From a59fc9e5bee577a62b7c6ede8339315885a3838f Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 5 Oct 2026 19:42:29 -0400 Subject: [PATCH 01/11] feat: NK / group 1 ILC and plasmablast marker audit (Dr. Diehl, 2026-10-05) Task A + D of the 2026-10-05 meeting plan. - pro_marker_species_support.tsv: new columns human_status / mouse_status (supported, contradicted, no_evidence_found, not_applicable), counter_citation / counter_quote (other side of a contradiction) and audit_batch. Legacy 10 columns unchanged on all 87 original rows. - 66 directly asserted pairs on the 28 marker-bearing terms under CL:0001067 (Ubergraph, 2026-10-05) plus the 4 plasmablast pairs; 57 new rows. 34 quotes, all checked verbatim against Europe PMC full text (abstract for Chiossone 2009). - HLA-DRA: CL:0000938 and CL:0000939 both assert "lacks HLA-DRA"; no CL term asserts HLA-DR+ NK; neither definition source supports the axiom; human evidence contradicts it for a minority subset. One-sheet export in nk_hladr_conflicts_2026-10.tsv. - nk_marker_audit_2026-10.md: counts per status, requested cases, 9 other issue candidates, open questions. - plasmablast_marker_audit_2026-10.md: lineage (inherits in-taxon Mammalia via CL:0001200), verdicts, proposed human/mouse children. - Skill and reports README document the new vocabulary. Co-Authored-By: Claude Opus 5.5 --- .../pro-marker-species-support/SKILL.md | 35 ++- reports/README.md | 5 +- reports/nk_hladr_conflicts_2026-10.tsv | 3 + reports/nk_marker_audit_2026-10.md | 142 +++++++++++ reports/plasmablast_marker_audit_2026-10.md | 83 +++++++ reports/pro_marker_species_support.tsv | 233 +++++++++++------- 6 files changed, 408 insertions(+), 93 deletions(-) create mode 100644 reports/nk_hladr_conflicts_2026-10.tsv create mode 100644 reports/nk_marker_audit_2026-10.md create mode 100644 reports/plasmablast_marker_audit_2026-10.md diff --git a/.claude/skills/pro-marker-species-support/SKILL.md b/.claude/skills/pro-marker-species-support/SKILL.md index 1a7697a..502d701 100644 --- a/.claude/skills/pro-marker-species-support/SKILL.md +++ b/.claude/skills/pro-marker-species-support/SKILL.md @@ -120,12 +120,16 @@ own discipline here. `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 +`mappings/curated_mappings.tsv` (87 pairs as of 2026-09-28), plus every term +under group 1 ILC (`CL:0001067`, NK cells included) from the October 2026 NK +audit (`audit_batch = nk_2026-10`; see `reports/nk_marker_audit_2026-10.md`). +Extra terms can be added the same way: scope them from Ubergraph and pull +their labels from `cl_pro_relationships.tsv`. 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 +the original human-only check from issue #11. All new work goes in the 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`). @@ -134,11 +138,34 @@ columns after them. **Where the new columns disagree with the legacy |---|---| | `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. | +| `species_scope` | `human`, `mouse`, `both` or `unresolved` (blank = not yet assessed). Derived from the two status columns. | +| `human_status`, `mouse_status` | One value per species, from the controlled list below. | +| `human_citation`, `human_quote` | Citation (author, year, PMID, PMCID) and an exact quote: the evidence behind `human_status`. For `contradicted`, this is the contradicting quote. | | `mouse_citation`, `mouse_quote` | The same for mouse. | +| `counter_citation`, `counter_quote` | For a `contradicted` verdict, the strongest quote on the other side (supporting the assertion), so both sides are recorded. Blank if none was found. | | `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. | +| `audit_batch` | Which audit last set the row, e.g. `nk_2026-10`. Blank for earlier rows. | + +Status values for `human_status` / `mouse_status` (Dr. Diehl, 2026-10-05). +Keep these four