s28ale-maker · Sep 28, 2026 · Sep 29, 2026 · Sep 29, 2026
diff --git a/.claude/skills/pro-marker-species-support/SKILL.md b/.claude/skills/pro-marker-species-support/SKILL.md
@@ -118,21 +118,60 @@ own discipline here.
 
 ## Step 4 — write the row
 
-Append to `reports/pro_marker_species_support.tsv`
-(tab-separated, one row per pair):
+`reports/pro_marker_species_support.tsv` has one row per directly asserted
+(CL term, PRO marker) pair for every CL term in
+`mappings/curated_mappings.tsv` (87 pairs as of 2026-09-28). The question is
+Dr. Diehl's: **is each marker, as CL asserts it, valid in human, mouse, or
+both?**
+
+**Never edit the first 10 (legacy) columns** of an existing row. They record
+the original human-only check from issue #11. All new work goes in the 7
+columns after them. **Where the new columns disagree with the legacy
+`species_support` value, the new columns take precedence** (e.g. plasmablast
+"lacks CD138", where the legacy value still says `human`).
 
 | Column | Meaning |
 |---|---|
-| `cl_id`, `cl_label`, `pr_id`, `pr_label`, `cd_synonym` | From `get_scoped_pairs()` — don't hand-retype these, pull them programmatically to avoid transcription errors (a real bug caught during the first run: hand-typed PR labels didn't match `cl_pro_relationships.tsv`). |
-| `species_support` | `human` / `mouse` / `both` / `insufficient_evidence`. |
-| `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` | `literature/evidence.tsv#<evidence_id>` for M2 reuse (older rows cite `archive/2026-09_literature_narratives/<file>.md`), an EuropePMC article URL for a fresh search, or `reports/citation_traversal/<run_id>/` for a traversal — or, for `insufficient_evidence`, a one-line note on what was tried. |
+| `cl_id`, `cl_label`, `pr_id`, `pr_label`, `cd_synonym` | From `cl_pro_relationships.tsv` — pull them programmatically, don't retype them. |
+| `species_support`, `evidence_source`, `citation`, `quote`, `source_ref` | **Legacy** (issue #11 human-only check). Read-only. |
+| `species_scope` | `human`, `mouse`, `both` or `unresolved` (blank = not yet assessed). |
+| `human_citation`, `human_quote` | Citation (author, year, PMID, PMCID) and an exact quote for the human side. |
+| `mouse_citation`, `mouse_quote` | The same for mouse. |
+| `note` | Free text explaining the verdict, e.g. "not tested in mouse, no reagent", "ortholog exists but not expressed", "contradicted in mouse", or "species from PRO label". |
+| `checked_on` | Date the row was last assessed. |
+
+Rules for `species_scope`:
+
+- **Judge against the assertion as CL states it.** For a negative pair
+  ("lacks CD14"), evidence that the marker is absent in a species *supports*
+  it.
+- `both` only when **both** species have an exact quote supporting the
+  assertion.
+- `human` / `mouse` when that species is supported and the other is
+  contradicted by a quote (e.g. mouse NK cells are not classified by CD56).
+- `unresolved` whenever a species has no evidence, only "not tested", or
+  conflicting evidence. Explain which in `note`. **Never treat "not tested in
+  mouse" as human-only.**
+- Pairs whose PRO label is species-qualified, e.g. "(human)", get
+  `species_scope = human` and the note "species from PRO label".
+- **Human-specific CL terms** (label ending ", human", e.g. CL:0000938): the
+  mouse question doesn't apply. Set `species_scope = human` when the human
+  side is supported by a verified quote, otherwise `unresolved`, and start
+  `note` with "CL term is human-specific; mouse not applicable".
+- An existing mouse ortholog (Alliance of Genome Resources / MGI) is **not**
+  evidence that a marker works in mouse. It may go in `note` with its record
+  ID; mouse support needs literature.
+- Every quote is checked word for word against the paper's Europe PMC full
+  text (as `soulcap-evidence verify` does) before it is written. If none can
+  be verified, leave the quote blank and say so in `note`.
+
+Evidence sources, in order: references in `literature/reviews/` (Dr. Diehl's
+first); verified rows of `literature/evidence.tsv`; then open-access
+literature via `soulcap-europepmc` / Europe PMC full text.
 
