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New cl_pro module + CLI queries the Ubergraph SPARQL endpoint and writes two regenerable reports under reports/: - cl_pro_relationships.md — CL-centric, PR markers grouped by sense (positive/high/low/negative), with CD synonyms and mouse/human UniProt IDs, flagging inferred-only edges. - cl_pro_relationships.tsv — one row per (cell, relation, PR) for diffing. Covers both directly-asserted (nonredundant) and inferred (redundant) axioms, restricted to meaningful marker relations via a VALUES filter to drop generic super-property entailments. Includes both UniProt routes (species-specific PR xrefs + species-neutral subclass mining). SPARQL access uses SPARQLWrapper (certifi-backed SSL); all other functions are pure with an injectable query_fn. Tests fully mock the network; cl_pro.py at 97% coverage. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The redundant graph entails edges to generic PR superclasses (e.g. "has part some protein" / "amino acid chain") for any cell with a protein part. These are not useful markers, carry no cell-type-specific metadata, and showed up in the report with blank labels. Restrict edges to PR terms directly asserted as a marker on some cell (the nonredundant PR set). Specific markers inherited by subtypes are retained and still flagged inferred-only; only the never-asserted generalisations are dropped. Every remaining row now has a label/metadata. Report shrinks from 17,076 to 8,624 marker edges (296 distinct markers). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- Exclude the root PR "protein" (PR:000000001) via EXCLUDED_PRS; it is asserted on cells but useless as a marker across every relation. - TSV booleans now render as True/False instead of yes/no. - CD synonym detection: scan the label and all synonym scopes (exact / related / broad / narrow) for CD tokens via regex, instead of only related synonyms, and report the source scope alongside each token (e.g. "CD19 (related)"). This surfaces many CD ids PRO records outside related synonyms (the exact scope alone adds ~4.9k matches). Metadata query extended with broad/narrow synonyms. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…ion) The redundant graph materialises every super-property, so a (cell, PR) pair appears under a specific relation and all its ancestors — e.g. both "has part" and "has plasma membrane part" for the same protein, the former entailed by the latter. Fetch the transitive rdfs:subPropertyOf hierarchy among the marker relations from Ubergraph (new fetch_relation_ancestors + SUBPROPERTY_QUERY), then in fetch_relationships drop, per (cell, PR), any relation that is a super-property of another relation present for that pair. Removes ~2025 redundant edges (6542 -> 4517). Redundancy entailed via property chains is out of scope. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
dosumis
marked this pull request as draft
July 4, 2026 12:50
…vements - soulcap-lookup: new CLI to search CL terms via EBI OLS4 REST API - soulcap-tokens: new CLI to extract distinct marker tokens from the Marker Combinations CSV (M1 prerequisite) - extract_markers() / extract_markers_from_csv() added to marker_syntax - Fix __version__ duplication: read from importlib.metadata at runtime - Add mypy + pandas-stubs to dev deps; mypy clean across all 7 modules - Fix 4 type bugs surfaced by mypy (None narrowing, Hashable index, ExcelFile stubs, mixed params dict) - CI: split into lint + test jobs; add ruff format --check; add uv sync --frozen; add mypy type-check step - Add Dependabot config for Actions and pip deps - Add pre-commit config (ruff check + format) - Create marker_mappings/ directory for tracked mapping artifacts - Resolve merge conflicts from upstream (pyproject.toml, marker_syntax, marker_validation report) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
s28ale-maker
marked this pull request as ready for review
July 4, 2026 20:37