apart; they mean different things: + +| Value | Meaning | +|---|---| +| `supported` | An exact quote supports the assertion as CL states it. | +| `contradicted` | An exact quote goes against it. Put any supporting quote in `counter_*`. | +| `no_evidence_found` | Searched, found nothing. **Not** a contradiction. Say in `note` what was searched. | +| `not_applicable` | The species question doesn't apply: the CL term is limited to the other species (", human" / ", mouse"), the PRO term is the other species' protein, or the marker is human-only. Human-only markers so far: HLA-DRA (mouse ortholog H2-Ea is a different protein) and NCAM1/CD56 for NK cells. | +| *(blank)* | Not assessed. | + +Derive `species_scope` from them: `both` if both are `supported`; `human` +if human is `supported` and mouse is `not_applicable` or `contradicted` +(likewise `mouse`); otherwise `unresolved`. + +Lineage-negative markers (lacks CD3/CD19/CD20/CD14 on non-T, non-B, +non-myeloid cells) are generally safe across species (Dr. Diehl), but still +look for mouse evidence and record `no_evidence_found` if there is none. Never +mark them `supported` on expert opinion alone; put the opinion in `note`. Rules for `species_scope`: diff --git a/reports/README.md b/reports/README.md index c7757c7..f8a62d4 100644 --- a/reports/README.md +++ b/reports/README.md @@ -60,7 +60,10 @@ 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) | 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 | +| [pro_marker_species_support.tsv](pro_marker_species_support.tsv) | Is each CL marker assertion valid in human, mouse, or both? One row per directly asserted PRO marker on (a) every mapped CL term (87 pairs) and (b) every term under group 1 ILC, natural killer cell included (NK audit, `audit_batch = nk_2026-10`). The first 10 columns are the original human-only check (issue #11, read-only). `human_status` / `mouse_status` hold one value each: `supported`, `contradicted` (evidence against; any supporting quote goes in `counter_citation`/`counter_quote`), `no_evidence_found` (searched, nothing found; *not* a contradiction), `not_applicable` (term or PRO protein limited to the other species, or a human-only marker such as HLA-DRA or NCAM1/CD56 for mouse), or blank (not assessed). `species_scope` summarises them as `human`/`mouse`/`both`/`unresolved`. `human_*`/`mouse_*` hold the citation and exact quote, `note` and `checked_on` the reasoning and date. 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 or abstract | Curated | +| [nk_marker_audit_2026-10.md](nk_marker_audit_2026-10.md) | NK and group 1 ILC marker audit for Dr. Diehl (meeting 2026-10-05): counts per status, the HLA-DRA and CD56 cases, other CL issue candidates, open questions | Hand-written from `pro_marker_species_support.tsv` | Curated | +| [nk_hladr_conflicts_2026-10.tsv](nk_hladr_conflicts_2026-10.tsv) | One sheet of the conflicting "lacks HLA-DRA" NK assertions (`CL:0000938`, `CL:0000939`): definition PMIDs, what they say, quotes for and against. To attach to the CL issue | Hand-maintained | Curated | +| [plasmablast_marker_audit_2026-10.md](plasmablast_marker_audit_2026-10.md) | Plasmablast markers and lineage, with a proposal to move them from the generic term to a species-specific child (meeting 2026-10-05) | Hand-written | Curated | ## Not tracked diff --git a/reports/nk_hladr_conflicts_2026-10.tsv b/reports/nk_hladr_conflicts_2026-10.tsv new file mode 100644 index 0000000..4585d13 --- /dev/null +++ b/reports/nk_hladr_conflicts_2026-10.tsv @@ -0,0 +1,3 @@ +cl_id cl_label cl_assertion pr_id pr_label in_taxon definition_pmids what_definition_sources_say_about_hla_dr evidence_against_citation evidence_against_quote evidence_for_citation evidence_for_quote human_status mouse_status proposed_action checked_on +CL:0000938 CD16-negative, CD56-bright natural killer