC9A", - "source_ref": "reports/literature/dc_markers.md", - "evidence_links": [ - { - "label": "reports/literature/dc_markers.md", - "href": "../../literature/dc_markers.md" - } - ] - }, - { - "cl_id": "CL:0002399", - "cl_label": "CD1c-positive myeloid dendritic cell", - "pr_id": "PR:000002027", - "pr_label": "T-cell surface glycoprotein CD1c", - "cd_synonym": "CD1C (exact); CD1c (label)", - "species_support": "human", - "evidence_source": "m2_literature_report", - "citation": "Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573)", - "quote": "DC2 and DC3 correspond to new subdivisions of the CD1C/BDCA-1+ cDC2", - "source_ref": "reports/literature/dc_markers.md", - "evidence_links": [ - { - "label": "reports/literature/dc_markers.md", - "href": "../../literature/dc_markers.md" - } - ] - } - ], - "limitations": [ - "All mappings remain proposals; marker compatibility does not establish equivalence.", - "Marker usage is extracted only from valid cells. Invalid cells can hide additional marker usage.", - "Empty structured evidence fields do not mean that literature does not exist; consult the narrative.", - "CL reverse view covers proposed targets, not the entire Cell Ontology.", - "No upstream services were queried. Snapshot age is not proof that an ontology is outdated." - ], - "evaluation": { - "schema_version": 1, - "generated_utc": "2026-09-11T04:13:49.655515+00:00", - "inputs": { - "data/marker_combinations.csv": "29b476e499ac402094b3dbccc410d052010a9b804ca9865e2624dda3ba9bfc44", - "mappings/soulcap_entities.tsv": "b7d312081b5279669599ead19d3d201a1003ff4978eb814302f16c9783b659a8", - "mappings/curated_mappings.tsv": "2ce1d078ed3d374b0c96d04184bb3520d37a1970415ad08584e33bc26e31434e", - "reports/cl_pro_relationships.tsv": "293edb6a7dc435caf9d85a758425be9305eb4eb00c877074fdec4593ef0d1b3c", - "benchmark": "bb1ab9905205a1ab8738b6e9da0a8db382ad3a778eae1103a1279a75335aa706", - "marker_policy": "317578b4b7fb1a9837b9a61fa85c2dc1ea6469eab4404b0435476ba4a12a1f84", - "marker_map": "4d1982db77c57a9a9e43b1fc883c5b0b32f0d69184e081764880baacb37992b7" - }, - "benchmark_path": "C:\\Users\\s28al\\SOULCAP_CL_Mapping\\mappings\\matcher_benchmark.tsv", - "matcher": { - "version": "0.1.0", - "source_hashes": { - "cl_match.py": "4d447e860e8c500196b2859549b91dac9549afeaee236eedd5d63049ca7f7cec", - "phenotype.py": "6d3e7e59b884365fa48596fe1365b8630053b70a6259bb0e8f42413a55a9514a", - "marker_syntax.py": "e40620b1d804eec3c1f05251716092abd7f5a273e11ba91ce61a3345b1872ade", - "registry.py": "a225ca650e0278378566bf7134b3d8daa33dabee0c61c3d479d8affddf7a25fd", - "evaluation.py": "69dd3abd6c1bbf5a5ae453428269179a5cca8b991c1338bb51097dadf06555c5", - "audit.py": "4d2bfeff9583efd80c37d8fef51e06abb887410f4b9d88ce9b68bceace8bc9bb", - "candidate_index.py": "d4c58041cb4c4a4033d1457ae9f04d2e4d814a2d80469dd7aced2e696539e9a6", - "marker_resolution.py": "17feb8779da5a3d429c9d8326d26195cb66bb25cebf9cd005c79410d99efe050" - } - }, - "config": { - "ks": [ - 1, - 3, - 5 - ], - "ranking": "production order, including disqualified candidates", - "ties": "primary metrics use production order; bounds report tie sensitivity", - "denominator": "all cohort cases, including unscorable profiles and absent targets", - "marker_resolution": true, - "resolution_policy": "explicit_v1", - "local_lexical": false, - "lexical_limit": 20, - "lexical_min_jaccard": 0.5 - }, - "candidate_count": 826, - "marker_resolution_issues": [ - { - "marker": "CD15", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required." - }, - { - "marker": "CD16", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required." - }, - { - "marker": "CD1D-A-GALCER", - "reason": "policy_withheld", - "representation": "reagent_gate", - "rationale": "Registry notes describe a reagent, lipid antigen, or carbohydrate epitope rather than a single protein." - }, - { - "marker": "CD3", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required." - }, - { - "marker": "CD57", - "reason": "policy_withheld", - "representation": "reagent_gate", - "rationale": "Registry notes describe a reagent, lipid antigen, or carbohydrate epitope rather than a single protein." - }, - { - "marker": "CD8", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required." - }, - { - "marker": "HLA-DR", - "reason": "policy_withheld", - "representation": "complex", - "rationale": "Registry notes describe an assembled or multi-gene marker; component PRO identity cannot establish whole-marker equivalence." - }, - { - "marker": "IGA", - "reason": "policy_withheld", - "representation": "protein_family", - "rationale": "Registry notes document a non-single-protein or pan-marker representation." - }, - { - "marker": "IGD", - "reason": "policy_withheld", - "representation": "protein_family", - "rationale": "Registry notes document a non-single-protein or pan-marker representation." - }, - { - "marker": "IGE", - "reason": "policy_withheld", - "representation": "protein_family", - "rationale": "Registry notes document a non-single-protein or pan-marker representation." - }, - { - "marker": "IGG", - "reason": "policy_withheld", - "representation": "protein_family", - "rationale": "Registry notes document a non-single-protein or pan-marker representation." - }, - { - "marker": "IGM", - "reason": "policy_withheld", - "representation": "protein_family", - "rationale": "Registry notes document a non-single-protein or pan-marker representation." - }, - { - "marker": "MR1", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "Conservative hold: registry protein label or reagent context does not explicitly establish whole-marker identity; review required." - }, - { - "marker": "TCR", - "reason": "policy_withheld", - "representation": "protein_family", - "rationale": "Registry notes document a non-single-protein or pan-marker representation." - }, - { - "marker": "TCRVA24-JA18", - "reason": "policy_withheld", - "representation": "complex", - "rationale": "Registry notes describe an assembled or multi-gene marker; component PRO identity cannot establish whole-marker equivalence." - }, - { - "marker": "TCRAB", - "reason": "policy_withheld", - "representation": "complex", - "rationale": "Registry notes describe an assembled or multi-gene marker; component PRO identity cannot establish whole-marker equivalence." - }, - { - "marker": "TCRGD", - "reason": "policy_withheld", - "representation": "complex", - "rationale": "Registry notes describe an assembled or multi-gene marker; component PRO identity cannot establish whole-marker equivalence." - }, - { - "marker": "TETRAMER", - "reason": "policy_withheld", - "representation": "reagent_gate", - "rationale": "Registry notes describe a reagent, lipid antigen, or carbohydrate epitope rather than a single protein." - }, - { - "marker": "V", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "No PRO identity recorded; possible source artifact or unresolved marker requires clarification." - }, - { - "marker": "DELTA", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "No PRO identity recorded; possible source artifact or unresolved marker requires clarification." - }, - { - "marker": "DELTA1", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "No PRO identity recorded; possible source artifact or unresolved marker requires clarification." - }, - { - "marker": "GAMMA", - "reason": "policy_withheld", - "representation": "unresolved", - "rationale": "No PRO identity recorded; possible source artifact or unresolved marker requires clarification." - } - ], - "cases": [ - { - "case_id": "provisional/SOULCAP:SC000001/Exact", - "cohort": "provisional", - "subject_id": "SOULCAP:SC000001", - "match_type": "Exact", - "targets": [ - "CL:0000623" - ], - "evidence_reference": "mappings/curated_mappings.tsv", - "uncertain": false, - "rank": 6, - "rank_best": 6, - "rank_worst": 32, - "missing_targets": [], - "candidates": [ - { - "cl_id": "CL:0002338", - "label": "CD56-positive, CD161-positive immature natural killer cell, human", - "score": 19, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD34-", - "CD19-", - "CD56+ (1 of 2 alt.)" - ], - "gaps": [ - "CD3-", - "CD45+", - "CD127-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD123-", - "CD33-/CD64- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 3, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001003", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD34", - "tokens": [ - "CD34" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001003", - "tokens": [ - "CD34" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001289", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD20", - "tokens": [ - "CD20" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001289", - "tokens": [ - "CD20" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001889", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD14", - "tokens": [ - "CD14" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001889", - "tokens": [ - "CD14" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001024", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD56", - "tokens": [ - "CD56" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001024", - "tokens": [ - "CD56" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001381", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD122", - "tokens": [ - "CD122" - ] - } - ] - }, - { - "sense": "positive", - "pr": "PR:000001874", - "asserted": "True", - "paths": [] - }, - { - "sense": "positive", - "pr": "PR:000002065", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD117", - "tokens": [ - "CD117" - ] - }, - { - "via": "pro_id", - "pr": "PR:000002065", - "tokens": [ - "CD117" - ] - } - ] - } - ] - }, - { - "cl_id": "CL:0000938", - "label": "CD16-negative, CD56-bright natural killer cell, human", - "score": 15, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19-", - "CD56+ (hi) (1 of 2 alt.)" - ], - "gaps": [ - "CD34-", - "CD3-", - 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"CD19-/CD20- (no axiom on any alt.)", - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 3, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [], - "rank": 238, - "rank_best": 238, - "rank_worst": 247 - } - ], - "status": "below_top_5", - "note": "" - }, - { - "case_id": "provisional/SOULCAP:SC000099/Exact", - "cohort": "provisional", - "subject_id": "SOULCAP:SC000099", - "match_type": "Exact", - "targets": [ - "CL:0000913" - ], - "evidence_reference": "mappings/curated_mappings.tsv", - "uncertain": false, - "rank": 239, - "rank_best": 238, - "rank_worst": 247, - "missing_targets": [], - "candidates": [ - { - "cl_id": "CL:0001057", - "label": "myeloid dendritic cell, human", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0002000", - "label": "Kit-positive erythroid progenitor cell", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0001024", - "label": "CD34-positive, CD38-negative hematopoietic stem cell", - "score": 12, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 2, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0000938", - "label": "CD16-negative, CD56-bright natural killer cell, human", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0002343", - "label": "decidual natural killer cell, human", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - } - ], - "target_results": [ - { - "cl_id": "CL:0000913", - "label": "effector memory CD8-positive, alpha-beta T cell", - "score": 3, - "matched": [], - "gaps": [ - "CD14-/CD33-/CD64- (no axiom on any alt.)", - "CD19-/CD20- (no axiom on any alt.)", - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 3, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [], - "rank": 239, - "rank_best": 238, - "rank_worst": 247 - } - ], - "status": "below_top_5", - "note": "" - }, - { - "case_id": "provisional/SOULCAP:SC000103/Exact", - "cohort": "provisional", - "subject_id": "SOULCAP:SC000103", - "match_type": "Exact", - "targets": [ - "CL:4030002" - ], - "evidence_reference": "mappings/curated_mappings.tsv", - "uncertain": false, - "rank": null, - "rank_best": null, - "rank_worst": null, - "missing_targets": [ - "CL:4030002" - ], - "candidates": [ - { - "cl_id": "CL:0001057", - "label": "myeloid dendritic cell, human", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0002000", - "label": "Kit-positive erythroid progenitor cell", - "score": 13, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD123-" - ], - "gaps": [ - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD16-" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0000938", - "label": "CD16-negative, CD56-bright natural killer cell, human", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0001024", - "label": "CD34-positive, CD38-negative hematopoietic stem cell", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - }, - { - "cl_id": "CL:0002343", - "label": "decidual natural killer cell, human", - "score": 11, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD19- (1 of 2 alt.)", - "CD16-" - ], - "gaps": [ - "CD123-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 1, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [] - } - ], - "target_results": [], - "status": "target_not_in_index", - "note": "" - } - ], - "metrics": { - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.1524095320342756, - "statuses": { - "below_top_5": 42, - "hit_at_5": 19, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0875, - "hit_at_1_optimistic": 0.125, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.15, - "hit_at_3_optimistic": 0.2, - "hit_at_3_pessimistic": 0.0875, - "hit_at_5": 0.2375, - "hit_at_5_optimistic": 0.275, - "hit_at_5_pessimistic": 0.1 - } - }, - "by_relation": { - "reviewed/Exact": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Broad": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Exact": { - "cases": 50, - "mrr": 0.15217520145714408, - "statuses": { - "below_top_5": 26, - "hit_at_5": 12, - "invalid_profile": 6, - "target_not_in_index": 6 - }, - "cases_with_missing_targets": 8, - "top1_disqualified": 0, - "hit_at_1": 0.08, - "hit_at_1_optimistic": 0.14, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.16, - "hit_at_3_optimistic": 0.18, - "hit_at_3_pessimistic": 0.08, - "hit_at_5": 0.24, - "hit_at_5_optimistic": 0.24, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Broad": { - "cases": 30, - "mrr": 0.1528000829961614, - "statuses": { - "hit_at_5": 7, - "below_top_5": 16, - "target_not_in_index": 7 - }, - "cases_with_missing_targets": 7, - "top1_disqualified": 0, - "hit_at_1": 0.1, - "hit_at_1_optimistic": 0.1, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.13333333333333333, - "hit_at_3_optimistic": 0.23333333333333334, - "hit_at_3_pessimistic": 0.1, - "hit_at_5": 0.23333333333333334, - "hit_at_5_optimistic": 0.3333333333333333, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - } - } -} diff --git a/reports/resolver-refinement/legacy/matcher_evaluation.md b/reports/resolver-refinement/legacy/matcher_evaluation.md deleted file mode 100644 index 5ed8fdf..0000000 --- a/reports/resolver-refinement/legacy/matcher_evaluation.md +++ /dev/null @@ -1,195 +0,0 @@ -# Matcher evaluation - -Target retrieval only; provisional agreement is not validated accuracy. -All cohort cases remain in denominators, including invalid profiles and absent targets. -Primary ranks retain production tie ordering and disqualified candidates. Bounds show tie sensitivity. - -## Metrics - -```json -{ - "reviewed": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional": { - "cases": 80, - "mrr": 0.1524095320342756, - "statuses": { - "below_top_5": 42, - "hit_at_5": 19, - "invalid_profile": 6, - "target_not_in_index": 13 - }, - "cases_with_missing_targets": 15, - "top1_disqualified": 0, - "hit_at_1": 0.0875, - "hit_at_1_optimistic": 0.125, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.15, - "hit_at_3_optimistic": 0.2, - "hit_at_3_pessimistic": 0.0875, - "hit_at_5": 0.2375, - "hit_at_5_optimistic": 0.275, - "hit_at_5_pessimistic": 0.1 - } -} -``` - -## Relation breakdown - -```json -{ - "reviewed/Exact": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Broad": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "reviewed/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Exact": { - "cases": 50, - "mrr": 0.15217520145714408, - "statuses": { - "below_top_5": 26, - "hit_at_5": 12, - "invalid_profile": 6, - "target_not_in_index": 6 - }, - "cases_with_missing_targets": 8, - "top1_disqualified": 0, - "hit_at_1": 0.08, - "hit_at_1_optimistic": 0.14, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.16, - "hit_at_3_optimistic": 0.18, - "hit_at_3_pessimistic": 0.08, - "hit_at_5": 0.24, - "hit_at_5_optimistic": 0.24, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Broad": { - "cases": 30, - "mrr": 0.1528000829961614, - "statuses": { - "hit_at_5": 7, - "below_top_5": 16, - "target_not_in_index": 7 - }, - "cases_with_missing_targets": 7, - "top1_disqualified": 0, - "hit_at_1": 0.1, - "hit_at_1_optimistic": 0.1, - "hit_at_1_pessimistic": 0.0, - "hit_at_3": 0.13333333333333333, - "hit_at_3_optimistic": 0.23333333333333334, - "hit_at_3_pessimistic": 0.1, - "hit_at_5": 0.23333333333333334, - "hit_at_5_optimistic": 0.3333333333333333, - "hit_at_5_pessimistic": 0.1 - }, - "provisional/Narrow": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - }, - "provisional/Related": { - "cases": 0, - "mrr": null, - "statuses": {}, - "cases_with_missing_targets": 0, - "top1_disqualified": 0, - "hit_at_1": null, - "hit_at_1_optimistic": null, - "hit_at_1_pessimistic": null, - "hit_at_3": null, - "hit_at_3_optimistic": null, - "hit_at_3_pessimistic": null, - "hit_at_5": null, - "hit_at_5_optimistic": null, - "hit_at_5_pessimistic": null - } -} -``` - -See matcher_evaluation.tsv for per-case failures and matcher_evaluation.json for full evidence and provenance. diff --git a/reports/resolver-refinement/legacy/matcher_evaluation.tsv b/reports/resolver-refinement/legacy/matcher_evaluation.tsv deleted file mode 100644 index e878348..0000000 --- a/reports/resolver-refinement/legacy/matcher_evaluation.tsv +++ /dev/null @@ -1,81 +0,0 @@ -case_id cohort subject_id match_type targets status rank rank_best rank_worst missing_targets note candidates target_results -provisional/SOULCAP:SC000001/Exact provisional SOULCAP:SC000001 Exact "[""CL:0000623""]" below_top_5 6 6 32 [] "[{""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD56+ (1 of 2 alt.)""], ""gaps"": [""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 19, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (hi) (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 19, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim) (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 19, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (hi) (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 17, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD56+ (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000623"", ""label"": ""natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+/CD56:high (no axiom on any alt.)"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-"", ""CD33-/CD64- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 6, ""rank_best"": 6, ""rank_worst"": 32}]" -provisional/SOULCAP:SC000002/Exact provisional SOULCAP:SC000002 Exact "[""CL:0000938""]" hit_at_5 1 1 2 [] "[{""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56:high (hi)"", ""CD16- (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56:high (hi)"", ""CD16- (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 19, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD56:high"", ""CD127-"", ""CD16-/CD16:low (no axiom on any alt.)"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000623"", ""label"": ""natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56:high"", ""CD127-"", ""CD16-/CD16:low (no axiom on any alt.)"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000823"", ""label"": ""immature natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56:high"", ""CD127-"", ""CD16-/CD16:low (no axiom on any alt.)"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56:high (hi)"", ""CD16- (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000003/Exact provisional SOULCAP:SC000003 Exact "[""CL:0000939""]" hit_at_5 1 1 2 [] "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim) (1 of 2 alt.)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD56+ (1 of 2 alt.)""], ""gaps"": [""CD45+"", ""CD127-"", ""CD16+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 17, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD56+ (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD45+"", ""CD127-"", ""CD16+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000623"", ""label"": ""natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+/CD56:high (no axiom on any alt.)"", ""CD127-"", ""CD16+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000823"", ""label"": ""immature natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+/CD56:high (no axiom on any alt.)"", ""CD127-"", ""CD16+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim) (1 of 2 alt.)