…profiles Takes the four SOULCAP marker columns (required/ideal exclusions and phenotypic markers) plus --parent and --subset name hints, scores every CL term in cl_pro_relationships.tsv by marker matches/contradictions/gaps, and returns ranked candidates. Name hints add a small label-match bonus to break ties. 201 tests passing, 93.8 percent coverage. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds hgnc_id and hgnc_symbol columns to reports/cl_pro_relationships.tsv by querying the Monarch Node Normalizer (nodenormalization-sri.renci.org) with UniProtKB CURIEs (primary) and PR CURIEs as fallback for rows missing a human UniProt ID. 239/295 unique PR markers resolved to HGNC on first run; 56 blanks are isoform-specific accessions or mouse-only proteins. 236 tests passing, 94% coverage. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add reports/cl_term_issues.md to document proposed CL label/definition changes identified during SOULCAP mapping (issue #13: CL:4052055 -> CD56-positive T cell, CL:0000814 -> iNKT cell). Link from ROADMAP.md CL corrections table. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds soulcap-map CLI (marker_map.py) that maps all 75 SOULCAP marker tokens to PR, UniProt, HGNC, and gene identifiers, writing the curated deliverable at marker_mappings/marker_protein_gene.csv. Results: 39 fully resolved (PR+HGNC), 17 gene-only (cytokines, TCR segments), 4 PR-only (CD16/CD198/FceR1a/HLA-DR), 15 unresolved (Ig classes, pan-TCR markers, parsing artifacts, CD1d-a-GalCer/Tetramer). Parsing artifacts (V, delta, gamma, delta1) flagged as data quality issues. Sources: cl_pro_relationships.tsv (36 CD markers), OLS4 PR ontology, Monarch Node Normalizer, HGNC REST API. 287 tests passing, 95% coverage. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add reports/literature/nk_cell_markers.md with verbatim-quoted evidence for all 10 NK cell markers used in SOULCAP (CD56+, CD3-, CD19-, CD14-, CD127-, CD16, CD57, HLA-DR, CD11c, CD56bright/dim subsets), drawn from 3 open-access papers (Rebuffet 2024 Nat Immunol, Scoville 2017 Front Immunol, Van Acker 2017 Front Immunol). Two paywalled papers (Vivier 2024 Nature, Aranami 2006 J Immunol) noted as not accessed. Key finding: CD127 and HLA-DR caveated as ideal rather than required exclusions based on the evidence. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Four new verbatim-quote reports under reports/literature/: - ilc_markers.md — 4 open-access papers (Krabbendam 2021, Alkon 2022, Bonne-Année 2019, Bento 2025); covers CD127, CD3, CD161, CD294/CRTH2, CD117/c-Kit, CD56, and lineage-exclusion markers - dc_markers.md — 3 open-access papers (Rhodes 2019, Villani 2017, Guilliams 2016); covers CD11c, HLA-DR, CD1c, CD141, CD172a/SIRPα, FceR1a, CD123, CD303, CD33, CD64, CD14/CD16, and Lin dump - inkt_markers.md — 2 open-access papers (Lal 2018 OMIP-046, Zhou 2022); covers CD3, TCRVα24-Jα18, TCRVβ11, CD1d pentamer; also documents the iNKT vs Type II NKT distinction relevant to CL issue #13 - t_cell_markers.md — 12 open-access sources; covers CD3, CD4/CD8, TCRαβ/TCRγδ, CXCR3/CD183, CXCR5/CD185, CCR4/CD194, CCR6/CD196, CRTH2/CD294, CD25+CD127lo (Treg), CD45RA+CCR7, CD27+CD28 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
CL:4052055 -> obophenotype/cell-ontology#3663 CL:0000814 -> obophenotype/cell-ontology#3664 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
CL:0000576/0000860/0002393/0000875 -> obophenotype/cell-ontology#3665 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…hgnc Isoform-suffixed accessions like UniProtKB:P16871-1 were sent to the Monarch Node Normalizer verbatim; Monarch only resolves canonical accessions (P16871). Adding strip_isoform_suffix() and applying it in collect_pr_mappings() raises HGNC coverage from 3919 to 4084/4517 rows, resolving CD34, CD127, CD56, CD117, NKp46, NKp44, CD161 and others. Closes #9 (remaining 36 unmapped rows are mouse-specific PRO terms or rare human proteins Monarch cannot resolve — documented in TSV notes). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…idate mappings (issue #6) - soulcap-match --batch scores every SOULCAP cell type against all CL terms in one pass; --lexical adds an independent OLS4 name-search candidate and writes a marker/lexical agreement report. - Fix scoring: required-marker conflicts now disqualify a candidate instead of just subtracting points, so shared exclusion markers can no longer outrank a term that outright contradicts a required marker. - Fix scoring: CL's "high"/"low" expression-level axioms are no longer treated as equivalent to "negative" (absent). - Add extract_marker_clauses(): SOULCAP's `(A+|B+|C-)` OR-groups were being flattened into independently-required markers instead of "at least one must hold" — this silently suppressed good matches (e.g. CL:0000043 mature basophil never scored for SOULCAP's Basophil profile). Clauses are now evaluated with proper OR semantics. - Fix OLS4 lexical search: exact label matches were buried by OLS4's default relevance ranking; now promoted to rank 1 when present in a wider pool. - Extend marker_map.py's PRO lookups (cytokines, MR1, TCR V-gene segments) via UniProt-accession-based PRO term fetch, closing most of the marker->gene mapping gaps tracked in issue #1. - Add reports/candidate_cl_mappings.md (Milestone 4 draft mappings with rationale/evidence) and log a new CL gap (missing human-specific "group 1 innate lymphoid cell" term, filed as issue #14). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