cell, human lacks_plasma_membrane_part (CL:4030046) PR:000002015 MHC class II histocompatibility antigen alpha chain DRA NCBITaxon:9606 Homo sapiens PMID:19796267; PMID:22343568 "PMID:19796267 (Verneris MR et al. 2009, PMC2770803): HLA-DR not mentioned in the full text. PMID:22343568 (Maecker HT et al. 2012, PMC3409649): mentions HLA-DR on NK cells only as an activation marker: ""The similar use of HLA-DR to track activated NK cells is a possibility that has been less well explored, but that might be equally fruitful."" Neither source states that NK cells lack HLA-DR." Erokhina SA et al. 2018 (PMID: 29363179; PMC8063572) We have observed that HLA-DR expression in freshly isolated circulating NK cells was mostly associated with less differentiated CD56brightCD57− cells, although in some individuals it could also be found in terminally differentiated CD57+ cells. Evans JH et al. 2011 (PMID: 21491418; PMC3549558) In contrast, only 2–5.5% (median 3.5%) of fresh NK cells ex vivo expressed HLA-DR contradicted not_applicable Remove (or disable) the 'lacks_plasma_membrane_part HLA-DRA' axiom until a source is found (Dr. Diehl, 2026-10-05). HLA-DR+ cells are a minority but are concentrated in this subset. 2026-10-05 +CL:0000939 CD16-positive, CD56-dim natural killer cell, human lacks_plasma_membrane_part (CL:4030046) PR:000002015 MHC class II histocompatibility antigen alpha chain DRA NCBITaxon:9606 Homo sapiens PMID:19796267; PMID:22343568 "PMID:19796267 (Verneris MR et al. 2009, PMC2770803): HLA-DR not mentioned in the full text. PMID:22343568 (Maecker HT et al. 2012, PMC3409649): mentions HLA-DR on NK cells only as an activation marker: ""The similar use of HLA-DR to track activated NK cells is a possibility that has been less well explored, but that might be equally fruitful."" Neither source states that NK cells lack HLA-DR." Erokhina SA et al. 2018 (PMID: 29363179; PMC8063572) However, in some individuals CD56dimCD57+HLA-DR+ cells were observed, which comprise terminally differentiated but at the same time activated NK cells. Erokhina SA et al. 2018 (PMID: 29363179; PMC8063572) The proportion of HLA-DR-positive cells in peripheral blood was much higher in CD56bright cells than in CD56dim cells for the most part of the volunteers contradicted not_applicable Same axiom, same definition sources, weaker contradiction (HLA-DR+ CD56dim cells only in some individuals). Decide together with CL:0000938. 2026-10-05 diff --git a/reports/nk_marker_audit_2026-10.md b/reports/nk_marker_audit_2026-10.md new file mode 100644 index 0000000..5f03c00 --- /dev/null +++ b/reports/nk_marker_audit_2026-10.md @@ -0,0 +1,142 @@ +# NK and group 1 ILC marker audit, October 2026 + +Dr. Diehl's request from the 5 October 2026 meeting: re-check every marker +that CL asserts on natural killer cell terms and group 1 ILC terms, keeping +human and mouse verdicts apart. Row-level results are in +[pro_marker_species_support.tsv](pro_marker_species_support.tsv) (rows with +`audit_batch = nk_2026-10`). The HLA-DR conflicts are exported on one sheet in +[nk_hladr_conflicts_2026-10.tsv](nk_hladr_conflicts_2026-10.tsv). The +plasmablast part of the same request is in +[plasmablast_marker_audit_2026-10.md](plasmablast_marker_audit_2026-10.md). + +## Scope and method + +- **Terms:** `CL:0001067` group 1 innate lymphoid cell and every CL subclass + of it, pulled from Ubergraph on 2026-10-05: 37 terms, including + `CL:0000623` natural killer cell and all its descendants. 