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000004/Broad provisional SOULCAP:SC000004 Broad "[""CL:0000939""]" hit_at_5 1 1 2 [] "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD56+""], ""gaps"": [""CD45+"", ""CD127-"", ""CD16+"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 17, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD45+"", ""CD127-"", ""CD16+"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002346"", ""label"": ""Dx5-negative, NK1.1-positive immature natural killer cell, mouse"", ""score"": 16, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+"", ""CD127-"", ""CD16+"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002438"", ""label"": ""NK1.1-positive natural killer cell, mouse"", ""score"": 16, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+"", ""CD127-"", ""CD16+"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000005/Broad provisional SOULCAP:SC000005 Broad "[""CL:0000939""]" hit_at_5 1 1 2 [] "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD56+""], ""gaps"": [""CD45+"", ""CD127-"", ""CD16+"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 17, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD45+"", ""CD127-"", ""CD16+"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000623"", ""label"": ""natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+"", ""CD127-"", ""CD16+"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000823"", ""label"": ""immature natural killer cell"", ""score"": 15, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD56+"", ""CD127-"", ""CD16+"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000939"", ""label"": ""CD16-positive, CD56-dim natural killer cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD56+ (dim)"", ""CD16+""], ""gaps"": [""CD34-"", ""CD45+"", ""CD127-"", ""CD57+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000006/Broad provisional SOULCAP:SC000006 Broad "[""CL:0001074""]" hit_at_5 3 3 3 [] "[{""cl_id"": ""CL:0001073"", ""label"": ""CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human"", ""score"": 15, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001076"", ""label"": ""NKp46-positive innate lymphoid cell, human"", ""score"": 15, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001074"", ""label"": ""CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human"", ""score"": 14, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002338"", ""label"": ""CD56-positive, CD161-positive immature natural killer cell, human"", ""score"": 13, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001072"", ""label"": ""CD34-negative, CD117-positive innate lymphoid cell, human"", ""score"": 11, ""matched"": [""CD3-"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD56+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001074"", ""label"": ""CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human"", ""score"": 14, ""matched"": [""CD3-"", ""CD56+"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 3, ""rank_best"": 3, ""rank_worst"": 3}]" -provisional/SOULCAP:SC000007/Exact provisional SOULCAP:SC000007 Exact "[""CL:0001065""]" below_top_5 155 155 159 [] "[{""cl_id"": ""CL:0000989"", ""label"": ""CD11c-low plasmacytoid dendritic cell"", ""score"": 23, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000992"", ""label"": ""immature CD11c-low plasmacytoid dendritic cell"", ""score"": 23, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000993"", ""label"": ""mature CD11c-low plasmacytoid dendritic cell"", ""score"": 23, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 23, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD123-""], ""gaps"": [""CD45+"", ""CD127+"", ""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002089"", ""label"": ""group 2 innate lymphoid cell, mouse"", ""score"": 23, ""matched"": [""CD33- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD127+""], ""gaps"": [""CD34-"", ""CD45+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001065"", ""label"": ""innate lymphoid cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD19-"", ""CD3-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD34-"", ""CD45+"", ""CD127+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 155, ""rank_best"": 155, ""rank_worst"": 159}]" -provisional/SOULCAP:SC000008/Exact provisional SOULCAP:SC000008 Exact "[""CL:0001067""]" below_top_5 161 150 165 [] "[{""cl_id"": ""CL:0000989"", ""label"": ""CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117-"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000992"", ""label"": ""immature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117-"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000993"", ""label"": ""mature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117-"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 27, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD56-"", ""CD123-""], ""gaps"": [""CD45+"", ""CD127+"", ""CD117-"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002089"", ""label"": ""group 2 innate lymphoid cell, mouse"", ""score"": 27, ""matched"": [""CD33- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD127+"", ""CD56-""], ""gaps"": [""CD34-"", ""CD45+"", ""CD117-"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001067"", ""label"": ""group 1 innate lymphoid cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD19-"", ""CD3-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD34-"", ""CD45+"", ""CD127+"", ""CD56-"", ""CD117-"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 161, ""rank_best"": 150, ""rank_worst"": 165}]" -provisional/SOULCAP:SC000009/Exact provisional SOULCAP:SC000009 Exact "[""CL:0001081""]" below_top_5 26 25 32 [] "[{""cl_id"": ""CL:0002029"", ""label"": ""Fc-epsilon RIalpha-low mast cell progenitor"", ""score"": 29, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD117:low (dim) (1 of 2 alt.)""], ""gaps"": [""CD34-"", ""CD127+"", ""CD294+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000989"", ""label"": ""CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117:low/CD117- (no axiom on any alt.)"", ""CD294+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000992"", ""label"": ""immature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117:low/CD117- (no axiom on any alt.)"", ""CD294+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000993"", ""label"": ""mature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56-"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117:low/CD117- (no axiom on any alt.)"", ""CD294+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 27, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD56-"", ""CD123-""], ""gaps"": [""CD45+"", ""CD127+"", ""CD117:low/CD117- (no axiom on any alt.)"", ""CD294+"", ""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001081"", ""label"": ""group 2 innate lymphoid cell, human"", ""score"": 23, ""matched"": [""CD3-"", ""CD19-"", ""CD3-"", ""CD127+"", ""CD294+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD34-"", ""CD45+"", ""CD56-"", ""CD117:low/CD117- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 26, ""rank_best"": 25, ""rank_worst"": 32}]" -provisional/SOULCAP:SC000010/Exact provisional SOULCAP:SC000010 Exact "[""CL:0001078""]" below_top_5 118 118 120 [] "[{""cl_id"": ""CL:0002029"", ""label"": ""Fc-epsilon RIalpha-low mast cell progenitor"", ""score"": 29, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD117+ (dim)""], ""gaps"": [""CD34-"", ""CD127+"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002344"", ""label"": ""CD56-negative, CD161-positive immature natural killer cell, human"", ""score"": 29, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD34-"", ""CD3-"", ""CD19-"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD117+""], ""gaps"": [""CD45+"", ""CD127+"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000989"", ""label"": ""CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117+"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000992"", ""label"": ""immature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117+"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000993"", ""label"": ""mature CD11c-low plasmacytoid dendritic cell"", ""score"": 27, ""matched"": [""CD34-"", ""CD3-"", ""CD19-"", ""CD45+"", ""CD3-"", ""CD56- (1 of 2 alt.)"", ""CD11C:not:high (dim) (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD127+"", ""CD117+"", ""CD294-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001078"", ""label"": ""group 3 innate lymphoid cell, human"", ""score"": 19, ""matched"": [""CD3-"", ""CD19-"", ""CD3-"", ""CD127+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD34-"", ""CD45+"", ""CD56:low/CD56- (no axiom on any alt.)"", ""CD117+"", ""CD294-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 118, ""rank_best"": 118, ""rank_worst"": 120}]" -provisional/SOULCAP:SC000011/Exact provisional SOULCAP:SC000011 Exact "[""CL:0000990""]" below_top_5 18 15 21 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 21, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD3-"", ""CD19-"", ""CD56-"", ""CD127-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""CD11C:high"", ""HLA-DR+""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000782"", ""label"": ""myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002394"", ""label"": ""CD141-positive myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002399"", ""label"": ""CD1c-positive myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000990"", ""label"": ""conventional dendritic cell"", ""score"": 13, ""matched"": [""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD123:not:high/CD193- (no axiom on any alt.)"", ""CD123:not:high/CD303- (no axiom on any alt.)"", ""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 18, ""rank_best"": 15, ""rank_worst"": 21}]" -provisional/SOULCAP:SC000012/Exact provisional SOULCAP:SC000012 Exact "[""CL:0002394""]" hit_at_5 2 1 2 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD141+"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002394"", ""label"": ""CD141-positive myeloid dendritic cell"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD141+"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 21, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD3-"", ""CD19-"", ""CD56-"", ""CD127-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""CD11C:high"", ""HLA-DR+"", ""CD1C-"", ""CD141+"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000782"", ""label"": ""myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD141+"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0011031"", ""label"": ""monocyte-derived dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD141+"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0002394"", ""label"": ""CD141-positive myeloid dendritic cell"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD141+"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C-"", ""CD127-"", ""CD172A-"", ""FCER1A-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 2, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000013/Exact provisional SOULCAP:SC000013 Exact "[""CL:0002399""]" hit_at_5 2 1 2 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002399"", ""label"": ""CD1c-positive myeloid dendritic cell"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD1C+"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 21, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD14-"", ""CD3-"", ""CD19-"", ""CD56-"", ""CD127-""], ""gaps"": [""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""CD11C:high"", ""HLA-DR+"", ""CD1C+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000782"", ""label"": ""myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002394"", ""label"": ""CD141-positive myeloid dendritic cell"", ""score"": 20, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD1C+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0002399"", ""label"": ""CD1c-positive myeloid dendritic cell"", ""score"": 24, ""matched"": [""CD123:not:high (1 of 2 alt.)"", ""CD123:not:high (1 of 2 alt.)"", ""CD11C:high (hi)"", ""CD1C+"", ""CD3-"", ""CD19-"", ""CD56-""], ""gaps"": [""CD14-"", ""CD16-"", ""CD45+"", ""CD33:high/CD64+ (no axiom on any alt.)"", ""HLA-DR+"", ""CD141:low/CD141- (no axiom on any alt.)"", ""CD127-"", ""CD172A+"", ""FCER1A:low/FCER1A- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 2, ""rank_best"": 1, ""rank_worst"": 2}]" -provisional/SOULCAP:SC000014/Exact provisional SOULCAP:SC000014 Exact "[""CL:0001058""]" below_top_5 34 27 42 [] "[{""cl_id"": ""CL:0000991"", ""label"": ""CD11c-negative plasmacytoid dendritic cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD303+ (1 of 3 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000994"", ""label"": ""immature CD11c-negative plasmacytoid dendritic cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD303+ (1 of 3 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000996"", ""label"": ""mature CD11c-negative plasmacytoid dendritic cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD303+ (1 of 3 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002008"", ""label"": ""CD34-positive, CD38-positive eosinophil progenitor cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD56-"", ""CD19-"", ""CD14-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD193-/FCER1A-/CD303+ (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002029"", ""label"": ""Fc-epsilon RIalpha-low mast cell progenitor"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD56-"", ""CD19-"", ""CD14-""], ""gaps"": [""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD193-/FCER1A-/CD303+ (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0001058"", ""label"": ""plasmacytoid dendritic cell, human"", ""score"": 12, ""matched"": [""CD3-"", ""CD56-"", ""CD19-"", ""CD14-""], ""gaps"": [""CD45+"", ""CD33:low/CD33+/CD123:high (no axiom on any alt.)"", ""CD193-/FCER1A-/CD303+ (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 34, ""rank_best"": 27, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000015/Exact provisional SOULCAP:SC000015 Exact "[""CL:0000043""]" hit_at_5 3 3 7 [] "[{""cl_id"": ""CL:0000614"", ""label"": ""basophilic myelocyte"", ""score"": 18, ""matched"": [""CD3-"", ""CD33+ (1 of 2 alt.)"", ""CD193+ (hi) (1 of 4 alt.)"", ""CD56-"", ""CD19-"", ""CD16-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD14-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [""CD15-/CD66B- (all alt. conflict)""], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002008"", ""label"": ""CD34-positive, CD38-positive eosinophil progenitor cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD123+ (1 of 2 alt.)"", ""CD56-"", ""CD19-"", ""CD14-""], ""gaps"": [""CD193+/FCER1A+/HLA-DR-/CD303- (no axiom on any alt.)"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000043"", ""label"": ""mature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD123+ (hi) (1 of 2 alt.)"", ""CD193+ (hi) (1 of 4 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000612"", ""label"": ""eosinophilic myelocyte"", ""score"": 17, ""matched"": [""CD3-"", ""CD33+ (1 of 2 alt.)"", ""CD193+ (1 of 4 alt.)"", ""CD56-"", ""CD19-"", ""CD16-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD14-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [""CD15-/CD66B- (all alt. conflict)""], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000767"", ""label"": ""basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD123+ (hi) (1 of 2 alt.)"", ""CD193+ (hi) (1 of 4 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000043"", ""label"": ""mature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD123+ (hi) (1 of 2 alt.)"", ""CD193+ (hi) (1 of 4 alt.)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD127-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD14-"", ""CD16-"", ""FCER1A+"", ""HLA-DR-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 3, ""rank_best"": 3, ""rank_worst"": 7}]" -provisional/SOULCAP:SC000016/Exact provisional SOULCAP:SC000016 Exact "[""CL:0000043""]" hit_at_5 1 1 4 [] "[{""cl_id"": ""CL:0000043"", ""label"": ""mature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000767"", ""label"": ""basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000768"", ""label"": ""immature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000770"", ""label"": ""band form basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000942"", ""label"": ""thymic plasmacytoid dendritic cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD45+"", ""CD123+"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD193+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000043"", ""label"": ""mature basophil"", ""score"": 17, ""matched"": [""CD3-"", ""CD193+ (hi)"", ""CD123+ (hi)"", ""CD56-"", ""CD19-""], ""gaps"": [""CD15-/CD66B- (no axiom on any alt.)"", ""CD45+"", ""CD127-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 4}]" -provisional/SOULCAP:SC000017/Exact provisional SOULCAP:SC000017 Exact "[""CL:0000576""]" invalid_profile "[""CL:0000576""]" invalid expression in Required exclusion: unexpected ')' in group [] [] -provisional/SOULCAP:SC000018/Exact provisional SOULCAP:SC000018 Exact "[""CL:0000860""]" invalid_profile [] invalid expression in Required exclusion: unexpected ')' in group [] [] -provisional/SOULCAP:SC000019/Exact provisional SOULCAP:SC000019 Exact "[""CL:0000875""]" invalid_profile [] invalid expression in Required exclusion: unexpected ')' in group [] [] -provisional/SOULCAP:SC000020/Exact provisional SOULCAP:SC000020 Exact "[""CL:0002393""]" invalid_profile [] invalid expression in Required exclusion: unexpected ')' in group [] [] -provisional/SOULCAP:SC000021/Exact provisional SOULCAP:SC000021 Exact "[""CL:0000775""]" below_top_5 9 7 16 [] "[{""cl_id"": ""CL:0000582"", ""label"": ""neutrophilic metamyelocyte"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD19-"", ""CD33+ (1 of 2 alt.)""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001021"", ""label"": ""CD34-positive, CD38-positive common lymphoid progenitor"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD14- (1 of 2 alt.)"", ""CD45+"", ""CD19-""], ""gaps"": [""CD123-"", ""CD15:high/CD66B+ (no axiom on any alt.)"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD14- (1 of 2 alt.)"", ""CD123-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD15:high/CD66B+ (no axiom on any alt.)"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD14- (1 of 2 alt.)"", ""CD123-"", ""CD19-""], ""gaps"": [""CD45+"", ""CD15:high/CD66B+ (no axiom on any alt.)"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002029"", ""label"": ""Fc-epsilon RIalpha-low mast cell progenitor"", ""score"": 18, ""matched"": [""CD3-"", ""CD56-"", ""CD14- (1 of 2 alt.)"", ""CD45+"", ""CD19-""], ""gaps"": [""CD123-"", ""CD15:high/CD66B+ (no axiom on any alt.)"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000775"", ""label"": ""neutrophil"", ""score"": 16, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD193-"", ""CD16:high"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 9, ""rank_best"": 7, ""rank_worst"": 16}]" -provisional/SOULCAP:SC000022/Exact provisional SOULCAP:SC000022 Exact "[""CL:0000771""]" hit_at_5 4 2 7 [] "[{""cl_id"": ""CL:0000612"", ""label"": ""eosinophilic myelocyte"", ""score"": 26, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD16-"", ""CD19-"", ""CD33+ (1 of 2 alt.)""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000041"", ""label"": ""mature eosinophil"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD16-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000580"", ""label"": ""neutrophilic myelocyte"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD16-"", ""CD19-"", ""CD33+ (1 of 2 alt.)""