- soulcap-oak-match: lexical/synonym CL search via OAK's sqlite:obo:cl adapter, an independent second opinion to soulcap-match --lexical (OLS4). Verified live: ranks exact label/synonym matches cleanly where OLS4's relevance ranking buries them behind subtype noise. - soulcap-sssom: exports the curated Milestone 4 mapping decisions as SSSOM TSV instead of writing OWL axioms directly. confidence/comment are derived automatically from whether CL directly asserts the matched marker axiom(s), only has them by inference, or has none at all — not hand-typed. - write_robot_template(): converts SSSOM rows into true logical OWL axioms (equivalentClass/subClassOf) for reasoner QC, since SSSOM's own OWL writer only emits skos:exactMatch as a non-logical annotation a reasoner ignores. - reports/gaps.tsv + .github/ISSUE_TEMPLATE/mapping_gap.yml (gap label): tracks cases with no reasonable CL match, CL/marker conflicts, CL axiom gaps, and sheet data issues, separate from the mapping table. - .github/workflows/robot-qc.yml: runs on every PR. One job audits upstream CL (cl-base.owl) standalone with robot report + robot reason (ELK); a second merges our SSSOM-derived mapping axioms into CL and re-checks, to catch problems our own proposed mappings would introduce. - New skill: soulcap-cl-matching, encoding the cross-check workflow (never trust either method's rank-1 blindly, verify via direct OLS4 lookup when uncertain). - Fix a pre-existing mypy gap in cl_match.py (_lexical_query_for_row typing). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…pings - 7 new mappings via the soulcap-cl-matching skill workflow, verified via OAK (soulcap-oak-match) after OLS4 REST search started timing out mid-run. - Eosinophil -> CL:0000771 is a strong marker-confirmed match (CD193/CCR3 directly asserted, not inferred, matching SOULCAP's defining marker). - Monocyte subset terms (CL:0000860/0000875/0002393) are lexical-only matches; CL's own markers for them are already known-incomplete per repo issue #12, cited rather than re-flagged. - Logged 4 new gaps.tsv entries: axiom gaps on the two more parent classes (Mono, B cell), and a malformed bracket shared across all four Monocyte rows' Required exclusion column (sheet data issue, not fixable here). - Extended the SSSOM curated table with the same 7 entries. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…y/naive tree) - Covers 57 of 83 remaining T cell rows via the soulcap-cl-matching skill. Marker-axiom scoring was uniformly useless across this entire branch (top candidates were consistently unrelated myeloid/NK terms); every mapping is lexical, OAK-verified directly rather than trusted from the raw batch output, which was wrong or missing for a large fraction of this branch too. - CD56+ T cell family (13 rows) ties back to repo issue #13: all Broad-match to CL:4052055, the term already flagged there for a pending rename to "CD56-positive T cell, human". - iNKT -> CL:0000814, the other term from issue #13 (pending rename to "iNKT cell"). - Several real CL gaps found and grouped in gaps.tsv: CL's CD4/CD8 vocabulary is alpha-beta-centric (no combined ab+gd, double-positive, or peripheral double-negative terms); no gamma-delta-specific or generic (non-CD4/CD8) differentiation-state terms; a likely CD8+-specific TEMRA term gap. - 26 rows have NO Full Name in the sheet at all (Conv TCRab family, Th1/2/9/17-like, Tfh, Vg9/Vd1/Vd2/Vd3, etc.) -- not mapped, since inventing a name isn't this report's call. Also found what looks like a genuine sheet data bug: Th1-like/Th2-like/Th9-like/Th17-like each appear TWICE, one copy with markers that look copy-pasted from an unrelated iNKT row. - SSSOM curated table extended with the 30 distinct (non-redundant) T cell mappings -> 80 total mappings. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…hon 3.11) and register SOULCAP: prefix in robot template David's agentic review caught a real bug I'd missed: my local dev environment runs Python 3.13, where uv.lock resolves eutils==0.6.1 (uses importlib.metadata). CI's test matrix includes Python 3.11, where uv.lock resolves the older eutils==0.6.0, which still does `import pkg_resources` at module load -- and setuptools>=81 removed pkg_resources entirely, so any import of oaklib (hence soulcap-oak-match) aborted pytest collection outright on 3.11, running 0 tests. Reproduced locally by installing Python 3.11 via uv and running the real test suite against it (matching CI's exact failure). Fixed by pinning setuptools<81 as a main dependency (not dev-only -- this also breaks the real soulcap-oak-match CLI on 3.11, not just tests) and confirmed the fix resolves cleanly under both 3.11 and the default 3.13 environment. Also found and fixed a second real CI failure while investigating (ROBOT ontology QC workflow, from actual run logs): `robot template` didn't know the SOULCAP: prefix used by write_robot_template()'s output, causing "UNKNOWN ENTITY ERROR could not interpret 'SOULCAP:NK'". Added --prefix "SOULCAP: https://soulcap.org/cell_type/" to register it, matching the CURIE_MAP already used in sssom_export.py. Could not fully dry-run the ROBOT fix locally (no Java available in this environment, and installing one hit a UAC prompt that can't be answered non-interactively) -- the setuptools/eutils fix is fully verified against a reproduced failure; the ROBOT prefix fix is a standard, well-documented fix applied directly against the real CI error, but not further dry-run. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
The --prefix fix from the last commit got the merge step passing; robot report on the merged ontology then surfaced two more real, verified issues (pulled the actual merged-report.tsv artifact from the failed run rather than guessing): - ERROR duplicate_label: SOULCAP:Basophil_(PBMC) and SOULCAP:Basophil_(WB) both got the literal rdfs:label "Basophil", since build_robot_template_rows used subject_label (SOULCAP's own Full Name column, not guaranteed unique -- both preps share the same Full Name) instead of something derived from subject_id (always unique, by construction). Fixed by deriving the ROBOT template LABEL from subject_id instead. Added a regression test against the real CURATED_MAPPINGS table, not just a synthetic example. - 3x ERROR missing_ontology_title/description/license: the merged.owl ontology declaration had no dc: metadata annotations. Added a chained `robot template ... annotate ...` step setting minimal title/description/ license on the merged QC artifact. Still can't fully dry-run locally (no Java in this environment) -- pushing to let the real CI run verify, same as the last fix. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
… over them David flagged this as overstepping scope during review — proposing mappings for human review is this repo's job, but unilaterally asserting them as true OWL axioms and merging them into CL (even as an ephemeral CI artifact) is not. Keep only the read-only upstream-CL audit job; drop the ROBOT-template/OWL-axiom code path from sssom_export.py since nothing calls it anymore. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…port (issue #11) Adds pro_species_support.get_scoped_pairs()/group_by_cell(): restricts the "does literature support this marker for human/mouse/both" question to CL terms this project actually maps SOULCAP cell types to, rather than all of CL. Against the current cl_pro_relationships.tsv and CURATED_MAPPINGS this resolves to 77 (CL cell type, marker) pairs across 33 distinct CL terms. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…support TSV (issue #11) The Asta MCP server wasn't reachable this session (project MCP connections never came up), so this adds europepmc_search.py -- a free, keyless literature search against Europe PMC's REST API -- as the "general search" fallback tier issue #11 already allows when citation-traversal has nothing to seed from. Compiled reports/pro_marker_species_support.tsv for all 77 scoped (CL cell type, PRO marker) pairs: 54 rows reuse already-verbatim-verified quotes from the Milestone 2 literature reports (the strongest available tier), 5 rows come from fresh Europe PMC searches, and 18 are recorded as insufficient_evidence rather than forced -- a real finding (mainly the monocyte subset marker panel, which has no clean definitional literature turned up by either route) rather than a search failure to hide. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Formalizes the method proven across all 77 pairs in the first full run: check the M2 literature reports first (best tier, already vetted), fall back to citation-traversal if Asta is reachable, otherwise the keyless soulcap-europepmc search, and record insufficient_evidence rather than force a weak match when nothing turns up. Registers the skill and the two supporting modules (pro_species_support.py, europepmc_search.py) in CLAUDE.md. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…aluation harness Move curated mapping decisions from Python into mappings/curated_mappings.tsv and mappings/soulcap_entities.tsv, with phenotype.py providing a shared AST for marker validation, token extraction, and scoring. Add soulcap-audit (a self-contained HTML dashboard), soulcap-evaluate (offline matcher retrieval metrics against a reviewed benchmark), and opt-in alias/protein-aware matching via candidate_index.py. Fix mapping_evidence.assess() double- counting bare/unqualified required markers as unscorable gaps, which incorrectly suppressed the required_markers_supported status even when every checkable required marker was directly asserted in CL; also cache per-row CL indexes instead of rebuilding one per matched clause. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…d evidence-reviewed follow-up Add marker_resolution.py + marker_mappings/marker_resolution.tsv: every registry marker token gets an explicit, SHA-256-fingerprinted policy (single_protein/protein_family/complex/reagent_gate/unresolved) with an allow/withhold protein-equivalence call, rationale, and source ref, wired into candidate scoring, mapping evidence, SSSOM export, and the audit via --marker-map. Add soulcap-resolution-audit (resolution_audit.py) to diff legacy vs. policy-driven resolution per marker. Add regression_triage.py, an offline diagnostic that isolates enhanced token-evidence additions, legacy token-evidence removals, and semantic- clause deduplication across 8 combinations without re-running lexical search, to explain matcher ranking changes without altering any mode. Add a hand-reviewed regression follow-up (reports/regression-followup/) covering the three top-5 targets lost under the stricter resolver: cites CL/PRO axioms and OMIP-060 for context, and implements one narrowly-scoped correction (whole_cd8_surface_positive_v1) rather than loosening policy broadly. Add benchmark scaffolding (marker_assertion_benchmark.json as regression tests, benchmark_reserve.json as a documented five-entity prospective reserve) with results reported as provisional retrieval metrics, not validated biological accuracy. No source-sheet values, marker identifiers, or curated mapping decisions changed; legacy matcher mode remains the default. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Break the Fall 2026 (Oct-Dec) working plan into concrete sub-tasks with acceptance criteria, grounded in ROADMAP.md, gaps.tsv, and issues #5-#14, flagging what's blocked on Dr. Diehl/sheet admin/upstream reviewers vs. independently actionable. Linked from CLAUDE.md, README.md, and ROADMAP.md. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…a/ cache test_reserve_is_reproducible_and_separate_from_development asserted a hash for data/marker_combinations.csv, a gitignored sync-only cache that CI never has (no Sheets credentials to regenerate it) — this broke CI on every Python version while passing locally only because this machine has a synced data/. Match the existing convention elsewhere (evaluation.py's dashboard_evaluation) of treating a missing data/ file as unverifiable rather than a hard failure; tracked mapping files under mappings/ still fail hard if missing. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Sheet re-sync (2026-09-18) now populates the Subset/Abbreviation column for the 26 previously-flagged invalid marker cells; same 26 errors, no new or resolved ones. Auto-generated by soulcap-sync, no manual edits. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Closing this in favor of a stack of smaller PRs, per our conversation about breaking this branch down instead of reviewing it all at once — it had ballooned to ~1M additions across 140 files since it's been open since July 4th tracking every commit on First piece is up: #15 (just the |
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@s28ale-maker - looks like a copy of the CL_to_PRO branch? Was hoping to see the draft SOULCAP to CL mappings you worked on last week & maybe something on #6