28 of them carry + directly asserted marker axioms (`has plasma membrane part`, + `lacks_plasma_membrane_part`, high/low amount, `has part`), giving + **66 term–marker pairs**. The other 9 have no marker axioms of their own. +- **Evidence:** every `supported` or `contradicted` verdict has a quote checked + word for word against the paper's Europe PMC full text, or against the + abstract where no open-access full text exists (Chiossone 2009 only). The + build script stops if any quote is not verbatim. +- **Status values** (`human_status`, `mouse_status`, one per species): + +| Value | Meaning | +|---|---| +| `supported` | A quote supports the assertion as CL states it. For "lacks X", evidence that X is absent counts as support. | +| `contradicted` | A quote goes against the assertion. When there is also a supporting quote, it goes in `counter_quote`, so both sides are recorded. | +| `no_evidence_found` | Searched and found nothing. **This is not a contradiction.** `note` says what was searched. | +| `not_applicable` | The question doesn't apply to this species: the CL term is limited to the other species (label ends ", human" or ", mouse"), the PRO term is the other species' protein, or the marker is human-only (HLA-DRA, NCAM1/CD56 for NK cells). | +| *(blank)* | Not assessed yet. | + +## Counts + +| Term group | Pairs | Human: supported / contradicted / no evidence / not applicable | Mouse: supported / contradicted / no evidence / not applicable | +|---|---|---|---| +| Generic (no species in label) | 5 | 5 / 0 / 0 / 0 | 0 / 1 / 4 / 0 | +| Human-specific (", human") | 34 | 21 / 2 / 11 / 0 | 0 / 0 / 0 / 34 | +| Mouse-specific (", mouse") | 27 | 0 / 0 / 0 / 27 | 21 / 1 / 5 / 0 | +| **All NK / group 1 ILC** | **66** | **26 / 2 / 11 / 27** | **21 / 2 / 9 / 34** | + +Only 5 pairs sit on generic terms: the two lineage-negative markers on +`CL:0000623` and the three positive markers on `CL:0000937` pre-natural killer +cell. Generic `CL:0000623` asserts no positive marker, which matches Dr. +Diehl's principle that high-level terms stay (near) markerless. + +## Cases requested in the meeting + +### HLA-DRA on the "CD16-negative" NK class + +- The "CD16-negative" class is **`CL:0000938` CD16-negative, CD56-bright + natural killer cell, human**. It asserts `lacks_plasma_membrane_part` + `PR:000002015` (HLA-DRA). +- **No CL term asserts that NK cells are HLA-DR positive.** The sibling + `CL:0000939` CD16-positive, CD56-dim natural killer cell, human *also* + asserts "lacks HLA-DRA". No NK or ILC definition in CL mentions HLA-DR, and + the only HLA-DRA-positive axioms in CL are on activated T cells and + "dendritic cell, human". The "two definitions, one positive and one + negative" Dr. Diehl described could not be found in current CL (Ubergraph, + 2026-10-05; local CL release 2026-03-26). See open question 1. +- **Neither definition source supports "lacks HLA-DRA".** Both terms cite + PMID:19796267 and PMID:22343568. The first never mentions HLA-DR. The second + mentions it on NK cells only as an activation marker: "The similar use of + HLA-DR to track activated NK cells is a possibility that has been less well + explored, but that might be equally fruitful." +- **Literature:** resting human NK cells are mostly HLA-DR negative: "only + 2–5.5% (median 3.5%) of fresh NK cells ex vivo expressed HLA-DR" (Evans + 2011, PMID:21491418). But an HLA-DR+ subset exists ex vivo, mainly CD56bright: + "HLA-DR expression in freshly isolated circulating NK cells was mostly + associated with less differentiated CD56brightCD57− cells" (Erokhina 2018, + PMID:29363179). CD56dim HLA-DR+ cells were seen "in some individuals". +- **Verdict:** `contradicted` in human for both terms (stronger for + `CL:0000938`); `not_applicable` in mouse. + +### NCAM1 / CD56 + +CD56 is asserted on 5 NK terms, all of them human-specific (`CL:0000938`, +`CL:0000939`, `CL:0002338`, `CL:0002343`, `CL:0002344`). All have +`mouse_status = not_applicable`. **No generic or cross-species NK term asserts +CD56.