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD193+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000771"", ""label"": ""eosinophil"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD16-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000772"", ""label"": ""immature eosinophil"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD16-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000771"", ""label"": ""eosinophil"", ""score"": 20, ""matched"": [""CD3-"", ""CD56-"", ""CD66B+ (1 of 2 alt.)"", ""CD193+"", ""CD19-""], ""gaps"": [""CD14:low/CD14- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD16-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD64-/CD33+ (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 4, ""rank_best"": 2, ""rank_worst"": 7}]" -provisional/SOULCAP:SC000023/Exact provisional SOULCAP:SC000023 Exact "[""CL:0000236""]" target_not_in_index "[""CL:0000236""]" "[{""cl_id"": ""CL:0000819"", ""label"": ""B-1 B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000820"", ""label"": ""B-1a B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000821"", ""label"": ""B-1b B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000843"", ""label"": ""follicular B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000024/Exact provisional SOULCAP:SC000024 Exact "[""CL:0000946""]" target_not_in_index "[""CL:0000946""]" "[{""cl_id"": ""CL:0000949"", ""label"": ""IgD plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000950"", ""label"": ""IgE plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000980"", ""label"": ""plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000982"", ""label"": ""IgG plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000983"", ""label"": ""IgM plasmablast"", ""score"": 18, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000025/Exact provisional SOULCAP:SC000025 Exact "[""CL:0000980""]" hit_at_5 3 1 7 [] "[{""cl_id"": ""CL:0000949"", ""label"": ""IgD plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000950"", ""label"": ""IgE plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000980"", ""label"": ""plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000982"", ""label"": ""IgG plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000983"", ""label"": ""IgM plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000980"", ""label"": ""plasmablast"", ""score"": 23, ""matched"": [""CD3-"", ""CD19+"", ""CD27+ (hi) (1 of 2 alt.)"", ""CD38:high (hi)"", ""CD138-"", ""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 3, ""rank_best"": 1, ""rank_worst"": 7}]" -provisional/SOULCAP:SC000026/Exact provisional SOULCAP:SC000026 Exact "[""CL:0000786""]" below_top_5 31 31 53 [] "[{""cl_id"": ""CL:0002047"", ""label"": ""fraction B precursor B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD45+"", ""CD19+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002049"", ""label"": ""fraction C precursor B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD45+"", ""CD19+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002050"", ""label"": ""fraction C' precursor B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD45+"", ""CD19+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002051"", ""label"": ""CD38-high pre-BCR positive cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD19+"", ""CD38:high (hi)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002052"", ""label"": ""fraction D precursor B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD45+"", ""CD19+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD138+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000786"", ""label"": ""plasma cell"", ""score"": 8, ""matched"": [""CD138+"", ""CD20-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD3-"", ""CD56-"", ""CD45+"", ""CD19+"", ""CD27+/CD27:high (no axiom on any alt.)"", ""CD38:high"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 31, ""rank_best"": 31, ""rank_worst"": 53}]" -provisional/SOULCAP:SC000028/Broad provisional SOULCAP:SC000028 Broad "[""CL:0000818""]" hit_at_5 1 1 6 [] "[{""cl_id"": ""CL:0000818"", ""label"": ""transitional stage B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000958"", ""label"": ""T1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000959"", ""label"": ""T2 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000960"", ""label"": ""T3 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:high/CD10:high (no axiom on any alt.)"", ""CD24:high"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000818"", ""label"": ""transitional stage B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38:high (hi) (1 of 2 alt.)"", ""CD24:high (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 6}]" -provisional/SOULCAP:SC000029/Exact provisional SOULCAP:SC000029 Exact "[""CL:0000785""]" below_top_5 43 43 45 [] "[{""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002055"", ""label"": ""CD38-negative immature B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000785"", ""label"": ""mature B cell"", ""score"": 10, ""matched"": [""CD3-"", ""CD19+ (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-"", ""CD20+""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 43, ""rank_best"": 43, ""rank_worst"": 45}]" -provisional/SOULCAP:SC000030/Exact provisional SOULCAP:SC000030 Exact "[""CL:0000960""]" below_top_5 20 13 26 [] "[{""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24+"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24+"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10:low (no axiom on any alt.)"", ""CD24+"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10:low (no axiom on any alt.)"", ""CD24+"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002054"", ""label"": ""fraction E immature B cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+"", ""CD127-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low/CD38-/CD10:low (no axiom on any alt.)"", ""IGD+"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000960"", ""label"": ""T3 B cell"", ""score"": 15, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+ (hi)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low (hi)/CD38- (hi)/CD10:low (no axiom on any alt.)"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 20, ""rank_best"": 13, ""rank_worst"": 26}]" -provisional/SOULCAP:SC000031/Exact provisional SOULCAP:SC000031 Exact "[""CL:0000788""]" hit_at_5 5 5 8 [] "[{""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000788"", ""label"": ""naive B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000788"", ""label"": ""naive B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 5, ""rank_best"": 5, ""rank_worst"": 8}]" -provisional/SOULCAP:SC000032/Exact provisional SOULCAP:SC000032 Exact "[""CL:0000981""]" hit_at_5 5 5 8 [] "[{""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 18, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 5, ""rank_best"": 5, ""rank_worst"": 8}]" -provisional/SOULCAP:SC000033/Broad provisional SOULCAP:SC000033 Broad "[""CL:0000981""]" below_top_5 12 12 19 [] "[{""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 23, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002055"", ""label"": ""CD38-negative immature B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD21+ (dim)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24+"", ""IGD-"", ""CD21+"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000843"", ""label"": ""follicular B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000959"", ""label"": ""T2 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+ (hi)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low (hi)/CD38- (hi)/CD10- (no axiom on any alt.)"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21+"", ""CD11C-"", ""CD185+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 12, ""rank_best"": 12, ""rank_worst"": 19}]" -provisional/SOULCAP:SC000034/Broad provisional SOULCAP:SC000034 Broad "[""CL:0000981""]" hit_at_5 4 4 6 [] "[{""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002103"", ""label"": ""IgG-positive double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24-"", ""IGD-"", ""CD21-"", ""CD11C+"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 4, ""rank_best"": 4, ""rank_worst"": 6}]" -provisional/SOULCAP:SC000035/Broad provisional SOULCAP:SC000035 Broad "[""CL:0000981""]" hit_at_5 5 5 12 [] "[{""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000958"", ""label"": ""T1 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+ (hi)"", ""CD21-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low (hi)/CD38- (hi)/CD10- (no axiom on any alt.)"", ""IGD-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002109"", ""label"": ""B220-positive CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002110"", ""label"": ""B220-low CD38-positive naive B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21-"", ""CD11C-"", ""CD185-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 5, ""rank_best"": 5, ""rank_worst"": 12}]" -provisional/SOULCAP:SC000036/Broad provisional SOULCAP:SC000036 Broad "[""CL:0000981""]" below_top_5 12 12 19 [] "[{""cl_id"": ""CL:0000961"", ""label"": ""Bm1 B cell"", ""score"": 23, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002055"", ""label"": ""CD38-negative immature B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD38- (1 of 3 alt.)"", ""CD21+ (dim)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002102"", ""label"": ""CD38-negative naive B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD38- (1 of 3 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD24+"", ""IGD-"", ""CD21+"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000843"", ""label"": ""follicular B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD27-"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000959"", ""label"": ""T2 B cell"", ""score"": 19, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD24+ (hi)"", ""CD21+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27-"", ""CD38:low (hi)/CD38- (hi)/CD10- (no axiom on any alt.)"", ""IGD-"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000981"", ""label"": ""double negative memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27-"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38-/CD10- (no axiom on any alt.)"", ""CD24+"", ""IGD-"", ""CD21+"", ""CD11C-"", ""CD185+"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 12, ""rank_best"": 12, ""rank_worst"": 19}]" -provisional/SOULCAP:SC000037/Exact provisional SOULCAP:SC000037 Exact "[""CL:0000787""]" below_top_5 39 39 42 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002108"", ""label"": ""CD38-negative IgG memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002111"", ""label"": ""CD38-negative unswitched memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002115"", ""label"": ""B220-positive CD38-positive unswitched memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000787"", ""label"": ""memory B cell"", ""score"": 12, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 39, ""rank_best"": 39, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000039/Exact provisional SOULCAP:SC000039 Exact "[""CL:0000970""]" below_top_5 13 13 14 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 25, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 25, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002111"", ""label"": ""CD38-negative unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002115"", ""label"": ""B220-positive CD38-positive unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002116"", ""label"": ""B220-low CD38-positive unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000970"", ""label"": ""unswitched memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD+"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 13, ""rank_best"": 13, ""rank_worst"": 14}]" -provisional/SOULCAP:SC000040/Exact provisional SOULCAP:SC000040 Exact "[""CL:0000971""]" below_top_5 33 33 39 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002108"", ""label"": ""CD38-negative IgG memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002111"", ""label"": ""CD38-negative unswitched memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002115"", ""label"": ""B220-positive CD38-positive unswitched memory B cell"", ""score"": 20, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000971"", ""label"": ""IgM memory B cell"", ""score"": 13, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD27+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 33, ""rank_best"": 33, ""rank_worst"": 39}]" -provisional/SOULCAP:SC000041/Exact provisional SOULCAP:SC000041 Exact "[""CL:0000972""]" below_top_5 14 13 18 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 25, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 25, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002111"", ""label"": ""CD38-negative unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002115"", ""label"": ""B220-positive CD38-positive unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002116"", ""label"": ""B220-low CD38-positive unswitched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000972"", ""label"": ""class switched memory B cell"", ""score"": 17, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 14, ""rank_best"": 13, ""rank_worst"": 18}]" -provisional/SOULCAP:SC000042/Exact provisional SOULCAP:SC000042 Exact "[""CL:0000973""]" below_top_5 18 17 19 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002118"", ""label"": ""CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002120"", ""label"": ""CD24-positive CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002121"", ""label"": ""CD24-negative CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000973"", ""label"": ""IgA memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""IGA+"", ""IGG-"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 18, ""rank_best"": 17, ""rank_worst"": 19}]" -provisional/SOULCAP:SC000043/Exact provisional SOULCAP:SC000043 Exact "[""CL:0000979""]" below_top_5 18 17 22 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002118"", ""label"": ""CD38-negative IgG-negative class switched memory B cell"", ""score"": 22, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002120"", ""label"": ""CD24-positive CD38-negative IgG-negative class switched memory B cell"", ""score"": 22, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002121"", ""label"": ""CD24-negative CD38-negative IgG-negative class switched memory B cell"", ""score"": 22, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 4, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000979"", ""label"": ""IgG memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG+"", ""IGE-"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 18, ""rank_best"": 17, ""rank_worst"": 22}]" -provisional/SOULCAP:SC000044/Exact provisional SOULCAP:SC000044 Exact "[""CL:0000948""]" below_top_5 17 17 19 [] "[{""cl_id"": ""CL:0002112"", ""label"": ""B220-positive CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002113"", ""label"": ""B220-low CD38-negative unswitched memory B cell"", ""score"": 24, ""matched"": [""CD3-"", ""CD45+ (dim)"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002118"", ""label"": ""CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002120"", ""label"": ""CD24-positive CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002121"", ""label"": ""CD24-negative CD38-negative IgG-negative class switched memory B cell"", ""score"": 21, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD38- (1 of 2 alt.)"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000948"", ""label"": ""IgE memory B cell"", ""score"": 16, ""matched"": [""CD3-"", ""CD20+ (1 of 2 alt.)"", ""CD27+"", ""CD20+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD56-"", ""CD45+"", ""CD38:low/CD38- (no axiom on any alt.)"", ""IGD-"", ""IGM-"", ""IGA-"", ""IGG-"", ""IGE+"", ""CD127-"", ""CD16-"", ""CD15-/CD66B- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD123-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 17, ""rank_best"": 17, ""rank_worst"": 19}]" -provisional/SOULCAP:SC000045/Exact provisional SOULCAP:SC000045 Exact "[""CL:0000084""]" target_not_in_index "[""CL:0000084""]" "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000786"", ""label"": ""plasma cell"", ""score"": 5, ""matched"": [""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000046/Broad provisional SOULCAP:SC000046 Broad "[""CL:4052055""]" below_top_5 34 2 34 [] "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD56+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000570"", ""label"": ""parafollicular cell"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 34, ""rank_best"": 2, ""rank_worst"": 34}]" -provisional/SOULCAP:SC000047/Broad provisional SOULCAP:SC000047 Broad "[""CL:4052055""]" below_top_5 42 13 42 [] "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002430"", ""label"": ""CD4-intermediate, CD8-positive double-positive thymocyte"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002431"", ""label"": ""CD4-positive, CD8-intermediate double-positive thymocyte"", ""score"": 9, ""matched"": [""CD4+"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD4+"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 42, ""rank_best"": 13, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000048/Broad provisional SOULCAP:SC000048 Broad "[""CL:4052055""]" below_top_5 63 39 63 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 14, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 14, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 14, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""CD4-"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 63, ""rank_best"": 39, ""rank_worst"": 63}]" -provisional/SOULCAP:SC000049/Broad provisional SOULCAP:SC000049 Broad "[""CL:4052055""]" below_top_5 34 2 34 [] "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000570"", ""label"": ""parafollicular cell"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 34, ""rank_best"": 2, ""rank_worst"": 34}]" -provisional/SOULCAP:SC000050/Broad provisional SOULCAP:SC000050 Broad "[""CL:4052055""]" below_top_5 70 42 70 [] "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD4+"", ""CD8-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 70, ""rank_best"": 42, ""rank_worst"": 70}]" -provisional/SOULCAP:SC000051/Broad provisional SOULCAP:SC000051 Broad "[""CL:4052055""]" below_top_5 63 34 63 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD4-"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 63, ""rank_best"": 34, ""rank_worst"": 63}]" -provisional/SOULCAP:SC000052/Broad provisional SOULCAP:SC000052 Broad "[""CL:4052055""]" below_top_5 42 9 42 [] "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD4+"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 42, ""rank_best"": 9, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000053/Broad provisional SOULCAP:SC000053 Broad "[""CL:4052055""]" below_top_5 54 30 54 [] "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD4-"", ""CD8-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 54, ""rank_best"": 30, ""rank_worst"": 54}]" -provisional/SOULCAP:SC000054/Broad provisional SOULCAP:SC000054 Broad "[""CL:4052055""]" below_top_5 34 2 34 [] "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000570"", ""label"": ""parafollicular cell"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 34, ""rank_best"": 2, ""rank_worst"": 34}]" -provisional/SOULCAP:SC000055/Broad provisional SOULCAP:SC000055 Broad "[""CL:4052055""]" below_top_5 70 42 70 [] "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD4+"", ""CD8-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 70, ""rank_best"": 42, ""rank_worst"": 70}]" -provisional/SOULCAP:SC000056/Broad provisional SOULCAP:SC000056 Broad "[""CL:4052055""]" below_top_5 63 34 63 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD4-"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 63, ""rank_best"": 34, ""rank_worst"": 63}]" -provisional/SOULCAP:SC000057/Broad provisional SOULCAP:SC000057 Broad "[""CL:4052055""]" below_top_5 42 9 42 [] "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD4+"", ""CD8+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 42, ""rank_best"": 9, ""rank_worst"": 42}]" -provisional/SOULCAP:SC000058/Broad provisional SOULCAP:SC000058 Broad "[""CL:4052055""]" below_top_5 54 30 54 [] "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD56+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:4052055"", ""label"": ""mature NK T cell, human"", ""score"": 5, ""matched"": [""CD56+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD4-"", ""CD8-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 54, ""rank_best"": 30, ""rank_worst"": 54}]" -provisional/SOULCAP:SC000059/Exact provisional SOULCAP:SC000059 Exact "[""CL:0000814""]" invalid_profile [] invalid expression in Required phenotypic markers: mixed '|' and space in a group [] [] -provisional/SOULCAP:SC000060/Exact provisional SOULCAP:SC000060 Exact "[""CL:0000789""]" target_not_in_index "[""CL:0000789""]" "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000786"", ""label"": ""plasma cell"", ""score"": 5, ""matched"": [""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000061/Exact provisional SOULCAP:SC000061 Exact "[""CL:0000798""]" target_not_in_index "[""CL:0000798""]" "[{""cl_id"": ""CL:0002467"", ""label"": ""Gr1-high myeloid suppressor cell"", ""score"": 7, ""matched"": [""CD45+"", ""CD11C:not:high (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000097"", ""label"": ""mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000484"", ""label"": ""connective tissue type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000485"", ""label"": ""mucosal type mast cell"", ""score"": 5, ""matched"": [""CD123-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000786"", ""label"": ""plasma cell"", ""score"": 5, ""matched"": [""CD20- (1 of 2 alt.)