Repository navigation
CL term-issue tracking, Milestone 1 table, Milestone 2 literature reports (part 3/9) - #17
Open
s28ale-maker wants to merge 8 commits into
Open
s28ale-maker wants to merge 8 commits into
s28ale-maker wants to merge 8 commits into
Conversation
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>
This was referenced Sep 29, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Commits
eaebb85..cb6993f:reports/cl_term_issues.mdand ROADMAP entries for CL corrections found during mapping.marker_mappings/marker_protein_gene.csv, the marker → PRO → UniProt → HGNC table.reports/literature/: NK; ILC, DC, iNKT and T cell; B cell and gdT + MAIT. These are docs only, so review can be light.soulcap-hgnc, which resolves some of the blanks noted in Add soulcap-match CLI and soulcap-hgnc gene-symbol mapping #16.Test plan
Checked in isolation with the same steps as CI (
uv sync --frozen --extra dev):uv run pytest: 293 passed, 94.9% coverageuv run ruff check .,ruff format --check ., anduv run mypy src/soulcap_cl_mappingpass🤖 Generated with Claude Code