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PRO marker species-specificity support, issue #11 (part 5/9) - #19
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…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>
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Summary
Commits
03cfdd4..4b0c9cf(issue #11, species specificity of CL's general PRO markers):pro_species_support.pyscopes the (CL term, PRO marker) pairs that SOULCAP's mappings touch.soulcap-europepmcadds a keyless Europe PMC search as a fallback literature source. The compiled verdicts are inreports/pro_marker_species_support.tsv.pro-marker-species-supportskill documents the workflow.Test plan
Checked in isolation with the same steps as CI (
uv sync --frozen --extra dev):uv run pytest: 408 passed, 94.9% coverageuv run ruff check .,ruff format --check ., anduv run mypy src/soulcap_cl_mappingpass🤖 Generated with Claude Code