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000062/Broad provisional SOULCAP:SC000062 Broad "[""CL:0000624""]" below_top_5 9 6 36 [] "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000624"", ""label"": ""CD4-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 9, ""rank_best"": 6, ""rank_worst"": 36}]" -provisional/SOULCAP:SC000063/Broad provisional SOULCAP:SC000063 Broad "[""CL:0000625""]" hit_at_5 4 4 27 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 4, ""rank_best"": 4, ""rank_worst"": 27}]" -provisional/SOULCAP:SC000064/Broad provisional SOULCAP:SC000064 Broad "[""CL:0000789""]" target_not_in_index "[""CL:0000789""]" "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000065/Broad provisional SOULCAP:SC000065 Broad "[""CL:0000084""]" target_not_in_index "[""CL:0000084""]" "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000066/Exact provisional SOULCAP:SC000066 Exact "[""CL:0000624""]" below_top_5 9 6 36 [] "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000624"", ""label"": ""CD4-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 9, ""rank_best"": 6, ""rank_worst"": 36}]" -provisional/SOULCAP:SC000067/Exact provisional SOULCAP:SC000067 Exact "[""CL:0000625""]" hit_at_5 4 4 27 [] "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 4, ""rank_best"": 4, ""rank_worst"": 27}]" -provisional/SOULCAP:SC000068/Broad provisional SOULCAP:SC000068 Broad "[""CL:0000789""]" target_not_in_index "[""CL:0000789""]" "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000069/Broad provisional SOULCAP:SC000069 Broad "[""CL:0000789""]" target_not_in_index "[""CL:0000789""]" "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 11, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB+/TCRGD- (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000070/Broad provisional SOULCAP:SC000070 Broad "[""CL:0000798""]" target_not_in_index "[""CL:0000798""]" "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001044"", ""label"": ""effector CD4-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001046"", ""label"": ""memory CCR4-positive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001204"", ""label"": ""CD4-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002677"", ""label"": ""naive regulatory T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4+"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000071/Broad provisional SOULCAP:SC000071 Broad "[""CL:0000798""]" target_not_in_index "[""CL:0000798""]" "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001050"", ""label"": ""effector CD8-positive, alpha-beta T cell"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001203"", ""label"": ""CD8-positive, alpha-beta memory T cell, CD45RO-positive"", ""score"": 13, ""matched"": [""CD45+"", ""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000625"", ""label"": ""CD8-positive, alpha-beta T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000794"", ""label"": ""CD8-positive, alpha-beta cytotoxic T cell"", ""score"": 9, ""matched"": [""CD4-"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000072/Broad provisional SOULCAP:SC000072 Broad "[""CL:0000798""]" target_not_in_index "[""CL:0000798""]" "[{""cl_id"": ""CL:0002039"", ""label"": ""immature NK T cell stage I, mouse"", ""score"": 9, ""matched"": [""CD4+ (dim)"", ""CD8+ (dim)""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000809"", ""label"": ""double-positive, alpha-beta thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002427"", ""label"": ""resting double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002428"", ""label"": ""double-positive blast"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002429"", ""label"": ""CD69-positive double-positive thymocyte"", ""score"": 8, ""matched"": [""CD4+"", ""CD8+""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 0, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] -provisional/SOULCAP:SC000073/Exact provisional SOULCAP:SC000073 Exact "[""CL:0000803""]" hit_at_5 1 1 6 [] "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000924"", ""label"": ""CD4-negative, CD8-negative type I NK T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000928"", ""label"": ""activated CD4-negative, CD8-negative type I NK T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000929"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000930"", ""label"": ""CD4-negative, CD8-negative type I NK T cell secreting interleukin-4"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000803"", ""label"": ""CD4-negative CD8-negative gamma-delta intraepithelial T cell"", ""score"": 10, ""matched"": [""CD4-"", ""CD8-""], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""CD45+"", ""CD3+"", ""TCRAB-/TCRGD+ (no axiom on any alt.)"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 1, ""rank_best"": 1, ""rank_worst"": 6}]" -provisional/SOULCAP:SC000074/Exact provisional SOULCAP:SC000074 Exact "[""CL:0000940""]" invalid_profile "[""CL:0000940""]" invalid expression in Required phenotypic markers: mixed '|' and space in a group [] [] -provisional/SOULCAP:SC000082/Exact provisional SOULCAP:SC000082 Exact "[""CL:0000904""]" below_top_5 238 238 243 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000904"", ""label"": ""central memory CD4-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 238, ""rank_best"": 238, ""rank_worst"": 243}]" -provisional/SOULCAP:SC000085/Exact provisional SOULCAP:SC000085 Exact "[""CL:0000907""]" below_top_5 239 238 243 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000907"", ""label"": ""central memory CD8-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 239, ""rank_best"": 238, ""rank_worst"": 243}]" -provisional/SOULCAP:SC000087/Exact provisional SOULCAP:SC000087 Exact "[""CL:0000898""]" below_top_5 252 243 261 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000898"", ""label"": ""naive T cell"", ""score"": 2, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 252, ""rank_best"": 243, ""rank_worst"": 261}]" -provisional/SOULCAP:SC000089/Exact provisional SOULCAP:SC000089 Exact "[""CL:0000895""]" below_top_5 238 238 242 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000895"", ""label"": ""naive thymus-derived CD4-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 238, ""rank_best"": 238, ""rank_worst"": 242}]" -provisional/SOULCAP:SC000092/Exact provisional SOULCAP:SC000092 Exact "[""CL:0000900""]" below_top_5 253 242 258 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000900"", ""label"": ""naive thymus-derived CD8-positive, alpha-beta T cell"", ""score"": 2, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 253, ""rank_best"": 242, ""rank_worst"": 258}]" -provisional/SOULCAP:SC000096/Exact provisional SOULCAP:SC000096 Exact "[""CL:0000905""]" below_top_5 238 238 247 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 12, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000905"", ""label"": ""effector memory CD4-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 238, ""rank_best"": 238, ""rank_worst"": 247}]" -provisional/SOULCAP:SC000099/Exact provisional SOULCAP:SC000099 Exact "[""CL:0000913""]" below_top_5 239 238 247 [] "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 12, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 2, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" "[{""cl_id"": ""CL:0000913"", ""label"": ""effector memory CD8-positive, alpha-beta T cell"", ""score"": 3, ""matched"": [], ""gaps"": [""CD14-/CD33-/CD64- (no axiom on any alt.)"", ""CD19-/CD20- (no axiom on any alt.)"", ""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 3, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": [], ""rank"": 239, ""rank_best"": 238, ""rank_worst"": 247}]" -provisional/SOULCAP:SC000103/Exact provisional SOULCAP:SC000103 Exact "[""CL:4030002""]" target_not_in_index "[""CL:4030002""]" "[{""cl_id"": ""CL:0001057"", ""label"": ""myeloid dendritic cell, human"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (hi) (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002000"", ""label"": ""Kit-positive erythroid progenitor cell"", ""score"": 13, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD123-""], ""gaps"": [""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)"", ""CD16-""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0000938"", ""label"": ""CD16-negative, CD56-bright natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0001024"", ""label"": ""CD34-positive, CD38-negative hematopoietic stem cell"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}, {""cl_id"": ""CL:0002343"", ""label"": ""decidual natural killer cell, human"", ""score"": 11, ""matched"": [""CD14- (1 of 3 alt.)"", ""CD19- (1 of 2 alt.)"", ""CD16-""], ""gaps"": [""CD123-"", ""HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)"", ""CD15-/CD66B- (no axiom on any alt.)""], ""contradictions"": [], ""hint_bonus"": 1, ""disqualified"": false, ""candidate_sources"": [""marker_axioms""], ""lexical_evidence"": null, ""resolution_evidence"": []}]" [] diff --git a/reports/resolver-refinement/pre_refinement_evaluation.json b/reports/resolver-refinement/pre_refinement_evaluation.json deleted file mode 100644 index 9072702..0000000 --- a/reports/resolver-refinement/pre_refinement_evaluation.json +++ /dev/null @@ -1,35723 +0,0 @@ -Warning: truncated output (original token count: 592769) -... 1322500 bytes omitted ... - -{ - "schema_version": 1, - "generated_utc": "2026-09-10T19:46:06.128515+00:00", - "inputs": { - "data/marker_combinations.csv": "29b476e499ac402094b3dbccc410d052010a9b804ca9865e2624dda3ba9bfc44", - "mappings/soulcap_entities.tsv": "b7d312081b5279669599ead19d3d201a1003ff4978eb814302f16c9783b659a8", - "mappings/curated_mappings.tsv": "2ce1d078ed3d374b0c96d04184bb3520d37a1970415ad08584e33bc26e31434e", - "reports/cl_pro_relationships.tsv": "293edb6a7dc435caf9d85a758425be9305eb4eb00c877074fdec4593ef0d1b3c", - "benchmark": "bb1ab9905205a1ab8738b6e9da0a8db382ad3a778eae1103a1279a75335aa706", - "marker_map": "4d1982db77c57a9a9e43b1fc883c5b0b32f0d69184e081764880baacb37992b7", - "term_cache": "148b2c3c6c4afce6d35e4d003bb3fbd1c30e2d7bcb43dad4a4a927e38233518d" - }, - "benchmark_path": "C:\\Users\\s28al\\SOULCAP_CL_Mapping\\mappings\\matcher_benchmark.tsv", - "matcher": { - "version": "0.1.0", - "source_hashes": { - "cl_match.py": "1bec5e9d880cfd34574ae55dfde29d4b62c745e9649a9b5d292d5697d848649f", - "phenotype.py": "6d3e7e59b884365fa48596fe1365b8630053b70a6259bb0e8f42413a55a9514a", - "marker_syntax.py": "e40620b1d804eec3c1f05251716092abd7f5a273e11ba91ce61a3345b1872ade", - "registry.py": "a225ca650e0278378566bf7134b3d8daa33dabee0c61c3d479d8affddf7a25fd", - "evaluation.py": "ad643e2b29d58e07d3e16b9c8aca15723f160cad346c751597cf52dec9526b25", - "audit.py": "86a7f3978446fe1122eec579b5a4c41ea3adf0086b5bcb642c195104e4125d4d", - "candidate_index.py": "b8ede03e76d0df09fd8735d1d45178c77a977c6ae40a61c38478bbb4be737ddc" - } - }, - "config": { - "ks": [ - 1, - 3, - 5 - ], - "ranking": "production order, including disqualified candidates", - "ties": "primary metrics use production order; bounds report tie sensitivity", - "denominator": "all cohort cases, including unscorable profiles and absent targets", - "marker_resolution": true, - "local_lexical": true, - "lexical_limit": 20, - "lexical_min_jaccard": 0.5 - }, - "candidate_count": 3327, - "marker_resolution_issues": [ - { - "marker": "CD1D-A-GALCER", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "CD57", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "HLA-DR", - "reason": "complex_or_reagent", - "pro_ids": [ - "PR:000002015" - ] - }, - { - "marker": "IGA", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "IGD", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "IGE", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "IGG", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "IGM", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "MR1", - "reason": "complex_or_reagent", - "pro_ids": [ - "PR:Q95460" - ] - }, - { - "marker": "TCR", - "reason": "multiple_or_missing_protein", - "pro_ids": [] - }, - { - "marker": "TCRAB", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "TCRGD", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "TETRAMER", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "V", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "DELTA", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "DELTA1", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "GAMMA", - "reason": "complex_or_reagent", - "pro_ids": [] - }, - { - "marker": "CCR4", - "reason": "ambiguous_alias", - "owners": [ - "CCR4", - "CD194" - ] - }, - { - "marker": "CD194", - "reason": "ambiguous_alias", - "owners": [ - "CCR4", - "CD194" - ] - }, - { - "marker": "CCR6", - "reason": "ambiguous_alias", - "owners": [ - "CCR6", - "CD196" - ] - }, - { - "marker": "CD196", - "reason": "ambiguous_alias", - "owners": [ - "CCR6", - "CD196" - ] - }, - { - "marker": "CD183", - "reason": "ambiguous_alias", - "owners": [ - "CD183", - "CXCR3" - ] - }, - { - "marker": "CXCR3", - "reason": "ambiguous_alias", - "owners": [ - "CD183", - "CXCR3" - ] - }, - { - "marker": "CD185", - "reason": "ambiguous_alias", - "owners": [ - "CD185", - "CXCR5" - ] - }, - { - "marker": "CXCR5", - "reason": "ambiguous_alias", - "owners": [ - "CD185", - "CXCR5" - ] - } - ], - "cases": [ - { - "case_id": "provisional/SOULCAP:SC000001/Exact", - "cohort": "provisional", - "subject_id": "SOULCAP:SC000001", - "match_type": "Exact", - "targets": [ - "CL:0000623" - ], - "evidence_reference": "mappings/curated_mappings.tsv", - "uncertain": false, - "rank": 6, - "rank_best": 6, - "rank_worst": 32, - "missing_targets": [], - "candidates": [ - { - "cl_id": "CL:0002338", - "label": "CD56-positive, CD161-positive immature natural killer cell, human", - "score": 23, - "matched": [ - "CD14- (1 of 3 alt.)", - "CD34-", - "CD3-", - "CD19-", - "CD56+ (1 of 2 alt.)" - ], - "gaps": [ - "CD45+", - "CD127-", - "HLA-DR:not:positive/CD11C:not:high (no axiom on any alt.)", - "CD15-/CD66B- (no axiom on any alt.)", - "CD123-", - "CD33-/CD64- (no axiom on any alt.)" - ], - "contradictions": [], - "hint_bonus": 3, - "disqualified": false, - "candidate_sources": [ - "marker_axioms" - ], - "lexical_evidence": null, - "resolution_evidence": [ - { - "sense": "negative", - "pr": "PR:000001002", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD19", - "tokens": [ - "CD19" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001002", - "tokens": [ - "CD19" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001003", - "asserted": "True", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD34", - "tokens": [ - "CD34" - ] - }, - { - "via": "pro_id", - "pr": "PR:000001003", - "tokens": [ - "CD34" - ] - } - ] - }, - { - "sense": "negative", - "pr": "PR:000001020", - "asserted": "False", - "paths": [ - { - "via": "exact_alias", - "source_token": "CD3", - "tokens": [ - "CD3" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": "exact_alias", - "source_token": "CD3E", - "tokens": [ - "CD3E" - ] - }, - { - "via": 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"provisional/SOULCAP:SC000070/Broad", - "change": "improved", - "before_rank": null, - "after_rank": 134, - "before_status": "target_not_in_index", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000071/Broad", - "change": "improved", - "before_rank": null, - "after_rank": 127, - "before_status": "target_not_in_index", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000072/Broad", - "change": "improved", - "before_rank": null, - "after_rank": 106, - "before_status": "target_not_in_index", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000073/Exact", - "change": "unchanged", - "before_rank": 1, - "after_rank": 1, - "before_status": "hit_at_5", - "after_status": "hit_at_5" - }, - { - "case_id": "provisional/SOULCAP:SC000074/Exact", - "change": "unchanged", - "before_rank": null, - "after_rank": null, - "before_status": "invalid_profile", - "after_status": "invalid_profile" - }, - { - "case_id": "provisional/SOULCAP:SC000082/Exact", - "change": "unchanged", - "before_rank": 238, - "after_rank": 238, - "before_status": "below_top_5", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000085/Exact", - "change": "unchanged", - "before_rank": 239, - "after_rank": 239, - "before_status": "below_top_5", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000087/Exact", - "change": "unchanged", - "before_rank": 252, - "after_rank": 252, - "before_status": "below_top_5", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000089/Exact", - "change": "unchanged", - "before_rank": 238, - "after_rank": 238, - "before_status": "below_top_5", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000092/Exact", - "change": "unchanged", - "before_rank": 253, - "after_rank": 253, - "before_status": "below_top_5", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000096/Exact", - "change": "unchanged", - "before_rank": 238, - "after_rank": 238, - "before_status": "below_top_5", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000099/Exact", - "change": "unchanged", - "before_rank": 239, - "after_rank": 239, - "before_status": "below_top_5", - "after_status": "below_top_5" - }, - { - "case_id": "provisional/SOULCAP:SC000103/Exact", - "change": "improved", - "before_rank": null, - "after_rank": 240, - "before_status": "target_not_in_index", - "after_status": "below_top_5" - } - ] - } -} diff --git a/src/soulcap_cl_mapping/audit.py b/src/soulcap_cl_mapping/audit.py index 7f4b992..27224d5 100644 --- a/src/soulcap_cl_mapping/audit.py +++ b/src/soulcap_cl_mapping/audit.py @@ -694,7 +694,7 @@ def add_links(data: dict, root: Path, out: Path) -> None: if not isinstance(value, str): continue for reference in re.findall( - r"https?://[^\s;<>\"]+|(?:reports|marker_mappings|data|mappings)/[^\s;<>\"]+", + r"https?://[^\s;<>\"]+|(?:reports|marker_mappings|data|mappings|literature|archive)/[^\s;<>\"]+", value, ): parsed = urlsplit(reference) diff --git a/src/soulcap_cl_mapping/marker_resolution.py b/src/soulcap_cl_mapping/marker_resolution.py index c3ade82..7d727f4 100644 --- a/src/soulcap_cl_mapping/marker_resolution.py +++ b/src/soulcap_cl_mapping/marker_resolution.py @@ -31,12 +31,12 @@ # denotes the whole CD8 coreceptor, unlike the CD8-alpha registry entry. # Require an explicit same-token label/exact synonym and this surface relation; # do not expand aliases, infer components, or convert generic has-part to surface. -# Review and frozen-source provenance: reports/regression-followup/README.md. +# Review and frozen-source provenance: archive/2026-09_resolver_experiments/regression-followup/README.md. REVIEWED_SURFACE_ASSERTIONS = { ("CD8", "PR:000025402", "RO:0002104", "positive"): { "rule_id": "whole_cd8_surface_positive_v1", "source_ref": "http://purl.obolibrary.org/obo/PR_000025402", - "review_ref": "reports/regression-followup/README.md#scoped-correction", + "review_ref": "archive/2026-09_resolver_experiments/regression-followup/README.md#scoped-correction", "interpretation": "marker_assertion_not_molecular_equivalence", } } diff --git a/tests/test_doc_links.py b/tests/test_doc_links.py new file mode 100644 index 0000000..9c7316d --- /dev/null +++ b/tests/test_doc_links.py @@ -0,0 +1,76 @@ +"""Every relative link in the hand-written Markdown docs must resolve.""" + +import re +from pathlib import Path + +import pytest + +ROOT = Path(__file__).resolve().parents[1] + +# Hand-written docs. Generated reports are excluded: they are rewritten by +# their CLI, and archived copies are frozen snapshots. +DOC_GLOBS = [ + "*.md", + "**/README.md", + "docs/**/*.md", + "cell_type_reviews/*.md", + "literature/*.md", + "reports/candidate_cl_mappings_narrative.md", + "reports/cl_term_issues.md", + "reports/marker_string_issues.md", +] +SKIP_DIRS = {".venv", ".uv-cache", ".test-runs", ".pytest_cache", "node_modules"} +LINK = re.compile(r"\[[^\]]*\]\(([^)\s]+)(?:\s+\"[^\"]*\")?\)") +FENCE = re.compile(r"^(```|~~~).*?^\1", re.MULTILINE | re.DOTALL) +INLINE_CODE = re.compile(r"`[^`\n]*`") + + +def doc_files() -> list[Path]: + found = set() + for pattern in DOC_GLOBS: + for path in ROOT.glob(pattern): + rel = path.relative_to(ROOT) + if not SKIP_DIRS.intersection(rel.parts): + found.add(path) + return sorted(found) + + +def relative_links(text: str) -> list[str]: + text = INLINE_CODE.sub("", FENCE.sub("", text)) + links = [] + for target in LINK.findall(text): + target = target.strip("<>") + if re.match(r"^[a-z][a-z0-9+.-]*:", target, re.IGNORECASE): + continue # http:, https:, mailto:, ... + path = target.split("#", 1)[0] + if path: + links.append(path) + return links + + +def test_finds_docs() -> None: + names = {p.relative_to(ROOT).as_posix() for p in doc_files()} + assert {"README.md", "CLAUDE.md", "reports/README.md"} <= names + + +def test_relative_links_extraction() -> None: + text = ( + "[a](x.md) [b](https://e.org) [c](#anchor) [d](y.md#s) `[e](no.md)`\n" + "```\n[f](fenced.md)\n```\n" + ) + assert relative_links(text) == ["x.md", "y.md"] + + +@pytest.mark.parametrize( + "doc", doc_files(), ids=lambda p: p.relative_to(ROOT).as_posix() +) +def test_relative_links_resolve(doc: Path) -> None: + missing = [] + for link in relative_links(doc.read_text(encoding="utf-8")): + target = (doc.parent / link).resolve() + # data/ is a gitignored cache that CI never has. + if target.is_relative_to(ROOT / "data"): + continue + if not target.exists(): + missing.append(link) + assert not missing, f"Broken links in {doc.relative_to(ROOT)}: {missing}" From 7a4c52ec50856460d40910d0ba2d2e1095b6ac65 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 28 Sep 2026 12:30:57 -0400 Subject: [PATCH 02/14] chore: finish Phase 1 - remove Notes.md, list every reports/ file - Notes.md removed (content was merged into README and MARKER_SYNTAX.md in 2dce48c); drop its CLAUDE.md layout row, which the link check caught. - reports/README.md now links every file by name (matcher_evaluation and marker_resolution_audit .tsv/.json were only shorthand). - Test that reports/README.md lists every file in reports/. Co-Authored-By: Claude Opus 5.5 --- CLAUDE.md | 1 - Notes.md | 23 ----------------------- reports/README.md | 4 ++-- tests/test_doc_links.py | 9 +++++++++ 4 files changed, 11 insertions(+), 26 deletions(-) delete mode 100644 Notes.md diff --git a/CLAUDE.md b/CLAUDE.md index cb22633..acc211d 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -58,7 +58,6 @@ AST in `marker_syntax.py`, compiled/evaluated by `phenotype.py`. | [README.md](README.md) | Project overview + setup (UV, Asta token). | | `CLAUDE.md` | This file — guidance for Claude. | | [ROADMAP.md](ROADMAP.md) | Planned work / milestones and their deliverables and dependencies. | -| [Notes.md](Notes.md) | Superseded: its sheet link is now in README.md and its quick reference in MARKER_SYNTAX.md. Pending removal. | | [MARKER_SYNTAX.md](MARKER_SYNTAX.md) | **Canonical spec** of the marker expression language (human-readable guide + EBNF). Cite this for anything parsing/validating marker strings. | | [reports/](reports/README.md) | **Current outputs only.** Every file is listed in [reports/README.md](reports/README.md) with its producer and whether it is curated or generated. Curated (hand-maintained): `gaps.tsv`, `cl_term_issues.md`, `marker_string_issues.md`, `pro_marker_species_support.tsv` (issue #11, built by the `pro-marker-species-support` skill), `proposed_marker_fixes.xlsx`, `candidate_cl_mappings_narrative.md`. Generated (don't hand-edit): `candidate_cl_mappings.md`/`.sssom.tsv` (`soulcap-sssom`, from `mappings/curated_mappings.tsv`), `candidate_cl_mappings_batch.tsv`/`_agreement.tsv` (`soulcap-match --batch [--lexical]`, unreviewed draft shortlists), `audit_*` (`soulcap-audit`), `matcher_evaluation.