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PubMed search CLI, Fall plan, cell_type_reviews scaffold (part 7/9) - #21
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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>
soulcap-pubmed wraps NCBI E-utilities as an alternative to
soulcap-europepmc when a task needs NCBI's own index/query syntax;
keyless by default, reads an optional PUBMED_API_KEY from .env for a
higher rate limit.
reports/fall_2026_semester_plan.{md,pdf,html} is the Sept 21 discussion
draft for Dr. Diehl expanding the sprint backlog into a plain-language
plan, recent-work summary, weekly schedule, and agent task instructions
- proposed for approval, not a confirmed commitment.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
… files Recovered from a cloud Claude session (patch 0001, commit 5b169aa) that built this folder but couldn't push it — no GitHub App write access on the Cellular-Semantics org. Applied by hand rather than git am since CLAUDE.md/README.md had diverged from that session's main base. One review file per SOULCAP cell type: definition, marker->protein/gene, verbatim literature support, CL axiom comparison, proposed verdict, and uncertainty triggers that route a review to Dr. Diehl for expert sign-off. _template.md and the folder README (workflow, statuses, index) are in; no individual reviews written yet. Deliberately NOT included here: the original patch's ROADMAP.md edits, which redefine Milestone 2's deliverable from reports/literature/ to this folder and assert "decided with Dr. Diehl" -- that framing isn't confirmed anywhere in the source conversation, and reports/literature/ already holds 7 real completed category reports plus a sprint-backlog item pointing at it. Flagging for confirmation before touching ROADMAP. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
SOULCAP's bare "CD8" (PR:000001084, alpha chain) can't separate CD8ab from CD8aa. This doesn't affect the CD8+ alpha-beta exactMatches, but it sharpens the CD8+ TCRgd gap: CL models CD8aa+ gamma-delta T cells only in the intraepithelial branch (CL:0000802), with no tissue-unrestricted term. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
Commits
aa4743b..fae3bd9:reports/marker_validation.mdfrom the latest sheet sync.soulcap-pubmed: a keyless NCBI E-utilities search CLI. It usesPUBMED_API_KEYfrom.envif set. Also adds the Fall 2026 semester plan draft.cell_type_reviews/scaffold: one review file per SOULCAP cell type, with a template and an index. No reviews are written yet.reports/gaps.tsvrefinement of the CD4/CD8 T cell gap (a CD8αα / γδ note).Test plan
Checked in isolation with the same steps as CI (
uv sync --frozen --extra dev):uv run pytest: 544 passed, 96.5% coverageuv run ruff check .,ruff format --check ., anduv run mypy src/soulcap_cl_mappingpass🤖 Generated with Claude Code