** For mouse: "Because mice lack CD56, murine NK cell subsets are +classified using alternative markers, particularly CD27 and Mac-1" (Kim 2026, +PMID:41898531). + +This conflicts with an earlier draft in this repo: the unfiled `NK` row in +[gaps.tsv](gaps.tsv) and the "Natural killer cell missing CD56 marker axiom" +entry in [cl_term_issues.md](cl_term_issues.md) propose *adding* CD56 to +generic `CL:0000623`. Under Dr. Diehl's rule, that proposal should be +withdrawn. + +### Terms that mix human-only and mouse-only markers + +**None found.** Every human-labelled term carries only human-applicable +markers, and every mouse-labelled term only mouse-applicable ones (NK1.1, +Ly49, DX5, CD27/CD11b subsets). The generic terms carry only lineage-negative +markers (`CL:0000623`) or progenitor markers (`CL:0000937`). + +### Lineage-negative markers on generic NK (`CL:0000623`) + +`lacks CD20` and `lacks CD14` are both `supported` in human and +`no_evidence_found` in mouse. Mouse NK studies gate out CD3/TCR and CD19, not +CD14 or CD20, so the literature is silent rather than contradictory. Dr. +Diehl's view that CD20 is safe for mouse is recorded in `note` as expert +opinion. + +## Other findings (issue candidates) + +| # | Term(s) | Finding | Status | +|---|---|---|---| +| 1 | `CL:0002348`, `CL:0002349` | The definitions cite **PMID:1994922**, which is an unrelated 1991 paper (Liang MH, pulmonary venoocclusive disease). This is probably a typo for PMID:19949422 (Andrews 2010), which `CL:0002345` and `CL:0002347` cite. | Citation error | +| 2 | `CL:0002439`–`CL:0002448` (10 terms) | The definitions read "A NK1.1-positive T cell that is …", but the terms are NK cells (parent `CL:0002438` NK1.1-positive natural killer cell, mouse). | Definition error | +| 3 | `CL:0002345` | Asserts DX5 (CD49b, `PR:000001008`) **positive** on an immature NK cell. Mouse iNK cells "lack CD49b expression" (Riggan 2019, PMID:31500958). Its sibling `CL:0002346` is DX5-negative. | Mouse contradicted | +| 4 | `CL:0000937` pre-NK (generic) | Asserts CD122 positive. The earliest mouse pre-NKP "does not express IL-2Rβ (CD122)" (Fathman 2011, PMID:21931117); only the later rNKP does. | Mouse contradicted | +| 5 | `CL:0002343` decidual NK, human | Asserts galectin-1 as `has plasma membrane part`. The cited source calls it one of "two secreted proteins". Its expression is supported but the relation isn't; `expresses` would fit the evidence. | Relation question | +| 6 | `CL:0002438` and children | NK1.1 is strain-restricted: "C57BL/6 and SJL mice use NK1.1 for identification, whereas BALB/c mice … rely on CD49b and NKp46" (Qin 2024, PMID:39628473). | Note for definition | +| 7 | `CL:0002338`, `CL:0002344` (human) | The definitions of these human immature NK terms cite only a mouse NK progenitor review (PMID:12457618). | Citation scope | +| 8 | `CL:0002442` | Unlike its siblings, its parent is `CL:0000623` rather than `CL:0002438`. | Hierarchy | +| 9 | `CL:0002426` vs `CL:0002347` | "CD11b-positive, CD27-positive natural killer cell, mouse" and "CD27-high, CD11b-high natural killer cell, mouse" may be the same population. | Possible duplicate | + +## Open questions for Alex and Dr. Diehl + +1. **Which term has the HLA-DR-positive definition?** Nothing in current CL + matches. Could it be a different resource, an older CL release, or + `CL:0000939` (which is also "lacks")? If it's the latter, the proposed + issue becomes "drop 'lacks HLA-DRA' from both CD56-bright and CD56-dim". +2. **CD14 in mouse NK:** `no_evidence_found`, not contradicted. Is that good + enough to keep the axiom on generic `CL:0000623`, or do you want a mouse + source before it stays? +3. **Pre-NK (`CL:0000937`):** its CD34/CD117/CD122 markers are supported in + human only if CL's "pre-NK" corresponds to human stage 2, and CD122 is + contradicted for the earliest mouse stage. Should these markers move to a + human child, as with plasmablast? +4. **ILC1, human (`CL:0001077`) IL-7Rα:** this is the standard gate, but + Riggan 2019 argues it may miss IL-7Rα-negative human ILC1. Keep as is? +5. **Withdraw the old "add CD56 to `CL:0000623`" draft?