*` (`soulcap-evaluate`), `marker_resolution_audit.*` (`soulcap-resolution-audit`), `marker_validation.md` (`soulcap-sync`/`soulcap-validate`), `cl_pro_relationships.md`/`.tsv` (`soulcap-cl-pro`, Ubergraph), `cl_lexical_cache.json` (`soulcap-cache-terms`). `reports/citation_traversal/` holds gitignored snippet caches from the `citation-traversal` skill. | | [cell_type_reviews/](cell_type_reviews/README.md) | **One review file per SOULCAP cell type** (tracked, curated — not a regenerable cache): definition, marker→protein, verbatim literature support, CL comparison, proposed verdict, uncertainty flags. Start from `_template.md` and keep the folder README's index in sync. Only reviews flagged **uncertain** go to Dr. Diehl for expert review. Scaffolded 2026-09-23, no reviews written yet; its relationship to the existing [`literature/`](literature/) Milestone 2 output is still being confirmed with Dr. Diehl — see ROADMAP.md before assuming one supersedes the other. | diff --git a/Notes.md b/Notes.md deleted file mode 100644 index 39ef7d1..0000000 --- a/Notes.md +++ /dev/null @@ -1,23 +0,0 @@ -Input data sources: - -https://docs.google.com/spreadsheets/d/1uWwczLxgbpWMmXycL8Thq5NVExzlib4A/edit?pli=1&gid=1187300939#gid=1187300939 - -Sheets: - -`Marker Combinations` is our master for SOULCAP cell type definition by negative positive cell flow cytometry markers - -`Citation Mgr` contains reference papers by major cell type. - - -Marker syntax (for the `Marker Combinations` sheet) is now specified in full in -MARKER_SYNTAX.md — both a human-readable guide and a formal EBNF grammar. - -Quick reference: - -`live/` - selection for live cell, not a marker -(x|y) = x OR y -space = AND -[ ] and ( ) = grouping (contents AND- or OR-joined); a postfix after a closing - bracket applies to the whole group, e.g. [A B]- = NOT(A AND B) -postfixes: -, + , lo, hi, int, `+/-` (=low to undetectable) -`/` = OR delimiter on postfix e.g. -/lo \ No newline at end of file diff --git a/reports/README.md b/reports/README.md index fb5def3..9bfc66b 100644 --- a/reports/README.md +++ b/reports/README.md @@ -26,8 +26,8 @@ literature evidence in [literature/](../literature/), and planning documents in | [audit_dashboard.html](audit_dashboard.html) | Offline, filterable dashboard of entities, proposals, findings, marker coverage, gaps and provenance | `uv run soulcap-audit` | Generated | | [audit_summary.md](audit_summary.md) | Text summary of the same audit | `uv run soulcap-audit` | Generated | | [audit_data.json](audit_data.json) | Data behind the dashboard | `uv run soulcap-audit` | Generated | -| [matcher_evaluation.md](matcher_evaluation.md) / `.tsv` / `.json` | How well the matcher retrieves the proposed CL targets (provisional agreement, not accuracy) | `uv run soulcap-evaluate` | Generated | -| [marker_resolution_audit.md](marker_resolution_audit.md) / `.tsv` / `.json` | Effect of the per-token resolution policies in [marker_mappings/marker_resolution.tsv](../marker_mappings/marker_resolution.tsv) on axiom links and mapping evidence | `uv run soulcap-resolution-audit` | Generated | +| [matcher_evaluation.md](matcher_evaluation.md), [matcher_evaluation.tsv](matcher_evaluation.tsv), [matcher_evaluation.json](matcher_evaluation.json) | How well the matcher retrieves the proposed CL targets (provisional agreement, not accuracy) | `uv run soulcap-evaluate` | Generated | +| [marker_resolution_audit.md](marker_resolution_audit.md), [marker_resolution_audit.tsv](marker_resolution_audit.tsv), [marker_resolution_audit.json](marker_resolution_audit.json) | Effect of the per-token resolution policies in [marker_mappings/marker_resolution.tsv](../marker_mappings/marker_resolution.tsv) on axiom links and mapping evidence | `uv run soulcap-resolution-audit` | Generated | `uv run python -m soulcap_cl_mapping.regression_triage` writes to `reports/regression-triage/` by default. No current run is committed; the diff --git a/tests/test_doc_links.py b/tests/test_doc_links.py index 9c7316d..437e243 100644 --- a/tests/test_doc_links.py +++ b/tests/test_doc_links.py @@ -74,3 +74,12 @@ def test_relative_links_resolve(doc: Path) -> None: if not target.exists(): missing.append(link) assert not missing, f"Broken links in {doc.relative_to(ROOT)}: {missing}" + + +def test_reports_readme_lists_every_report() -> None: + readme = (ROOT / "reports/README.md").read_text(encoding="utf-8") + listed = set(relative_links(readme)) + files = {p.name for p in (ROOT / "reports").iterdir() if p.is_file()} - { + "README.md" + } + assert not files - listed, f"Add to reports/README.md: {sorted(files - listed)}" From 98e1f94efb47b18f11ec63882a3446ea8a452303 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 28 Sep 2026 12:36:02 -0400 Subject: [PATCH 03/14] docs: short README, docs/ pages, folder READMEs, file-placement rules (Phase 2) Addresses Dr. Osumi-Sutherland's "Docs" to-do from the 2026-09-28 meeting. - README rewritten to 172 lines: aims, Mermaid pipeline, key files (naming the token->PRO registry and the resolution policy/audit), mapping machinery (deterministic CLIs vs agent skills vs human review vs reproducibility), all 7 skills, outputs, quick start, layout. - Detailed README sections moved verbatim into docs/setup.md, docs/pipeline.md, docs/marker_resolution.md and docs/matching_and_evaluation.md (links rebased). - New folder READMEs: docs/, archive/, literature/, marker_mappings/, src/. marker_mappings/README.md explains how marker_protein_gene.csv, marker_resolution.tsv and marker_resolution_audit.md relate, and what registry_sha256 is, with a command that recomputes it. - CLAUDE.md: "Where things go" placement rules and an updated layout table. No mapping decisions, CL IDs, quotes or citations changed. Co-Authored-By: Claude Opus 5.5 --- CLAUDE.md | 34 +- README.md | 619 ++++++++------------------------ archive/README.md | 16 + docs/README.md | 20 ++ docs/marker_resolution.md | 87 +++++ docs/matching_and_evaluation.md | 105 ++++++ docs/pipeline.md | 157 ++++++++ docs/setup.md | 65 ++++ literature/README.md | 44 +++ marker_mappings/README.md | 73 ++++ src/README.md | 33 ++ 11 files changed, 785 insertions(+), 468 deletions(-) create mode 100644 archive/README.md create mode 100644 docs/README.md create mode 100644 docs/marker_resolution.md create mode 100644 docs/matching_and_evaluation.md create mode 100644 docs/pipeline.md create mode 100644 docs/setup.md create mode 100644 literature/README.md create mode 100644 marker_mappings/README.md create mode 100644 src/README.md diff --git a/CLAUDE.md b/CLAUDE.md index acc211d..33ff20d 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -55,20 +55,21 @@ AST in `marker_syntax.py`, compiled/evaluated by `phenotype.py`. | Path | Purpose | |------|---------| -| [README.md](README.md) | Project overview + setup (UV, Asta token). | +| [README.md](README.md) | Short overview: aims, pipeline diagram, key files, mapping machinery (code vs skills vs human review), outputs, quick start. | | `CLAUDE.md` | This file — guidance for Claude. | | [ROADMAP.md](ROADMAP.md) | Planned work / milestones and their deliverables and dependencies. | | [MARKER_SYNTAX.md](MARKER_SYNTAX.md) | **Canonical spec** of the marker expression language (human-readable guide + EBNF). Cite this for anything parsing/validating marker strings. | | [reports/](reports/README.md) | **Current outputs only.** Every file is listed in [reports/README.md](reports/README.md) with its producer and whether it is curated or generated. Curated (hand-maintained): `gaps.tsv`, `cl_term_issues.md`, `marker_string_issues.md`, `pro_marker_species_support.tsv` (issue #11, built by the `pro-marker-species-support` skill), `proposed_marker_fixes.xlsx`, `candidate_cl_mappings_narrative.md`. Generated (don't hand-edit): `candidate_cl_mappings.md`/`.sssom.tsv` (`soulcap-sssom`, from `mappings/curated_mappings.tsv`), `candidate_cl_mappings_batch.tsv`/`_agreement.tsv` (`soulcap-match --batch [--lexical]`, unreviewed draft shortlists), `audit_*` (`soulcap-audit`), `matcher_evaluation.*` (`soulcap-evaluate`), `marker_resolution_audit.*` (`soulcap-resolution-audit`), `marker_validation.md` (`soulcap-sync`/`soulcap-validate`), `cl_pro_relationships.md`/`.tsv` (`soulcap-cl-pro`, Ubergraph), `cl_lexical_cache.json` (`soulcap-cache-terms`). `reports/citation_traversal/` holds gitignored snippet caches from the `citation-traversal` skill. | | [cell_type_reviews/](cell_type_reviews/README.md) | **One review file per SOULCAP cell type** (tracked, curated — not a regenerable cache): definition, marker→protein, verbatim literature support, CL comparison, proposed verdict, uncertainty flags. Start from `_template.md` and keep the folder README's index in sync. Only reviews flagged **uncertain** go to Dr. Diehl for expert review. Scaffolded 2026-09-23, no reviews written yet; its relationship to the existing [`literature/`](literature/) Milestone 2 output is still being confirmed with Dr. Diehl — see ROADMAP.md before assuming one supersedes the other. | | [mappings/](mappings/README.md) | Curated mapping decisions (`curated_mappings.tsv`), permanent local entity IDs (`soulcap_entities.tsv`), and matcher benchmark files. The decision source of truth for this repo. | -| `marker_mappings/` | Token → PRO/UniProt/gene registry (`marker_protein_gene.csv`), per-token resolution policy (`marker_resolution.tsv`), token list, and PRO→UniProt overrides. Tracked, curated. | -| [literature/](literature/) | Milestone 2 literature evidence (verbatim quotes with citations), one file per cell-type family. Moved from `reports/literature/` on 2026-09-28. | +| [marker_mappings/](marker_mappings/README.md) | Token → PRO/UniProt/gene registry (`marker_protein_gene.csv`), per-token resolution policy (`marker_resolution.tsv`), token list, and PRO→UniProt overrides. Tracked, curated. | +| [literature/](literature/README.md) | Milestone 2 literature evidence (verbatim quotes with citations), one file per cell-type family. Moved from `reports/literature/` on 2026-09-28. | +| [docs/](docs/README.md) | Detailed docs moved out of the README: `setup.md`, `pipeline.md`, `marker_resolution.md`, `matching_and_evaluation.md`. | | [docs/planning/](docs/planning/) | Planning documents: `fall_2026_sprint_backlog.md` (hand-maintained sprint breakdown of ROADMAP.md; update as items complete, not a generated report) and the Sept 21 `fall_2026_semester_plan` draft (`.md`, `.pdf`, `.html`). | -| [archive/](archive/2026-09_resolver_experiments/README.md) | Finished one-off experiments, one dated folder each with a README. Not current output; nothing regenerates it. | -| `src/soulcap_cl_mapping/` | All Python code. `sync_sheets.py` → `soulcap-sync`; `marker_syntax.py` → `soulcap-validate` (EBNF validator); `snippet_cache.py` → `soulcap-cache`; `report_validator.py` → `soulcap-validate-report`; `cl_pro.py` → `soulcap-cl-pro` (CL→PR relationships via Ubergraph SPARQL); `cl_match.py` → `soulcap-match` (marker-axiom + lexical CL candidate scoring, single-profile or `--batch`); `oak_match.py` → `soulcap-oak-match` (OAK sqlite-backed lexical/synonym CL search — downloads/caches a local CL database on first use, ~100MB); `sssom_export.py` → `soulcap-sssom` (curated mappings → SSSOM TSV, with confidence derived from CL marker-axiom assertion status); `pro_species_support.py` (scopes CL PRO markers needing species-specificity literature support — no CLI, called as a library from the `pro-marker-species-support` skill); `europepmc_search.py` → `soulcap-europepmc` (free, keyless Europe PMC search — fallback literature source when the Asta MCP server isn't reachable); `pubmed_search.py` → `soulcap-pubmed` (NCBI E-utilities search — reads `PUBMED_API_KEY` from `.env` if set for the higher rate limit, otherwise works keyless; use when a task specifically needs NCBI's own index/query syntax rather than Europe PMC's mirror of it). | +| [archive/](archive/README.md) | Finished one-off experiments, one dated folder each with a README. Not current output; nothing regenerates it. | +| [src/](src/README.md) `soulcap_cl_mapping/` | All Python code (module-by-stage table in `src/README.md`). `sync_sheets.py` → `soulcap-sync`; `marker_syntax.py` → `soulcap-validate` (EBNF validator); `snippet_cache.py` → `soulcap-cache`; `report_validator.py` → `soulcap-validate-report`; `cl_pro.py` → `soulcap-cl-pro` (CL→PR relationships via Ubergraph SPARQL); `cl_match.py` → `soulcap-match` (marker-axiom + lexical CL candidate scoring, single-profile or `--batch`); `oak_match.py` → `soulcap-oak-match` (OAK sqlite-backed lexical/synonym CL search — downloads/caches a local CL database on first use, ~100MB); `sssom_export.py` → `soulcap-sssom` (curated mappings → SSSOM TSV, with confidence derived from CL marker-axiom assertion status); `pro_species_support.py` (scopes CL PRO markers needing species-specificity literature support — no CLI, called as a library from the `pro-marker-species-support` skill); `europepmc_search.py` → `soulcap-europepmc` (free, keyless Europe PMC search — fallback literature source when the Asta MCP server isn't reachable); `pubmed_search.py` → `soulcap-pubmed` (NCBI E-utilities search — reads `PUBMED_API_KEY` from `.env` if set for the higher rate limit, otherwise works keyless; use when a task specifically needs NCBI's own index/query syntax rather than Europe PMC's mirror of it). | | `tests/` | Unit tests (mirror `src/` layout). | -| `.claude/skills/` | Project skills — see [citation-traversal](.claude/skills/citation-traversal/SKILL.md), `ontology-term-lookup`, [pro-marker-species-support](.claude/skills/pro-marker-species-support/SKILL.md), [gap-issue-filing](.claude/skills/gap-issue-filing/SKILL.md), [roadmap-status-sync](.claude/skills/roadmap-status-sync/SKILL.md), and [mapping-audit](.claude/skills/mapping-audit/SKILL.md). | +| `.claude/skills/` | Project skills — see [soulcap-cl-matching](.claude/skills/soulcap-cl-matching/SKILL.md), [citation-traversal](.claude/skills/citation-traversal/SKILL.md), `ontology-term-lookup`, [pro-marker-species-support](.claude/skills/pro-marker-species-support/SKILL.md), [gap-issue-filing](.claude/skills/gap-issue-filing/SKILL.md), [roadmap-status-sync](.claude/skills/roadmap-status-sync/SKILL.md), and [mapping-audit](.claude/skills/mapping-audit/SKILL.md). | | `.claude/hooks/` | Claude Code hooks. `validate_report_quotes.py` is a PreToolUse guard that blocks writing a citation-traversal report whose quotes aren't verbatim in the snippet cache. | | `data/` | Gitignored cache of the synced sheet (CSV + xlsx). | | `pyproject.toml` | Project metadata, deps, and the CLI entry points. | @@ -79,6 +80,27 @@ When you create a new artifact, put it in the established location and link it from here and the README so locations stay consistent. Do not scatter documents at the repo root. +### Where things go + +Follow these rules for every new or moved file. Update the relevant folder +README **in the same commit** as the change. + +| New file is… | Put it in | Also | +|---|---|---| +| A current generated output (report, export, dashboard) | `reports/` | Add a row to `reports/README.md` (a test enforces this). Never hand-edit generated files. | +| A one-off experiment, comparison run or diagnostic | `archive/_/` | Add a README saying what ran, what it showed, how to reproduce. Keep `.md`/`.tsv` summaries; leave out large JSON/HTML. Add a row to `archive/README.md`. | +| Literature evidence (quotes, review-paper notes) | `literature/` | Verbatim quotes with PMID/DOI only. No paywalled PDFs. | +| A mapping decision | `mappings/curated_mappings.tsv` (a row, not a new file) | Re-run `soulcap-sssom`. Never put decisions in Python or in `candidate_cl_mappings.md`. | +| A marker token → protein change | `marker_mappings/` | Review the token's policy row in `marker_resolution.tsv` before updating its `registry_sha256`. | +| A per-cell-type review | `cell_type_reviews/.md` | Update the index in `cell_type_reviews/README.md`. | +| Detailed documentation | `docs/` | Link it from `docs/README.md`. Keep the top-level README short. | +| A planning document | `docs/planning/` | | +| Python code / tests | `src/soulcap_cl_mapping/` / `tests/` | Add the module to `src/README.md`; CLIs go in `pyproject.toml`. | + +Never create a new top-level folder or root-level file without updating the +README's layout table and this table. `tests/test_doc_links.py` fails if a +relative link in the hand-written docs breaks. + The September 21 Fall 2026 planning draft for Dr. Diehl is `docs/planning/fall_2026_semester_plan.md`, with matching `.pdf` and `.html` versions. It summarizes recent work and proposes weekly deliverables and agent task diff --git a/README.md b/README.md index b603d82..91a64f9 100644 --- a/README.md +++ b/README.md @@ -1,477 +1,172 @@ # SOULCAP ↔ Cell Ontology Mapping -Warning - any mappings found on this repo or linked to from it are a work in progress. They are NOT official products of SOULCAP or the Cell Ontology +> **Warning:** any mappings found in this repo or linked from it are a work in +> progress. They are NOT official products of SOULCAP or the Cell Ontology. ## Aims Build mappings between [SOULCAP](https://soulcap.org/) and the -[Cell Ontology](https://github.com/obophenotype/cell-ontology), improving both -resources in the process. - -By aligning SOULCAP cell type definitions with Cell Ontology classes, this work -aims to: +[Cell Ontology](https://github.com/obophenotype/cell-ontology) (CL), improving +both resources in the process: - Give SOULCAP cell types stable, interoperable ontology identifiers. - Surface gaps and inconsistencies in both resources (missing cell types, ambiguous definitions, conflicting marker assertions) so they can be fixed upstream. -## Background - -**SOULCAP** ([soulcap.org](https://soulcap.org/)) is a resource that defines -cell types — including by their positive and negative cell-surface marker -combinations as measured by flow cytometry. Each cell type is backed by -reference literature. - -**Cell Ontology (CL)** -([github.com/obophenotype/cell-ontology](https://github.com/obophenotype/cell-ontology)) -is a community-developed OBO ontology providing a structured, cross-species -controlled vocabulary of cell types. It is widely used for annotating -single-cell datasets and is a standard reference for cell type identity across -the life sciences. +**SOULCAP** defines immune cell types by positive/negative cell-surface marker +combinations measured by flow cytometry, each backed by reference literature. +**CL** is the community OBO ontology of cell types; many CL terms carry logical +axioms linking them to Protein Ontology (PRO) marker proteins. + +**Status (2026-09-28):** 127 SOULCAP cell types have local IDs; 80 have a +proposed CL mapping (50 Exact, 30 Broad). All 80 are `needs_review`. See +[ROADMAP.md](ROADMAP.md) for milestones. + +## Pipeline + +```mermaid +flowchart TD + sheet[("Google Sheet
    Marker Combinations")] -->|soulcap-sync| data["data/*.csv
    (gitignored cache)"] + data -->|soulcap-validate| val["reports/marker_validation.md
    syntax errors for SOULCAP"] + data -->|soulcap-tokens| tokens["marker_mappings/marker_tokens.csv"] + tokens -->|soulcap-map| registry["marker_mappings/marker_protein_gene.csv
    token → PRO / UniProt / gene"] + registry --- policy["marker_mappings/marker_resolution.tsv
    allow / withhold per token"] + ubergraph[("Ubergraph
    CL + PRO")] -->|soulcap-cl-pro| clpro["reports/cl_pro_relationships.tsv
    CL marker axioms"] + data --> match + clpro --> match + policy -.->|"--marker-map (opt-in)"| match + match["soulcap-match
    marker-axiom + lexical scoring"] --> batch["reports/candidate_cl_mappings_batch.tsv
    unreviewed shortlist"] + batch -->|"agent skill + curator review"| curated["mappings/curated_mappings.tsv
    proposed decisions"] + curated -->|soulcap-sssom| sssom["reports/candidate_cl_mappings.sssom.tsv