 ## Step 5 — flag real findings
 
-If a `species_support` result is genuinely surprising (e.g. a marker CL
+If a `species_scope` result is genuinely surprising (e.g. a marker CL
 implicitly treats as pan-species turns out to only have mouse evidence, or a
 whole marker cluster comes back `insufficient_evidence` the way monocyte
 subset markers did), log it the same way other literature/CL gaps from this

diff --git a/docs/README.md b/docs/README.md
@@ -9,7 +9,7 @@ pages hold the full detail.
 | [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); agenda for the [12 Oct 2026 meeting](planning/2026-10-12_meeting_summary.md) |
+| [planning/](planning/) | Sprint backlog and semester plan (hand-maintained); agenda for the [12 Oct 2026 meeting](planning/2026-10-12_meeting_summary.md); [human/mouse marker pilot summary](planning/2026-10-02_diehl_summary.md) for Dr. Diehl |
 
 Related specs that live at the top level: [MARKER_SYNTAX.md](../MARKER_SYNTAX.md)
 (marker expression grammar) and [ROADMAP.md](../ROADMAP.md) (milestones).

diff --git a/docs/planning/2026-10-02_diehl_summary.md b/docs/planning/2026-10-02_diehl_summary.md
@@ -0,0 +1,76 @@
+# Human vs mouse validity of CL markers: pilot summary for 2 October 2026
+
+For Dr. Diehl. Your request from 28 September, a pilot on 3 CL terms, and
+three questions before the rest is done.
+
+## The task and how it's done
+
+For every CL term a SOULCAP cell type maps to, each PRO marker CL asserts
+directly (87 pairs) is checked: **is the assertion, as CL states it, valid in
+human, mouse, or both?** For a negative assertion such as "lacks CD14",
+absence in a species counts as support.
+
+- Each species needs its own **exact quote**, checked word for word against
+  the paper's full text in Europe PMC. Nothing is inferred from a marker's name
+  or from memory.
+- `both` requires a supporting quote for each species. "Not tested in mouse"
+  gives `unresolved`, never "human only". An existing mouse ortholog is not
+  counted as evidence.
+- Results are in `reports/pro_marker_species_support.tsv` (new columns
+  `species_scope`, `human_*`, `mouse_*`, `note`). The original human-only
+  check is kept unchanged alongside.
+
+## Pilot: 3 CL terms, 10 pairs
+
+| CL term: assertion | Human | Mouse | Scope |
+|---|---|---|---|
+| NK cell (CL:0000623): lacks CD20 | Supported | No evidence found | unresolved |
+| NK cell: lacks CD14 | Supported | No evidence found | unresolved |
+| Plasmablast (CL:0000980): CD38 high | Supported | No evidence found | unresolved |
+| Plasmablast: CD27 high | Supported | No evidence found | unresolved |
+| Plasmablast: lacks CD20 | Supported | No evidence found | unresolved |
+| Plasmablast: lacks CD138 | Conflicting | **Contradicted** | unresolved |
+| CD56-bright NK, human (CL:0000938): CD56 high | Supported | Contradicted | **human** |
+| CD56-bright NK: lacks CD16 | Supported | Not applicable | **human** |
+| CD56-bright NK: lacks HLA-DRA | **Not supported** | Not applicable | unresolved |
+| CD56-bright NK: CD84 positive | No evidence found | Not applicable | unresolved |
+
+Also, 10 pairs whose PRO term is itself human-specific, e.g. "(human)" in the
+label, are marked `human` from the label.
+
+## Three notable findings
+
+1. **CD56 is the clearest human-only marker.** "Because mice lack CD56, murine
+   NK cell subsets are classified using alternative markers, particularly CD27
+   and Mac-1." (PMID 41898531). The mouse gene *Ncam1* exists (MGI:97281), but
+   it isn't used for NK cells.
+2. **Plasmablast "lacks CD138" doesn't hold in mouse and is disputed in
+   human.** Mouse: "plasmablasts as B220+CD138+" (PMID 42774878). Human:
+   "short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)"
+   (PMID 41771939).
+3. **CD56-bright NK "lacks HLA-DRA" isn't well supported even in human:** "the
+   proportion of HLA-DR+CD56bright cells ex vivo" (PMID 42450353). PRO notes
+   the mouse counterpart is H2-Ea.
+
+Findings 2 and 3 are logged as unfiled candidates in
+`reports/cl_term_issues.md`.
+
+## Questions for you
+
+a. **Can you share your references?** They'll be used first, before any new
+   searching (they go in `literature/reviews/`).
+
+b. **Negative lineage markers.** For assertions like "lacks CD14 / CD19 / CD20"
+   on non-myeloid or non-B cells, will you accept `both` on biological
+   grounds, or require a quote for each species? The mouse literature rarely
+   states these absences, so requiring quotes leaves most of them
+   `unresolved`.
+
+c. **Human-specific CL terms.** For terms like CL:0000938 ("…, human"), is
+   "mouse not applicable", scoped `human` when the human side is supported,
+   the right rule?
+
+## Remaining scope
+
+**67 pairs on 30 CL terms**, waiting for your answers. Four of those pairs
+already have a corrected human quote; their mouse side is still to do.
diff --git a/reports/README.md b/reports/README.md
@@ -60,7 +60,7 @@ These are generated, but they are inputs to other code and need network access
 |---|---|---|---|
 | [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 |
+| [pro_marker_species_support.tsv](pro_marker_species_support.tsv) | For every directly asserted PRO marker on a mapped CL term (87 pairs): is the assertion valid in human, mouse, or both? The first 10 columns are the original human-only check (issue #11, read-only); `species_scope`, `human_*`/`mouse_*` citation and quote, `note` and `checked_on` hold the human/mouse assessment (Dr. Diehl's request, 2026-09-28; pilot on 3 CL terms so far). Where they disagree with the legacy `species_support`, the new columns take precedence | `pro-marker-species-support` skill; every quote checked against the paper's full text | Curated |
 