** (See NCAM1 above.) + +## Reproducing + +The subtree and marker axioms come from Ubergraph (SPARQL, 2026-10-05). The +literature came from Europe PMC. When Europe PMC's full-text endpoint returned +HTTP 500, the same JATS XML was fetched from NCBI PMC efetch. Quotes were +checked with `literature_evidence.check_quote`. diff --git a/reports/plasmablast_marker_audit_2026-10.md b/reports/plasmablast_marker_audit_2026-10.md new file mode 100644 index 0000000..563a8bf --- /dev/null +++ b/reports/plasmablast_marker_audit_2026-10.md @@ -0,0 +1,83 @@ +# Plasmablast marker audit, October 2026 + +Task D from Dr. Diehl's 5 October 2026 meeting. His principle: **B cell stays +markerless, "CD19-positive B cell" covers mammals, and the generic plasmablast +term loses CD27 and similar markers, which move to a mammal-specific child +term.** Row-level verdicts are in +[pro_marker_species_support.tsv](pro_marker_species_support.tsv) +(`cl_id = CL:0000980`, `audit_batch = nk_2026-10`). The status values are +defined in [nk_marker_audit_2026-10.md](nk_marker_audit_2026-10.md#scope-and-method). + +## Current CL lineage and markers + +Pulled from Ubergraph on 2026-10-05. Only directly asserted marker axioms are +shown; the `in taxon` values are as asserted. + +| Term | Asserted parents | Own markers | In taxon | +|---|---|---|---| +| lymphocyte of B lineage (`CL:0000945`) | lymphocyte | none | none | +| B cell (`CL:0000236`) | `CL:0000945` | none | none | +| lymphocyte of B lineage, CD19-positive (`CL:0001200`) | `CL:0000945` | CD19 positive, lacks CD3 | **Mammalia** (`NCBITaxon:40674`) | +| B cell, CD19-positive (`CL:0001201`) | `CL:0000236`, `CL:0001200` | none | none (inherits Mammalia) | +| mature B cell (`CL:0000785`) | `CL:0001201`, professional antigen presenting cell | none | none (inherits Mammalia) | +| antibody secreting cell (`CL:0000946`) | `CL:0000945` | none | none | +| **plasmablast** (`CL:0000980`) | `CL:0000785`, `CL:0000946` | CD38 high, CD27 high, lacks CD20, lacks CD138 | none (inherits Mammalia) | + +Plasmablast has two parents, mature B cell and antibody secreting cell. Its +asserted children are IgD, IgE, IgG, IgM and IgA plasmablast +(`CL:0000949`, `CL:0000950`, `CL:0000982`, `CL:0000983`, `CL:0000984`) and +CD86-positive plasmablast (`CL:0001202`). Their markers were not reviewed here. + +The definition reads "An activated mature (naive or memory) B cell that is +secreting immunoglobulin, typified by being CD27-positive, CD38-positive, +CD138-negative". It cites PMC2673126 (Jackson SM et al. 2009, PMID:19059880), +a study of **human** germinal centre B cells. The text available from Europe +PMC describes plasmablasts as "IgD−CD38++CD27+" and says nothing about CD138. + +## Finding: plasmablast is already mammal-only by inheritance + +`mature B cell` is a subclass of `B cell, CD19-positive`, which is a subclass +of `lymphocyte of B lineage, CD19-positive`, and that term is `in taxon +Mammalia`. So plasmablast, and every mature B cell, is already restricted to +mammals through its parents, whatever markers it carries. Removing CD27 from +plasmablast alone won't make it usable for zebrafish or other non-mammals; the +`mature B cell` → `B cell, CD19-positive` link would also have to change. This +is a bigger change than Dr. Diehl described, so it is flagged rather than +proposed (see question 1). + +## Marker verdicts on plasmablast (`CL:0000980`) + +| Assertion | Human | Mouse | Evidence | +|---|---|---|---| +| CD38 high (`PR:000001408`) | supported | no_evidence_found | Human: Georgopoulos 2026 (PMID:42653236). Mouse studies gate plasmablasts on B220/CD138 instead. | +| CD27 high (`PR:000001963`) | supported | no_evidence_found | Human: same