    + .md review + provenance hashes"] + curated -->|soulcap-audit| audit["reports/audit_dashboard.html"] + curated -->|soulcap-evaluate| evalr["reports/matcher_evaluation.md"] +``` + +Stage-by-stage commands and options: [docs/pipeline.md](docs/pipeline.md). + +## Key files + +| What | Where | +|---|---| +| Source definitions | The [Google Sheet](https://docs.google.com/spreadsheets/d/1uWwczLxgbpWMmXycL8Thq5NVExzlib4A/edit), synced into `data/`. Never edit `data/`; fix the Sheet. | +| Marker expression grammar | [MARKER_SYNTAX.md](MARKER_SYNTAX.md) | +| **Token → PRO mapping** | [marker_mappings/marker_protein_gene.csv](marker_mappings/marker_protein_gene.csv): each marker token with its PRO ID, UniProt ID and gene | +| **Which tokens are withheld, and why** | [marker_mappings/marker_resolution.tsv](marker_mappings/marker_resolution.tsv) (policy per token) and [reports/marker_resolution_audit.md](reports/marker_resolution_audit.md) (effect on matching). How the three relate, and what the SHA-256 column is: [marker_mappings/README.md](marker_mappings/README.md) | +| **Proposed CL mappings (decisions)** | [mappings/curated_mappings.tsv](mappings/curated_mappings.tsv), with local IDs in [mappings/soulcap_entities.tsv](mappings/soulcap_entities.tsv) | +| Proposed CL mappings (to read) | [reports/candidate_cl_mappings.md](reports/candidate_cl_mappings.md) and the SSSOM export [reports/candidate_cl_mappings.sssom.tsv](reports/candidate_cl_mappings.sssom.tsv) | +| CL's own marker axioms | [reports/cl_pro_relationships.md](reports/cl_pro_relationships.md) | +| Gaps in CL or SOULCAP | [reports/gaps.tsv](reports/gaps.tsv), [reports/cl_term_issues.md](reports/cl_term_issues.md) | +| Literature evidence | [literature/](literature/) | +| Audit dashboard | [reports/audit_dashboard.html](reports/audit_dashboard.html) (download and open in a browser) | + +## Mapping machinery + +The mapping work mixes deterministic code, LLM agent skills and human review. +Each has a clear boundary. + +**Deterministic Python** (`src/soulcap_cl_mapping/`, run with `uv run `). +Same inputs, same outputs; covered by unit tests at ≥80%. + +| Command | Does | +|---|---| +| `soulcap-sync` | Download the Sheet into `data/` and validate marker strings | +| `soulcap-validate`, `soulcap-tokens` | Check marker strings against the grammar; extract distinct tokens | +| `soulcap-map`, `soulcap-hgnc` | Build the token → PRO / UniProt / gene registry; add HGNC symbols to CL axioms | +| `soulcap-cl-pro` | Pull CL→PRO marker axioms from Ubergraph | +| `soulcap-match` | Rank CL terms against a SOULCAP marker profile (marker axioms, plus lexical with `--lexical`) | +| `soulcap-oak-match`, `soulcap-lookup`, `soulcap-cache-terms` | Name/synonym search in CL (local OAK database, OLS4, or cached labels) | +| `soulcap-sssom` | Turn `curated_mappings.tsv` into SSSOM + a readable review, with per-mapping marker evidence | +| `soulcap-audit`, `soulcap-evaluate`, `soulcap-resolution-audit` | Dashboard, matcher retrieval metrics, effect of marker policies | +| `soulcap-europepmc`, `soulcap-pubmed`, `soulcap-cache`, `soulcap-validate-report` | Literature search and snippet caching; quote verification | + +**Agent skills** (`.claude/skills/`, run by Claude Code). These do judgement +work: choosing between candidates, reading papers, writing rationale. They call +the commands above for anything that can be computed. + +| Skill | Purpose | Inputs → outputs | Runs | +|---|---|---|---| +| [soulcap-cl-matching](.claude/skills/soulcap-cl-matching/SKILL.md) | Propose a CL term for a SOULCAP cell type, cross-checking marker and lexical matching, verifying via OLS4 | Sheet rows, CL axioms → proposed mapping with rationale | Agent + `soulcap-match`, `soulcap-lookup` | +| [citation-traversal](.claude/skills/citation-traversal/SKILL.md) | Answer a question from seed papers by following their citations two levels deep | Question + seed DOIs/PMIDs → quoted summary in `reports/citation_traversal/` (gitignored) | Agent + Asta; a hook blocks any quote not verbatim in the cache | +| [pro-marker-species-support](.claude/skills/pro-marker-species-support/SKILL.md) | Check whether a CL PRO marker is supported in human, mouse or both | CL axioms, `literature/` → [reports/pro_marker_species_support.tsv](reports/pro_marker_species_support.tsv) | Agent + `pro_species_support.py`, `soulcap-europepmc` | +| [mapping-audit](.claude/skills/mapping-audit/SKILL.md) | Re-check proposed mappings against current CL axioms and literature; catch drift | SSSOM, CL axioms, `literature/` → `reports/mapping_audit.md` (not yet run) | Agent + `soulcap-match`, `soulcap-lookup` | +| [ontology-term-lookup](.claude/skills/ontology-term-lookup/SKILL.md) | Resolve a biological term to an exact ontology label | Term + ontology → matched ID and label | Agent + OLS4 MCP | +| [gap-issue-filing](.claude/skills/gap-issue-filing/SKILL.md) | File unfiled `gaps.tsv` rows as GitHub issues, avoiding duplicates | `reports/gaps.tsv` → GitHub issues, row updated | Agent + `gh` | +| [roadmap-status-sync](.claude/skills/roadmap-status-sync/SKILL.md) | Correct stale milestone markers in ROADMAP.md from what is on disk | Repo files, issues → ROADMAP.md | Agent | + +**Human review.** Every proposal starts as `review_status = needs_review` in +`curated_mappings.tsv`. Per-cell-type evidence and verdicts are written in +[cell_type_reviews/](cell_type_reviews/README.md); only reviews that hit an +uncertainty trigger go to Dr. Diehl. A verdict takes effect only once it is +entered in the Sheet. Gap issues and CL change requests are filed only after +review. (The review folder was scaffolded 2026-09-23 with no reviews yet; how +it relates to [literature/](literature/README.md) is still being confirmed with +Dr. Diehl.) + +**Reproducibility.** +- Generated outputs carry SHA-256 hashes of their inputs: the SSSOM export has + a `.provenance.json` sidecar, and the evaluation JSON records input and + matcher-source hashes. +- Each marker policy stores a fingerprint of its registry rows, so it fails + loudly if the registry changes. +- Literature quotes must be verbatim and cited; the citation-traversal hook + enforces this. +- No numeric confidence is assigned yet, pending calibration against reviewed + examples. + +## Outputs + +Every file in [reports/](reports/README.md) is listed in its README with the +command that produces it and whether it is curated or generated. The ones most +people want: + +| Output | Producer | Regenerable | For | +|---|---|---|---| +| [candidate_cl_mappings.md](reports/candidate_cl_mappings.md) / [.sssom.tsv](reports/candidate_cl_mappings.sssom.tsv) | `soulcap-sssom` | Yes | Reviewers; CL editors | +| [audit_dashboard.html](reports/audit_dashboard.html) | `soulcap-audit` | Yes (needs `data/`) | Reviewers | +| [gaps.tsv](reports/gaps.tsv), [cl_term_issues.md](reports/cl_term_issues.md) | Hand-curated | No | CL and SOULCAP maintainers | +| [marker_validation.md](reports/marker_validation.md), [marker_string_issues.md](reports/marker_string_issues.md) | `soulcap-sync` / hand-curated | Partly | SOULCAP curators | +| [pro_marker_species_support.tsv](reports/pro_marker_species_support.tsv) | `pro-marker-species-support` skill | No | CL editors | +| [matcher_evaluation.md](reports/matcher_evaluation.md) | `soulcap-evaluate` | Yes | Developers | + +## Quick start + +Install [UV](https://docs.astral.sh/uv/), then: + +```bash +uv sync # create the environment +uv run soulcap-sync # pull the Sheet into data/ (sheet must be link-viewable) +uv run soulcap-match --batch # candidate shortlist for every cell type +uv run soulcap-sssom # regenerate the mapping review + SSSOM from curated_mappings.tsv +uv run soulcap-audit # regenerate the dashboard +uv run pytest # tests (≥80% coverage enforced) +``` + +To change a mapping decision, edit +[mappings/curated_mappings.tsv](mappings/curated_mappings.tsv) and re-run +`soulcap-sssom`. MCP servers and API keys (Asta, optional PubMed): +[docs/setup.md](docs/setup.md). + +## Repository layout + +| Folder | Contents | +|---|---| +| [mappings/](mappings/README.md) | Curated mapping decisions and permanent local entity IDs | +| [marker_mappings/](marker_mappings/README.md) | Token → PRO registry and per-token resolution policy | +| [literature/](literature/README.md) | Literature evidence (verbatim quotes with citations) | +| [cell_type_reviews/](cell_type_reviews/README.md) | One evidence-and-verdict file per SOULCAP cell type | +| [reports/](reports/README.md) | Current outputs, each listed with its producer | +| [docs/](docs/README.md) | Detailed documentation and planning documents | +| [archive/](archive/README.md) | Finished experiments, kept for the record | +| [src/](src/README.md), `tests/` | Python package and its unit tests | + +Agent guidance, including where new files go, is in [CLAUDE.md](CLAUDE.md). ## Planning -Milestones and their status live in [ROADMAP.md](ROADMAP.md). The current -semester's sprint-level breakdown (sub-tasks, acceptance criteria, and what's -blocked on someone outside the repo) is -[docs/planning/fall_2026_sprint_backlog.md](docs/planning/fall_2026_sprint_backlog.md). - -The September 21 discussion draft for Dr. Diehl expands this into a -plain-language October–December plan, recent-work summary, weekly schedule, -and agent task instructions: [PDF](docs/planning/fall_2026_semester_plan.pdf), -[editable Markdown](docs/planning/fall_2026_semester_plan.md), or -[browser version](docs/planning/fall_2026_semester_plan.html). -Its workload and review targets are proposed for approval, not confirmed commitments. - -## Setup - -### 1. Clone this repo - -### 2. Install UV and create the environment - -Install [UV](https://docs.astral.sh/uv/), then use it to create a virtual -environment with the project dependencies: - -```bash -# Install UV (macOS / Linux) -curl -LsSf https://astral.sh/uv/install.sh | sh - -# Create the virtual environment and install dependencies -uv sync -``` - -### 2. MCP servers (Claude Code) - -The MCP servers used by this project — `Asta_semanticscholar` (literature -search), `artl-mcp`, and `ols4` — are defined in the committed -[.mcp.json](.mcp.json) and enabled for the project in the committed -`.claude/settings.json`. No per-developer action is needed to enable them. - -### 3. Configure the Asta API token - -The [Asta](https://allenai.org/asta/resources/mcp) tools require a personal API -key. Request one from , then add it to -your **local, gitignored** Claude Code settings at -`.claude/settings.local.json`: - -```json -{ - "env": { - "ASTA_API_KEY": "{token}" - } -} -``` - -Replace `{token}` with your actual key. Claude Code reads this `env` block at -startup and expands `${ASTA_API_KEY}` into the `x-api-key` header in -[.mcp.json](.mcp.json). - -`.claude/settings.local.json` is gitignored and must **never** be committed — -it is the only place the secret lives. Restart Claude Code after editing it so -the key is picked up. - -### Optional: PubMed (NCBI E-utilities) - -`soulcap-pubmed` (`src/soulcap_cl_mapping/pubmed_search.py`) works keyless, -same as `soulcap-europepmc`. An NCBI API key just raises the rate limit from -3 to 10 requests/second. If you want one, generate it from your -[NCBI account settings](https://www.ncbi.nlm.nih.gov/account/settings/) under -**API Key Management**, then add it to the **local, gitignored** `.env`: - -``` -PUBMED_API_KEY={token} -``` - -Unlike `ASTA_API_KEY`, this is read directly by Python (via `python-dotenv`), -not through Claude Code's MCP `env` substitution — it isn't an MCP server key. - -## Unified audit dashboard - -Generate an offline dashboard from the local data and mapping registries: - -```bash -uv run soulcap-audit -``` - -Open [reports/audit_dashboard.html](reports/audit_dashboard.html) in a browser. -It includes searchable, filterable review tables for SOULCAP entities, proposed -CL targets, prioritized findings, marker coverage, gaps, species evidence, and -input provenance. Expand a row to inspect its evidence and source references. -No server, network calls, or additional dashboard dependencies are required. - -The command also writes [audit_summary.md](reports/audit_summary.md) and -[audit_data.json](reports/audit_data.json). Use `--root PATH` for another repository -snapshot, `--out-dir PATH` for another output directory, or `--strict` to return -exit code 1 when error findings exist (reports are still generated). - -The audit recomputes marker evidence without changing source data or mappings. -Missing inputs are reported as unavailable, not zero. Local hashes and export -evidence are checked for drift; upstream freshness is not checked. Historical -agreement reports and family-level gaps are not silently joined to entity IDs. -Mapping proposals and marker compatibility do **not** establish equivalence. - -## Matcher evaluation - -```bash -uv run soulcap-evaluate -uv run soulcap-audit -``` - -The first command writes `reports/matcher_evaluation.md`, `.json`, and `.tsv`; -the second refreshes the dashboard's evaluation view. Evaluation is offline and -uses the production matcher unchanged, including its name hints and tie order. -It measures CL target retrieval, not the correctness of an equivalence relation. - -Existing mapping proposals automatically form a **provisional agreement** cohort. -The separate [benchmark TSV](mappings/matcher_benchmark.tsv) starts empty: no -proposal is automatically certified as ground truth. Add manually reviewed cases -with columns `subject_id`, `acceptable_cl_ids` (`|`-separated alternatives), -`match_type` (`Exact`, `Broad`, `Narrow`, `Related`), `review_status` (`reviewed` -or `provisional`), and `evidence_reference` (required for reviewed cases). -One case represents a subject/relation within a cohort. An explicit provisional -case overrides that subject/relation's proposal-derived targets. Review statuses -in the proposal registry never automatically promote cases to the reviewed cohort. - -Top-1/3/5 hit rates and mean reciprocal rank include every cohort case in their -denominators, with zero credit for unscorable profiles and absent targets. Empty -cohorts report unavailable metrics. Best/worst tie bounds expose ordering -sensitivity; disqualified candidates are retained and flagged, not endorsed. -Exact/Broad/Narrow/Related results are reported separately. Profile drift requires -review before scoring; benchmark targets must be re-reviewed if definitions change. - -To compare against a saved JSON baseline without overwriting it: - -```bash -uv run soulcap-evaluate --baseline reports/matcher_evaluation.json --out-dir reports/evaluation-next -``` - -Use `--root PATH` or `--benchmark PATH` for other snapshots/case files. The JSON -records input and matcher-source hashes. Input/configuration drift marks baseline -comparisons non-equivalent; rank changes are descriptive, not significance tests. -The dashboard reads the default report location and checks local hashes; a custom -benchmark is unverified unless its contents match the default benchmark. -Missing or malformed required inputs fail before reports are written. - -## Alias/protein-aware matching and local candidate coverage - -The enhanced modes are explicit opt-ins; omitting the flags preserves the legacy -marker scorer. They do not change curated mapping decisions. Candidate scoring, -mapping evidence, SSSOM export, and the audit now share the same resolver when -`--marker-map` is explicitly enabled for each command; defaults remain legacy. - -```bash -uv run soulcap-match --batch --marker-map marker_mappings/marker_protein_gene.csv --term-cache reports/cl_lexical_cache.json --batch-out reports/candidate_cl_mappings_enhanced.tsv # archived Sept run: archive/2026-09_resolver_experiments/ -uv run soulcap-evaluate --marker-map marker_mappings/marker_protein_gene.csv --term-cache reports/cl_lexical_cache.json --baseline SAVED_BASELINE.json --out-dir reports/evaluation-next -uv run soulcap-audit -``` - -Marker resolution uses explicit registry aliases and exact PRO identity, preserving -positive/negative and expression-level distinctions. Its sibling policy file, -[marker_resolution.tsv](marker_mappings/marker_resolution.tsv), must classify -every normalized registry marker as `single_protein`, `protein_family`, `complex`, -`reagent_gate`, or `unresolved`, with an explicit `allow`/`withhold` protein policy, -rationale, source reference, and SHA-256 of the original registry rows. Runtime -resolution does not interpret free-text notes to decide protein identity. Only -single-protein policies with exactly one PRO ID can allow protein expansion. -Missing, conflicting, or stale policies fail rather than silently guessing. - -Initial policies preserve existing single-PRO representations as computational -assumptions, not biological sign-offs. CD3, CD8, CD15, CD16, and MR1 have conservative -holds because the registry's component/family/reagent representation needs review; -no source identifiers have been changed. Complex, family, and reagent policies -cannot inherit a component-protein assertion through an alias. An explicit -same-marker assertion without a component PRO remains distinguishable evidence. -Related/broad ontology synonyms do not imply identity. No gene-symbol, -cross-species, or protein-hierarchy equivalence is inferred. - -Compatible duplicate aliases with the same allowed PRO identity are merged; -conflicting owners remain unresolved. Identical semantic clauses count once across -required/ideal columns (required takes precedence), while contradictory signs, -different levels, and distinct OR constraints remain separate. Original source -spelling is retained for evidence display. After a registry edit, review and update -the affected policy and its fingerprint; do not simply refresh hashes to bypass review. -Resolution paths are recorded in candidate evidence; withheld cases are listed in -evaluation JSON under `marker_resolution_issues`. - -Isolate resolver changes from lexical coverage and inspect detailed differences. -The September 2026 run of these commands is archived in -[archive/2026-09_resolver_experiments/resolver-refinement/](archive/2026-09_resolver_experiments/resolver-refinement/README.md): - -```bash -uv run soulcap-resolution-audit -uv run soulcap-evaluate --out-dir reports/resolver-refinement/legacy -uv run soulcap-evaluate --marker-map marker_mappings/marker_protein_gene.csv --out-dir reports/resolver-refinement/enhanced --baseline reports/resolver-refinement/legacy/matcher_evaluation.json -uv run soulcap-sssom --marker-map marker_mappings/marker_protein_gene.csv --out reports/resolver-refinement/enhanced.sssom.tsv -uv run soulcap-audit --marker-map marker_mappings/marker_protein_gene.csv --out-dir reports/resolver-refinement/audit -``` - -The [resolution audit](reports/marker_resolution_audit.md) includes per-marker -gains/losses and JSON with per-mapping before/after evidence. Case-normalized -resolution covers 73 marker groups from 75 registry rows. Comparison runs use -identical source/axiom snapshots and no lexical expansion; modes intentionally -differ, so the general evaluation comparison flags them as non-equivalent runs. -Enhanced SSSOM export requires a separate output path to protect the default export. -The audit explicitly distinguishes export/audit mode differences from evidence drift. - -The local lexical cache contains active CL labels and exact synonyms from a local -OAK SQLite snapshot, with a source-database hash. To rebuild from your own snapshot: - -```bash -uv run soulcap-cache-terms --database PATH_TO_CL_DB --out reports/cl_lexical_cache.json -``` - -No network services are contacted. The cache extraction timestamp is not an -ontology release date or upstream freshness check. Lexical candidates use the source -full name (abbreviation fallback), never expected mapping targets: normalized exact -matches first, then word overlap of at least 0.5, limited to 20 candidates per row. -They are unioned with marker candidates and scored with the existing weights; -missing axioms remain unknown, not supporting evidence. Invalid/no-qualified-marker -profiles remain unscored. Single-profile CLI searches use `--subset` or `--parent`. - -The evaluation distinguishes targets absent from the global index from targets -present but not retrieved for a row. Candidate-source labels, lexical evidence, -and protein-resolution paths are exported in batch TSV and evaluation JSON. -The original baseline and the controlled legacy/alias runs are archived in -[archive/2026-09_resolver_experiments/](archive/2026-09_resolver_experiments/README.md) (summaries only; JSON recoverable from git history). -Mode/input changes make comparisons descriptive rather than equivalent-condition -regression tests. Broader coverage alone does not establish better ranking. - -## Offline regression triage - -```bash -uv run python -m soulcap_cl_mapping.regression_triage -``` - -Writes `regression_triage.md`, JSON evidence, and a per-case TSV under -`reports/regression-triage/` (not currently committed; the September 2026 run is -[archived](archive/2026-09_resolver_experiments/regression-triage/README.md)). Optional -`--root` and `--out-dir` select another snapshot or report location. This is a -diagnostic tool, not a production matcher mode: it does not change policies, -mapping decisions, scoring weights, or existing audit/evaluation reports. - -All eight combinations separate enhanced token-evidence additions, legacy -token-evidence removals, and semantic-clause deduplication. Candidates, their order, -source profiles, and scoring weights remain fixed; no lexical search is run. -Both endpoints must reproduce the production matchers. The report includes ties, -changed expected-target and competitor evidence, policy references, pairwise -factor effects, and input/code hashes. These computational findings do not validate -the provisional targets or establish biological correctness of a policy. - -## Input data - -The single source of truth is a -[Google Sheet](https://docs.google.com/spreadsheets/d/1uWwczLxgbpWMmXycL8Thq5NVExzlib4A/edit) -(ask for edit access). - -Key tabs: - -- **`Marker Combinations`** — master definition of SOULCAP cell types by - positive/negative flow-cytometry markers. The `OLS CL identifier` and - `CL Mapping Notes` columns are the targets this project populates. The marker - expression language used in this sheet is specified in - [MARKER_SYNTAX.md](MARKER_SYNTAX.md). -- **`Citation Mgr`** — reference papers per major cell type. - -**Do not hand-edit the local copies — edit the Google Sheet instead.