 ## Not tracked
 

diff --git a/reports/cl_term_issues.md b/reports/cl_term_issues.md
@@ -185,6 +185,44 @@ confirmed)? The same question applies to CD57 (HNK-1 epitope, made by
 B3GAT1, PR:000001440): CL has one such axiom, CL:4033092 "CD57-positive
 enterocyte" `expresses` PR:000001440.
 
+### Plasmablast "lacks CD138" — CL:0000980, PR:000001935 (syndecan-1)
+
+**Status:** candidate — not filed
+
+CL asserts CL:0000980 "plasmablast" `lacks_plasma_membrane_part`
+PR:000001935 "syndecan-1" (CD138). Found during the human/mouse marker
+review (2026-09-28; row in
+[pro_marker_species_support.tsv](pro_marker_species_support.tsv)). Both
+quotes were checked word for word against the Europe PMC full text:
+
+- **Contradicted in mouse:** "plasmablasts as B220+CD138+" (PMID 42774878;
+  PMC13594723, 2026).
+- **Conflicting in human:** one human scheme defines plasmablasts as CD138++:
+  "short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)" (PMID
+  41771939; PMC13066544, 2026). The earlier human quote supporting the
+  assertion (Woodruff 2020 gating labels) could not be verified.
+
+**Question for review:** should this axiom be removed, weakened (e.g. "low"),
+or restricted to human?
+
+### CD56-bright NK "lacks HLA-DRA" — CL:0000938, PR:000002015
+
+**Status:** candidate — not filed
+
+CL asserts CL:0000938 "CD16-negative, CD56-bright natural killer cell, human"
+`lacks_plasma_membrane_part` PR:000002015 "MHC class II histocompatibility
+antigen alpha chain DRA". Human evidence reports HLA-DR+ CD56-bright cells:
+"the proportion of HLA-DR+CD56bright cells ex vivo" (PMID 42450353;
+PMC13362507, 2026; checked word for word against the full text). The
+supporting quote from the earlier check (Rebuffet 2024) concerns a different
+NK cluster (NK3B) and does not address CD56-bright cells.
+
+**Question for review:** is "lacks HLA-DRA" right for resting CD56-bright NK
+cells, with HLA-DR appearing only on an activated subset, or should the axiom
+be dropped? This is also Dr. Diehl's example of HLA-DRA as a human-only proxy
+for MHC class II: PRO notes "The mouse ortholog is called H2-Ea"
+(PR:000002015, OLS4).
+
 ---
 
 ## Resolved issues