** Pull the -latest snapshot at any time with: - -```bash -uv run soulcap-sync -``` - -This downloads the workbook to `data/soulcap_source.xlsx` and explodes each tab -into a CSV under `data/` (e.g. `data/marker_combinations.csv`). The entire -`data/` directory is a regenerable cache and is gitignored. - -Options: - -```bash -uv run soulcap-sync --no-csv # download the raw .xlsx only -uv run soulcap-sync --sheet-id # pull a different sheet -SOULCAP_SHEET_ID= uv run soulcap-sync -``` - -> The sheet must be shared as *"anyone with the link can view"* for the -> unauthenticated export to work. - -## CL ↔ PR (Cell Ontology → PRO) marker relationships - -The Cell Ontology already defines many cell types by their protein markers via -logical axioms. To use these as a SOULCAP↔CL mapping reference, pull them from -the [Ubergraph](https://ubergraph.apps.renci.org/sparql) SPARQL endpoint: - -```bash -uv run soulcap-cl-pro -``` - -This regenerates two artifacts under `reports/`: - -- **`cl_pro_relationships.md`** — CL-centric: each cell type with its PR markers - grouped by sense (positive / negative / high / low), annotated with CD - synonyms and mouse/human UniProt IDs, flagging inferred-only edges. -- **`cl_pro_relationships.tsv`** — one row per (cell, relation, PR) for diffing - across CL/PRO releases. - -```bash -uv run soulcap-cl-pro --reports-dir other/ # write elsewhere -uv run soulcap-cl-pro --endpoint # use a different SPARQL endpoint -``` - -## Candidate CL matching (`soulcap-match`) - -Validation, token extraction, and scoring share one phenotype AST. Boolean -negation and expression levels are preserved. Malformed profiles are flagged -without producing marker candidates; missing axioms remain unknown. Batch -outputs include stable `subject_id` and specimen context so duplicate -abbreviations cannot be merged accidentally. Token regeneration also refuses -invalid source expressions. See [MARKER_SYNTAX.md](MARKER_SYNTAX.md#4-implementation-semantics). - -The committed agreement TSV predates this parser/identity migration. Regenerate -it with `soulcap-match --batch --lexical` before comparing it with current -batch results; cached old lexical results cannot safely distinguish all -duplicated source rows. - -Ranks CL terms against a SOULCAP marker profile, scored from -`cl_pro_relationships.tsv`. Single-profile mode (paste the four marker columns -for one cell type): - -```bash -uv run soulcap-match --req-excl "CD14- CD3- CD19-" --req-pheno "CD45+ CD56+/hi" --parent "NK cell" -``` - -Batch mode scores every row of `data/marker_combinations.csv` in one pass: - -```bash -uv run soulcap-match --batch # -> reports/candidate_cl_mappings_batch.tsv -uv run soulcap-match --batch --lexical # + name-based OLS4 CL search and an - # agreement report (reports/candidate_cl_mappings_agreement.tsv) -``` - -Marker-axiom scoring can only rank CL terms that already have a PR axiom in -`cl_pro_relationships.tsv` — many CL terms (including some "obvious" parent -classes) have none and are invisible to it. `--lexical` adds an independent -name-based candidate per row; rows where both approaches agree are a much -stronger signal than either alone. **Treat batch output as an unreviewed draft -shortlist** — check the `contradictions`/`marker_conflict` columns before -trusting a rank-1 pick, since shared exclusion markers can inflate scores for -biologically wrong candidates. - -## OAK lexical/synonym matching (`soulcap-oak-match`) - -A second, independent lexical matcher using [OAK](https://incatools.github.io/ontology-access-kit/) -(Ontology Access Kit) instead of the OLS4 REST API: - -```bash -uv run soulcap-oak-match "Natural Killer Cell" -uv run soulcap-oak-match "NK cell" --top 5 -``` - -Uses OAK's `sqlite:obo:cl` adapter — a search-optimised local database that -ranks exact label/synonym matches first by construction (OLS4's free-text -relevance ranking, by contrast, can bury an exact match behind dozens of -more-specific subtype variants). Downloads and caches a local CL database -(~100MB) on first use; instant afterwards. - -## SSSOM mapping export (`soulcap-sssom`) - -The decision source is [mappings/curated_mappings.tsv](mappings/curated_mappings.tsv). -The [entity registry](mappings/soulcap_entities.tsv) supplies permanent local -SOULCAP IDs; [registry documentation](mappings/README.md) explains identity -resolution, migration aliases, review status, and evidence fields. - -```bash -uv run soulcap-sssom -``` - -This generates `reports/candidate_cl_mappings.sssom.tsv`, the readable -`reports/candidate_cl_mappings.md`, and an input-hash provenance sidecar. -The original detailed rationale, including sheet-confirmation notes, is -preserved in [the narrative archive](reports/candidate_cl_mappings_narrative.md). - -Evidence is evaluated against each source phenotype: required-marker matches, -contradictions, unknown clauses, ideal-marker conflicts, and direct versus -inferred support. Current sheet confirmation, lexical evidence, and literature -evidence remain separate. Missing or malformed profiles are explicitly flagged. -Numeric confidence is omitted pending calibration, and all mappings remain -proposals requiring review. Marker compatibility alone does not prove that two -cell-type definitions are equivalent. - -Use `--source`, `--mappings`, `--tsv`, `--out`, and `--review-out` to -select inputs and output locations. Existing abbreviation-based subject IDs -are retained in the registry's `legacy_subject_id` column. - -## Evidence-reviewed regression follow-up - -The [steps 3–6 follow-up](archive/2026-09_resolver_experiments/regression-followup/README.md) reviews the -three lost top-five targets, retains a narrowly scoped whole-CD8 surface -assertion in opt-in policy mode, and records controlled before/after results. -Top-five provisional agreement remains 16/80; this is not a validated ranking -improvement. Two proposed mapping relations lack sufficient support. - -[Resolver constraint examples](mappings/marker_assertion_benchmark.json) run -as regression tests. A [five-entity prospective reserve](mappings/benchmark_reserve.json) -is kept separate from development proposals and identical profiles. It still -needs independent annotation; no gold-standard mappings or held-out accuracy -are claimed. The report explains the remaining curator decisions. - -## ROBOT ontology QC - -`.github/workflows/robot-qc.yml` runs on every PR and audits upstream CL — -downloads CL's `cl-base.owl` (import-free release artifact) and runs -`robot report` + `robot reason` (ELK) on it standalone, independent of -anything in this repo. Catches pre-existing CL bugs (e.g. duplicate -equivalence/subclass axioms) worth reporting upstream. It never touches our -own candidate mappings — those stay as SSSOM, a proposal for human review, -not something this repo should unilaterally convert into OWL axioms and merge -into CL as if already accepted. - -## Cell-type reviews - -[`cell_type_reviews/`](cell_type_reviews/README.md) holds one review file per -SOULCAP cell type. Each file gathers the marker definition, marker → protein/gene -mappings, verbatim literature support, a comparison against Cell Ontology terms -and their marker axioms, and a proposed CL mapping. Reviews that meet an -uncertainty trigger (weak literature, a conflict with CL axioms, no exact CL term, -etc.) are sent for expert review; confident mappings go straight into the Google -Sheet. See the folder README for the workflow, statuses, and template. Scaffolded -2026-09-23 — no reviews written yet, and how it relates to the existing -[`literature/`](literature/) Milestone 2 reports is still being confirmed with Dr. Diehl -(see [ROADMAP.md](ROADMAP.md)). - -## Skills & literature workflows - -This repo ships Claude Code skills under `.claude/skills/`: - -- **`citation-traversal`** — answer a specific research question from a set of - seed papers via a two-round ASTA (Semantic Scholar) citation traversal: - `snippet_search` the seeds, follow the inline references that support the - answering sentences, `snippet_search` those cited papers, cache every snippet, - then synthesise a referenced summary. Every quote in the summary must be - verbatim from a cached snippet — a PreToolUse hook - (`.claude/hooks/validate_report_quotes.py`) blocks the report otherwise. Caches - and reports land under `reports/citation_traversal//` (gitignored). - Supporting CLIs: `soulcap-cache` (persist snippet results) and - `soulcap-validate-report` (manual quote check). See the - [skill](.claude/skills/citation-traversal/SKILL.md). -- **`ontology-term-lookup`** — resolve biological terms to ontology labels via OLS4. +- Milestones and status: [ROADMAP.md](ROADMAP.md) +- Fall 2026 sprint backlog: [docs/planning/fall_2026_sprint_backlog.md](docs/planning/fall_2026_sprint_backlog.md) +- Sept 21 semester plan draft for Dr. Diehl (proposed, not confirmed): + [Markdown](docs/planning/fall_2026_semester_plan.md), + [PDF](docs/planning/fall_2026_semester_plan.pdf), + [HTML](docs/planning/fall_2026_semester_plan.html) diff --git a/archive/README.md b/archive/README.md new file mode 100644 index 0000000..4b2b1fd --- /dev/null +++ b/archive/README.md @@ -0,0 +1,16 @@ +# archive/ + +Finished one-off experiments, kept for the record. Nothing here is a current +output, and no command regenerates it. Current results live in +[reports/](../reports/README.md). + +| Folder | What it was | +|---|---| +| [2026-09_resolver_experiments/](2026-09_resolver_experiments/README.md) | Comparisons of the legacy marker matcher with the stricter token-to-PRO resolver, and the regression investigation that followed (Sept 10–18, 2026) | + +## Adding an experiment + +Use `archive/_/` with a README that says what was run, what it +showed, and how to reproduce it. Keep human-readable summaries (`.md`, `.tsv`); +leave large machine-readable JSON/HTML out unless something depends on it, and +say how to recover it from git history. diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..f40e159 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,20 @@ +# docs/ + +Detailed documentation. The [README](../README.md) is the short overview; these +pages hold the full detail. + +| Page | Covers | +|---|---| +| [setup.md](setup.md) | Environment, MCP servers, Asta and PubMed API keys | +| [pipeline.md](pipeline.md) | Each pipeline stage and its command: sheet sync, CL→PRO axioms, candidate matching, OAK lexical search, SSSOM export, ROBOT QC | +| [marker_resolution.md](marker_resolution.md) | Token → PRO resolution rules, policies, lexical cache | +| [matching_and_evaluation.md](matching_and_evaluation.md) | Audit dashboard, matcher evaluation, regression triage and follow-up | +| [planning/](planning/) | Sprint backlog and semester plan (hand-maintained) | + +Related specs that live at the top level: [MARKER_SYNTAX.md](../MARKER_SYNTAX.md) +(marker expression grammar) and [ROADMAP.md](../ROADMAP.md) (milestones). +File-level docs live next to the files: [mappings/](../mappings/README.md), +[marker_mappings/](../marker_mappings/README.md), [reports/](../reports/README.md). + +Documentation is hand-written. Update the relevant page in the same commit as +the change it describes. diff --git a/docs/marker_resolution.md b/docs/marker_resolution.md new file mode 100644 index 0000000..cd34881 --- /dev/null +++ b/docs/marker_resolution.md @@ -0,0 +1,87 @@ +# Marker resolution (token → PRO) + +How marker tokens from the sheet are resolved to Protein Ontology (PRO) terms, and when that resolution is withheld. The files themselves are described in [marker_mappings/README.md](../marker_mappings/README.md). + +## Alias/protein-aware matching and local candidate coverage + +The enhanced modes are explicit opt-ins; omitting the flags preserves the legacy +marker scorer. They do not change curated mapping decisions. Candidate scoring, +mapping evidence, SSSOM export, and the audit now share the same resolver when +`--marker-map` is explicitly enabled for each command; defaults remain legacy. + +```bash +uv run soulcap-match --batch --marker-map marker_mappings/marker_protein_gene.csv --term-cache reports/cl_lexical_cache.json --batch-out reports/candidate_cl_mappings_enhanced.tsv # archived Sept run: archive/2026-09_resolver_experiments/ +uv run soulcap-evaluate --marker-map marker_mappings/marker_protein_gene.csv --term-cache reports/cl_lexical_cache.json --baseline SAVED_BASELINE.json --out-dir reports/evaluation-next +uv run soulcap-audit +``` + +Marker resolution uses explicit registry aliases and exact PRO identity, preserving +positive/negative and expression-level distinctions. Its sibling policy file, +[marker_resolution.tsv](../marker_mappings/marker_resolution.tsv), must classify +every normalized registry marker as `single_protein`, `protein_family`, `complex`, +`reagent_gate`, or `unresolved`, with an explicit `allow`/`withhold` protein policy, +rationale, source reference, and SHA-256 of the original registry rows. Runtime +resolution does not interpret free-text notes to decide protein identity. Only +single-protein policies with exactly one PRO ID can allow protein expansion. +Missing, conflicting, or stale policies fail rather than silently guessing. + +Initial policies preserve existing single-PRO representations as computational +assumptions, not biological sign-offs. CD3, CD8, CD15, CD16, and MR1 have conservative +holds because the registry's component/family/reagent representation needs review; +no source identifiers have been changed. Complex, family, and reagent policies +cannot inherit a component-protein assertion through an alias. An explicit +same-marker assertion without a component PRO remains distinguishable evidence. +Related/broad ontology synonyms do not imply identity. No gene-symbol, +cross-species, or protein-hierarchy equivalence is inferred. + +Compatible duplicate aliases with the same allowed PRO identity are merged; +conflicting owners remain unresolved. Identical semantic clauses count once across +required/ideal columns (required takes precedence), while contradictory signs, +different levels, and distinct OR constraints remain separate. Original source +spelling is retained for evidence display. After a registry edit, review and update +the affected policy and its fingerprint; do not simply refresh hashes to bypass review. +Resolution paths are recorded in candidate evidence; withheld cases are listed in +evaluation JSON under `marker_resolution_issues`. + +Isolate resolver changes from lexical coverage and inspect detailed differences. +The September 2026 run of these commands is archived in +[archive/2026-09_resolver_experiments/resolver-refinement/](../archive/2026-09_resolver_experiments/resolver-refinement/README.md): + +```bash +uv run soulcap-resolution-audit +uv run soulcap-evaluate --out-dir reports/resolver-refinement/legacy +uv run soulcap-evaluate --marker-map marker_mappings/marker_protein_gene.csv --out-dir reports/resolver-refinement/enhanced --baseline reports/resolver-refinement/legacy/matcher_evaluation.json +uv run soulcap-sssom --marker-map marker_mappings/marker_protein_gene.csv --out reports/resolver-refinement/enhanced.sssom.tsv +uv run soulcap-audit --marker-map marker_mappings/marker_protein_gene.csv --out-dir reports/resolver-refinement/audit +``` + +The [resolution audit](../reports/marker_resolution_audit.md) includes per-marker +gains/losses and JSON with per-mapping before/after evidence. Case-normalized +resolution covers 73 marker groups from 75 registry rows. Comparison runs use +identical source/axiom snapshots and no lexical expansion; modes intentionally +differ, so the general evaluation comparison flags them as non-equivalent runs. +Enhanced SSSOM export requires a separate output path to protect the default export. +The audit explicitly distinguishes export/audit mode differences from evidence drift. + +The local lexical cache contains active CL labels and exact synonyms from a local +OAK SQLite snapshot, with a source-database hash. To rebuild from your own snapshot: + +```bash +uv run soulcap-cache-terms --database PATH_TO_CL_DB --out reports/cl_lexical_cache.json +``` + +No network services are contacted. The cache extraction timestamp is not an +ontology release date or upstream freshness check. Lexical candidates use the source +full name (abbreviation fallback), never expected mapping targets: normalized exact +matches first, then word overlap of at least 0.5, limited to 20 candidates per row. +They are unioned with marker candidates and scored with the existing weights; +missing axioms remain unknown, not supporting evidence. Invalid/no-qualified-marker +profiles remain unscored. Single-profile CLI searches use `--subset` or `--parent`. + +The evaluation distinguishes targets absent from the global index from targets +present but not retrieved for a row. Candidate-source labels, lexical evidence, +and protein-resolution paths are exported in batch TSV and evaluation JSON. +The original baseline and the controlled legacy/alias runs are archived in +[archive/2026-09_resolver_experiments/](../archive/2026-09_resolver_experiments/README.md) (summaries only; JSON recoverable from git history). +Mode/input changes make comparisons descriptive rather than equivalent-condition +regression tests. Broader coverage alone does not establish better ranking. diff --git a/docs/matching_and_evaluation.md b/docs/matching_and_evaluation.md new file mode 100644 index 0000000..b0c33ef --- /dev/null +++ b/docs/matching_and_evaluation.md @@ -0,0 +1,105 @@ +# Audit, evaluation and regression tools + +Tools for checking the proposed mappings and measuring the matcher. None of them change mapping decisions. Every metric here measures agreement with *provisional* mappings, not biological accuracy. + +## Unified audit dashboard + +Generate an offline dashboard from the local data and mapping registries: + +```bash +uv run soulcap-audit +``` + +Open [reports/audit_dashboard.html](../reports/audit_dashboard.html) in a browser. +It includes searchable, filterable review tables for SOULCAP entities, proposed +CL targets, prioritized findings, marker coverage, gaps, species evidence, and +input provenance. Expand a row to inspect its evidence and source references. +No server, network calls, or additional dashboard dependencies are required. + +The command also writes [audit_summary.md](../reports/audit_summary.md) and +[audit_data.json](../reports/audit_data.json). Use `--root PATH` for another repository +snapshot, `--out-dir PATH` for another output directory, or `--strict` to return +exit code 1 when error findings exist (reports are still generated). + +The audit recomputes marker evidence without changing source data or mappings. +Missing inputs are reported as unavailable, not zero. Local hashes and export +evidence are checked for drift; upstream freshness is not checked. Historical +agreement reports and family-level gaps are not silently joined to entity IDs. +Mapping proposals and marker compatibility do **not** establish equivalence. + +## Matcher evaluation + +```bash +uv run soulcap-evaluate +uv run soulcap-audit +``` + +The first command writes `reports/matcher_evaluation.md`, `.json`, and `.tsv`; +the second refreshes the dashboard's evaluation view. Evaluation is offline and +uses the production matcher unchanged, including its name hints and tie order. +It measures CL target retrieval, not the correctness of an equivalence relation. + +Existing mapping proposals automatically form a **provisional agreement** cohort. +The separate [benchmark TSV](../mappings/matcher_benchmark.tsv) starts empty: no +proposal is automatically certified as ground truth. Add manually reviewed cases +with columns `subject_id`, `acceptable_cl_ids` (`|`-separated alternatives), +`match_type` (`Exact`, `Broad`, `Narrow`, `Related`), `review_status` (`reviewed` +or `provisional`), and `evidence_reference` (required for reviewed cases). +One case represents a subject/relation within a cohort. An explicit provisional +case overrides that subject/relation's proposal-derived targets. Review statuses +in the proposal registry never automatically promote cases to the reviewed cohort. + +Top-1/3/5 hit rates and mean reciprocal rank include every cohort case in their +denominators, with zero credit for unscorable profiles and absent targets. Empty +cohorts report unavailable metrics. Best/worst tie bounds expose ordering +sensitivity; disqualified candidates are retained and flagged, not endorsed. +Exact/Broad/Narrow/Related results are reported separately. Profile drift requires +review before scoring; benchmark targets must be re-reviewed if definitions change. + +To compare against a saved JSON baseline without overwriting it: + +```bash +uv run soulcap-evaluate --baseline reports/matcher_evaluation.json --out-dir reports/evaluation-next +``` + +Use `--root PATH` or `--benchmark PATH` for other snapshots/case files. The JSON +records input and matcher-source hashes. Input/configuration drift marks baseline +comparisons non-equivalent; rank changes are descriptive, not significance tests. +The dashboard reads the default report location and checks local hashes; a custom +benchmark is unverified unless its contents match the default benchmark. +Missing or malformed required inputs fail before reports are written. + +## Offline regression triage + +```bash +uv run python -m soulcap_cl_mapping.regression_triage +``` + +Writes `regression_triage.md`, JSON evidence, and a per-case TSV under +`reports/regression-triage/` (not currently committed; the September 2026 run is +[archived](../archive/2026-09_resolver_experiments/regression-triage/README.md)). Optional +`--root` and `--out-dir` select another snapshot or report location. This is a +diagnostic tool, not a production matcher mode: it does not change policies, +mapping decisions, scoring weights, or existing audit/evaluation reports. + +All eight combinations separate enhanced token-evidence additions, legacy +token-evidence removals, and semantic-clause deduplication. Candidates, their order, +source profiles, and scoring weights remain fixed; no lexical search is run. +Both endpoints must reproduce the production matchers. The report includes ties, +changed expected-target and competitor evidence, policy references, pairwise +factor effects, and input/code hashes. These computational findings do not validate +the provisional targets or establish biological correctness of a policy. + +## Evidence-reviewed regression follow-up + +The [steps 3–6 follow-up](../archive/2026-09_resolver_experiments/regression-followup/README.md) reviews the +three lost top-five targets, retains a narrowly scoped whole-CD8 surface +assertion in opt-in policy mode, and records controlled before/after results. +Top-five provisional agreement remains 16/80; this is not a validated ranking +improvement. Two proposed mapping relations lack sufficient support. + +[Resolver constraint examples](../mappings/marker_assertion_benchmark.json) run +as regression tests. A [five-entity prospective reserve](../mappings/benchmark_reserve.json) +is kept separate from development proposals and identical profiles. It still +needs independent annotation; no gold-standard mappings or held-out accuracy +are claimed. The report explains the remaining curator decisions. diff --git a/docs/pipeline.md b/docs/pipeline.md new file mode 100644 index 0000000..0e6132e --- /dev/null +++ b/docs/pipeline.md @@ -0,0 +1,157 @@ +# Pipeline and commands + +How SOULCAP marker definitions become proposed CL mappings, one stage at a time. See the [README](../README.md#pipeline) for the diagram, [marker_resolution.md](marker_resolution.md) for the token-to-PRO step, and [matching_and_evaluation.md](matching_and_evaluation.md) for the audit and evaluation tools. + +## Input data + +The single source of truth is a +[Google Sheet](https://docs.google.com/spreadsheets/d/1uWwczLxgbpWMmXycL8Thq5NVExzlib4A/edit) +(ask for edit access). + +Key tabs: + +- **`Marker Combinations`** — master definition of SOULCAP cell types by + positive/negative flow-cytometry markers. The `OLS CL identifier` and + `CL Mapping Notes` columns are the targets this project populates. The marker + expression language used in this sheet is specified in + [MARKER_SYNTAX.md](../MARKER_SYNTAX.md). +- **`Citation Mgr`** — reference papers per major cell type. + +**Do not hand-edit the local copies — edit the Google Sheet instead.** Pull the +latest snapshot at any time with: + +```bash +uv run soulcap-sync +``` + +This downloads the workbook to `data/soulcap_source.xlsx` and explodes each tab +into a CSV under `data/` (e.g. `data/marker_combinations.csv`). The entire +`data/` directory is a regenerable cache and is gitignored. + +Options: + +```bash +uv run soulcap-sync --no-csv # download the raw .xlsx only +uv run soulcap-sync --sheet-id # pull a different sheet +SOULCAP_SHEET_ID= uv run soulcap-sync +``` + +> The sheet must be shared as *"anyone with the link can view"* for the +> unauthenticated export to work. + +## CL ↔ PR (Cell Ontology → PRO) marker relationships + +The Cell Ontology already defines many cell types by their protein markers via +logical axioms. To use these as a SOULCAP↔CL mapping reference, pull them from +the [Ubergraph](https://ubergraph.apps.renci.org/sparql) SPARQL endpoint: + +```bash +uv run soulcap-cl-pro +``` + +This regenerates two artifacts under `reports/`: + +- **`cl_pro_relationships.md`** — CL-centric: each cell type with its PR markers + grouped by sense (positive / negative / high / low), annotated with CD + synonyms and mouse/human UniProt IDs, flagging inferred-only edges. +- **`cl_pro_relationships.tsv`** — one row per (cell, relation, PR) for diffing + across CL/PRO releases. + +```bash +uv run soulcap-cl-pro --reports-dir other/ # write elsewhere +uv run soulcap-cl-pro --endpoint # use a different SPARQL endpoint +``` + +## Candidate CL matching (`soulcap-match`) + +Validation, token extraction, and scoring share one phenotype AST. Boolean +negation and expression levels are preserved. Malformed profiles are flagged +without producing marker candidates; missing axioms remain unknown. Batch +outputs include stable `subject_id` and specimen context so duplicate +abbreviations cannot be merged accidentally. Token regeneration also refuses +invalid source expressions. See [MARKER_SYNTAX.md](../MARKER_SYNTAX.md#4-implementation-semantics). + +The committed agreement TSV predates this parser/identity migration. Regenerate +it with `soulcap-match --batch --lexical` before comparing it with current +batch results; cached old lexical results cannot safely distinguish all +duplicated source rows. + +Ranks CL terms against a SOULCAP marker profile, scored from +`cl_pro_relationships.tsv`. Single-profile mode (paste the four marker columns +for one cell type): + +```bash +uv run soulcap-match --req-excl "CD14- CD3- CD19-" --req-pheno "CD45+ CD56+/hi" --parent "NK cell" +``` + +Batch mode scores every row of `data/marker_combinations.csv` in one pass: + +```bash +uv run soulcap-match --batch # -> reports/candidate_cl_mappings_batch.tsv +uv run soulcap-match --batch --lexical # + name-based OLS4 CL search and an + # agreement report (reports/candidate_cl_mappings_agreement.tsv) +``` + +Marker-axiom scoring can only rank CL terms that already have a PR axiom in +`cl_pro_relationships.tsv` — many CL terms (including some "obvious" parent +classes) have none and are invisible to it. `--lexical` adds an independent +name-based candidate per row; rows where both approaches agree are a much +stronger signal than either alone. **Treat batch output as an unreviewed draft +shortlist** — check the `contradictions`/`marker_conflict` columns before +trusting a rank-1 pick, since shared exclusion markers can inflate scores for +biologically wrong candidates. + +## OAK lexical/synonym matching (`soulcap-oak-match`) + +A second, independent lexical matcher using [OAK](https://incatools.github.io/ontology-access-kit/) +(Ontology Access Kit) instead of the OLS4 REST API: + +```bash +uv run soulcap-oak-match "Natural Killer Cell" +uv run soulcap-oak-match "NK cell" --top 5 +``` + +Uses OAK's `sqlite:obo:cl` adapter — a search-optimised local database that +ranks exact label/synonym matches first by construction (OLS4's free-text +relevance ranking, by contrast, can bury an exact match behind dozens of +more-specific subtype variants). Downloads and caches a local CL database +(~100MB) on first use; instant afterwards. + +## SSSOM mapping export (`soulcap-sssom`) + +The decision source is [mappings/curated_mappings.tsv](../mappings/curated_mappings.tsv). +The [entity registry](../mappings/soulcap_entities.tsv) supplies permanent local +SOULCAP IDs; [registry documentation](../mappings/README.md) explains identity +resolution, migration aliases, review status, and evidence fields. + +```bash +uv run soulcap-sssom +``` + +This generates `reports/candidate_cl_mappings.sssom.tsv`, the readable +`reports/candidate_cl_mappings.md`, and an input-hash provenance sidecar. +The original detailed rationale, including sheet-confirmation notes, is +preserved in [the narrative archive](../reports/candidate_cl_mappings_narrative.md). + +Evidence is evaluated against each source phenotype: required-marker matches, +contradictions, unknown clauses, ideal-marker conflicts, and direct versus +inferred support. Current sheet confirmation, lexical evidence, and literature +evidence remain separate. Missing or malformed profiles are explicitly flagged. +Numeric confidence is omitted pending calibration, and all mappings remain +proposals requiring review. Marker compatibility alone does not prove that two +cell-type definitions are equivalent. + +Use `--source`, `--mappings`, `--tsv`, `--out`, and `--review-out` to +select inputs and output locations. Existing abbreviation-based subject IDs +are retained in the registry's `legacy_subject_id` column. + +## ROBOT ontology QC + +`.github/workflows/robot-qc.yml` runs on every PR and audits upstream CL — +downloads CL's `cl-base.owl` (import-free release artifact) and runs +`robot report` + `robot reason` (ELK) on it standalone, independent of +anything in this repo. Catches pre-existing CL bugs (e.g. duplicate +equivalence/subclass axioms) worth reporting upstream. It never touches our +own candidate mappings — those stay as SSSOM, a proposal for human review, +not something this repo should unilaterally convert into OWL axioms and merge +into CL as if already accepted. diff --git a/docs/setup.md b/docs/setup.md new file mode 100644 index 0000000..b70689b --- /dev/null +++ b/docs/setup.md @@ -0,0 +1,65 @@ +# Setup + +Full setup for this repository. The [README](../README.md#quick-start) has the short version. + +## Setup + +### 1. Clone this repo + +### 2. Install UV and create the environment + +Install [UV](https://docs.astral.sh/uv/), then use it to create a virtual +environment with the project dependencies: + +```bash +# Install UV (macOS / Linux) +curl -LsSf https://astral.sh/uv/install.sh | sh + +# Create the virtual environment and install dependencies +uv sync +``` + +### 2. MCP servers (Claude Code) + +The MCP servers used by this project — `Asta_semanticscholar` (literature +search), `artl-mcp`, and `ols4` — are defined in the committed +[.mcp.json](../.mcp.json) and enabled for the project in the committed +`.claude/settings.json`. No per-developer action is needed to enable them. + +### 3. Configure the Asta API token + +The [Asta](https://allenai.org/asta/resources/mcp) tools require a personal API +key. Request one from , then add it to +your **local, gitignored** Claude Code settings at +`.claude/settings.local.json`: + +```json +{ + "env": { + "ASTA_API_KEY": "{token}" + } +} +``` + +Replace `{token}` with your actual key. Claude Code reads this `env` block at +startup and expands `${ASTA_API_KEY}` into the `x-api-key` header in +[.mcp.json](../.mcp.json). + +`.claude/settings.local.json` is gitignored and must **never** be committed — +it is the only place the secret lives. Restart Claude Code after editing it so +the key is picked up. + +### Optional: PubMed (NCBI E-utilities) + +`soulcap-pubmed` (`src/soulcap_cl_mapping/pubmed_search.py`) works keyless, +same as `soulcap-europepmc`. An NCBI API key just raises the rate limit from +3 to 10 requests/second. If you want one, generate it from your +[NCBI account settings](https://www.ncbi.nlm.nih.gov/account/settings/) under +**API Key Management**, then add it to the **local, gitignored** `.env`: + +``` +PUBMED_API_KEY={token} +``` + +Unlike `ASTA_API_KEY`, this is read directly by Python (via `python-dotenv`), +not through Claude Code's MCP `env` substitution — it isn't an MCP server key. diff --git a/literature/README.md b/literature/README.md new file mode 100644 index 0000000..733887d --- /dev/null +++ b/literature/README.md @@ -0,0 +1,44 @@ +# literature/ + +Literature evidence that SOULCAP's markers define the cell types they claim to +(Milestone 2). Every quote is copied verbatim from its source and carries a +PMID or DOI. Moved here from `reports/literature/` on 2026-09-28. + +## Current files + +One narrative file per cell-type family, built mostly from the SOULCAP cell +sorting papers listed in the Sheet's `Citation Mgr` tab and the papers they cite. + +| File | Covers | +|---|---| +| [b_cell_markers.md](b_cell_markers.md) | B cells | +| [dc_markers.md](dc_markers.md) | Dendritic cells | +| [gdt_mait_markers.md](gdt_mait_markers.md) | γδ T cells and MAIT cells | +| [ilc_markers.md](ilc_markers.md) | Innate lymphoid cells | +| [inkt_markers.md](inkt_markers.md) | iNKT cells | +| [nk_cell_markers.md](nk_cell_markers.md) | NK cells | +| [t_cell_markers.md](t_cell_markers.md) | T cells and T helper subsets | + +Not yet covered: monocyte, neutrophil, basophil, mast cell, granulocyte, MDSC +(see [ROADMAP.md](../ROADMAP.md) Milestone 2). + +**Caveat:** the ILC and T cell files say their quotes were extracted with +WebFetch, which uses an AI model to copy page text. They have not yet been +checked against the primary PDFs. + +## Rules + +- Quotes are verbatim, never paraphrased, and always cited (PMID or DOI plus a + locator where possible). If a paper could not be accessed, say so; never quote + from memory or from an abstract you have not retrieved. +- Paywalled papers are listed as inaccessible. Do not commit paywalled PDFs. +- "No evidence found" is a valid, recorded result. +- The `pro-marker-species-support` and `mapping-audit` skills read these files, + and [reports/pro_marker_species_support.tsv](../reports/pro_marker_species_support.tsv) + cites them by path. Update those references if a file is renamed. + +## Planned (tidy plan Phase 6) + +These narrative files will be migrated into a structured table with one row +per (cell type, marker, quote), plus generated per-cell-type and per-marker +views. A `reviews/` subfolder will hold review papers, starting with NK cells. diff --git a/marker_mappings/README.md b/marker_mappings/README.md new file mode 100644 index 0000000..423b0e8 --- /dev/null +++ b/marker_mappings/README.md @@ -0,0 +1,73 @@ +# marker_mappings/ + +How each marker token in the SOULCAP sheet (e.g. `CD56`, `CCR7`) is linked to a +protein, and when that link is trusted for matching. All files here are tracked +and curated; none are in the gitignored `data/` cache. + +| File | What it is | Produced by | +|---|---|---| +| [marker_tokens.csv](marker_tokens.csv) | Every distinct marker token used in the sheet's four marker columns | `uv run soulcap-tokens` (from `data/marker_combinations.csv`) | +| [marker_protein_gene.csv](marker_protein_gene.csv) | **The token → PRO registry.** One row per (token, protein): PRO ID, UniProt ID, gene symbol, HGNC/NCBI IDs, method, confidence, notes. 75 rows | `uv run soulcap-map`, then hand-corrected | +| [marker_resolution.tsv](marker_resolution.tsv) | **The resolution policy.** One row per token: is it a single protein, and may the matcher treat it as that PRO term? 73 rows | Hand-curated | +| [pr_uniprot_overrides.csv](pr_uniprot_overrides.csv) | Manual PRO → human UniProt links where the automatic lookup fails | Hand-curated; read by `soulcap-hgnc` | + +## How the registry, the policy and the audit relate + +Think of it as three questions asked in order. + +1. **What protein does this token name?** + `marker_protein_gene.csv` answers this. It records the best available PRO, + UniProt and gene IDs for each token, including awkward cases (a family, a + complex, a tetramer reagent) with a note. It is a lookup table, not a + judgement about whether the ID is safe to use. + +2. **Is it safe to treat the token as exactly that protein when matching?** + `marker_resolution.tsv` answers this, one row per token: + - `representation`: `single_protein`, `protein_family`, `complex`, + `reagent_gate` (e.g. a tetramer), or `unresolved`. + - `protein_resolution`: `allow` or `withhold`. Only a `single_protein` + token with exactly one PRO ID may be `allow`. Everything else is + `withhold`: the matcher then compares the token only by name, never by + protein identity. + - `rationale` and `source_ref`: why. + + Today 51 tokens are `allow` and 22 are `withhold` (9 unresolved, 6 family, + 4 complex, 3 reagent gate). CD16, CD15, CD3, CD8 and MR1 are held + deliberately until their representation is reviewed. + +3. **What difference does the policy make?** + [reports/marker_resolution_audit.md](../reports/marker_resolution_audit.md) + (from `uv run soulcap-resolution-audit`) compares matching with and without + the policies: which tokens gain or lose links to CL marker axioms, and how + each mapping's evidence changes. It reads the two files above; it never + edits them. + +The policy is used only when a command is given `--marker-map +marker_mappings/marker_protein_gene.csv`. Without that flag the matcher runs in +its default (legacy) mode, which uses the CD synonyms in CL's own axioms. See +[docs/marker_resolution.md](../docs/marker_resolution.md) for the full rules. + +## The `registry_sha256` column (the long numbers on the right) + +Each policy row stores a SHA-256 fingerprint of the registry rows it was +written for. It is computed over every column of every +`marker_protein_gene.csv` row with that token (case-insensitive; `TCRVA24` and +`VB11` each have two rows). + +If anyone later edits those registry rows, even a note, the fingerprint no +longer matches and every `--marker-map` command stops with +`Stale marker policy: ; review registry changes`. That is deliberate: a +policy that said "CD16 is safe" should not silently carry over to a changed +CD16 entry. + +After editing the registry: + +1. Re-read the policy row for each changed token and update it if needed. +2. Only then recompute its fingerprint: + + ```bash + uv run python -c "import csv,sys; from soulcap_cl_mapping.marker_resolution import signature; t=sys.argv[1].upper(); rows=[r for r in csv.DictReader(open('marker_mappings/marker_protein_gene.csv',encoding='utf-8-sig',newline='')) if r['marker_token'].strip().upper()==t]; print(signature(rows))" CD16 + ``` + +Do not refresh fingerprints just to make the error go away; that defeats the +review step. diff --git a/src/README.md b/src/README.md new file mode 100644 index 0000000..2585972 --- /dev/null +++ b/src/README.md @@ -0,0 +1,33 @@ +# src/ + +All Python code, in the package `soulcap_cl_mapping`. Command-line entry points +are declared in [pyproject.toml](../pyproject.toml) and run with +`uv run `. Tests live in `tests/` (one `test_.py` per module) +and must keep coverage at or above 80%. + +## Modules by pipeline stage + +| Stage | Module | Command | +|---|---|---| +| Source data | `sync_sheets.py` | `soulcap-sync` | +| Marker grammar | `marker_syntax.py` (parser, validator, token extraction) | `soulcap-validate`, `soulcap-tokens` | +| | `phenotype.py` (evaluates parsed marker expressions against evidence) | library | +| Token → protein | `marker_map.py` | `soulcap-map` | +| | `hgnc_map.py` | `soulcap-hgnc` | +| | `marker_resolution.py` (per-token allow/withhold policies) | library | +| CL reference data | `cl_pro.py` (CL→PRO axioms from Ubergraph) | `soulcap-cl-pro` | +| | `candidate_index.py` (alias/protein resolution, lexical cache) | `soulcap-cache-terms` | +| Matching | `cl_match.py` | `soulcap-match` | +| | `oak_match.py`, `ols4_lookup.py` | `soulcap-oak-match`, `soulcap-lookup` | +| Mapping decisions | `registry.py` (entity IDs, curated decisions) | library | +| | `mapping_evidence.py` (marker evidence per mapping) | library | +| | `mapping_export.py`, `sssom_export.py` (entry point) | `soulcap-sssom` | +| Audit and evaluation | `audit.py` + `audit_dashboard.html` (template) | `soulcap-audit` | +| | `evaluation.py` | `soulcap-evaluate` | +| | `resolution_audit.py` | `soulcap-resolution-audit` | +| | `regression_triage.py` | `uv run python -m soulcap_cl_mapping.regression_triage` | +| Literature | `europepmc_search.py`, `pubmed_search.py` | `soulcap-europepmc`, `soulcap-pubmed` | +| | `snippet_cache.py`, `report_validator.py` (citation-traversal support) | `soulcap-cache`, `soulcap-validate-report` | +| | `pro_species_support.py` (used by the `pro-marker-species-support` skill) | library | + +See [docs/pipeline.md](../docs/pipeline.md) for how the stages connect. From fb1bc3ac95191d84e746a10bc46513273bfaedd7 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 28 Sep 2026 12:38:22 -0400 Subject: [PATCH 04/14] docs: soulcap-cl-matching skill records decisions in curated_mappings.tsv The skill still told agents to append entries to reports/candidate_cl_mappings.md, which is now generated by soulcap-sssom from mappings/curated_mappings.tsv. Step 4 now adds/edits a registry row (with column guidance: permanent subject_id, review_status always needs_review, no invented citations) and runs soulcap-sssom, and says never to edit the generated report. CLAUDE.md's Skills entry updated to match. Co-Authored-By: Claude Opus 5.5 --- .claude/skills/soulcap-cl-matching/SKILL.md | 59 ++++++++++++--------- CLAUDE.md | 4 +- 2 files changed, 38 insertions(+), 25 deletions(-) diff --git a/.claude/skills/soulcap-cl-matching/SKILL.md b/.claude/skills/soulcap-cl-matching/SKILL.md index e066ea0..7d06a36 100644 --- a/.claude/skills/soulcap-cl-matching/SKILL.md +++ b/.claude/skills/soulcap-cl-matching/SKILL.md @@ -1,6 +1,6 @@ --- name: soulcap-cl-matching -description: Propose a Cell Ontology (CL) match for a SOULCAP cell type (one, several, or all of them) using both marker-axiom scoring and name-based lexical search, cross-checking the two before trusting either, and writing the result into reports/candidate_cl_mappings.md with rationale and evidence. Invoke when asked to map/match a SOULCAP cell type to CL, propose a CL ID, or extend Milestone 4 candidate mappings. +description: Propose a Cell Ontology (CL) match for a SOULCAP cell type (one, several, or all of them) using both marker-axiom scoring and name-based lexical search, cross-checking the two before trusting either, and recording the result as a row in mappings/curated_mappings.tsv (then regenerating reports with soulcap-sssom) with rationale and evidence. Invoke when asked to map/match a SOULCAP cell type to CL, propose a CL ID, or extend Milestone 4 candidate mappings. --- You propose SOULCAP → Cell Ontology (CL) mappings the way they were actually @@ -109,32 +109,43 @@ because it needed an OR-group marker check ## Step 4 — write the result -Append an entry to `reports/candidate_cl_mappings.md` following the existing -format (one `##` section per cell type or closely related family): +Record the decision as a row in +[`mappings/curated_mappings.tsv`](../../../mappings/curated_mappings.tsv), then +regenerate the outputs: -```markdown -## — - -**SOULCAP definition:** - -| Field | Value | -|---|---| -| Proposed CL term |