quote. | +| lacks CD20 (`PR:000001289`) | supported | no_evidence_found | Human: Griffin & Rothstein 2012 (PMID:22654880). | +| lacks CD138 (`PR:000001935`) | **contradicted** | **contradicted** | Human: "short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)" (PMID:41771939). Mouse: "plasmablasts as B220+CD138+" (PMID:42774878). No supporting quote found. | + +None of the four markers has mouse support, so the evidence does not yet +justify a **mammal**-level child. It supports a **human** child. + +## Proposal + +| Term | Proposed parent | Markers | Taxon | Evidence status | New term? | +|---|---|---|---|---|---| +| plasmablast (`CL:0000980`) | unchanged (mature B cell; antibody secreting cell) | **none**: remove CD38 high, CD27 high, lacks CD20, lacks CD138 | none | n/a | no | +| plasmablast, human *(proposed)* | plasmablast (`CL:0000980`) | CD38 high, CD27 high, lacks CD20 | in taxon Homo sapiens | All three supported in human | **yes** | +| plasmablast, mouse *(optional, proposed)* | plasmablast (`CL:0000980`) | CD138 (syndecan-1) positive | in taxon Mus musculus | Mouse supported ("plasmablasts as B220+CD138+", PMID:42774878); B220 not proposed as an axiom until its PRO term is looked up | yes | + +- **Drop "lacks CD138" everywhere.** It is contradicted in both species and its + definition source does not mention CD138. +- **Naming:** follows the existing ", human" / ", mouse" convention (no + Hsap/Mmus renaming). If Dr. Diehl prefers a single mammal-level child, it + would need mouse evidence for CD27 and CD38, which wasn't found. +- **Children:** the IgX plasmablast terms and CD86-positive plasmablast stay + under the generic term until their own markers are reviewed. + +## Questions for Alex and Dr. Diehl + +1. Should `mature B cell` stay under `B cell, CD19-positive` (making all + mature B cells, plasmablasts included, mammal-only), or be moved so that + plasmablast can be used outside mammals? +2. Should the child be "plasmablast, human" (what the evidence supports) or a + mammal-level term (what was asked for, but with no mouse support yet)? +3. Is a "plasmablast, mouse" term worth proposing now, or later? diff --git a/reports/pro_marker_species_support.tsv b/reports/pro_marker_species_support.tsv index 80309a8..c64177f 100644 --- a/reports/pro_marker_species_support.tsv +++ b/reports/pro_marker_species_support.tsv @@ -1,88 +1,145 @@ -cl_id cl_label pr_id pr_label cd_synonym species_support evidence_source citation quote source_ref species_scope human_citation human_quote mouse_citation mouse_quote note checked_on -CL:0000623 natural killer cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303). archive/2026-09_literature_narratives/nk_cell_markers.md unresolved Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303).""" Human supported (verified quote, reused from the legacy check). Mouse: no evidence found in open-access literature (Europe PMC search for mouse NK cells with CD20/CD14); not tested as far as found. 2026-09-28 -CL:0000623 natural killer cell PR:000001889 CD14 molecule CD14 (label) human m2_literature_report Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes archive/2026-09_literature_narratives/nk_cell_markers.md unresolved Van Acker HH et al. 2017 (PMID: 28791027; PMC5522883) """there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes""" Human supported (verified quote, reused from the legacy check). Mouse: no evidence found in open-access literature; not tested as far as found. 2026-09-28 -CL:0000624 CD4-positive, alpha-beta T cell PR:000025402 T cell receptor co-receptor CD8 CD8 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000624 CD4-positive, alpha-beta T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000625 CD8-positive, alpha-beta T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000625 CD8-positive, alpha-beta T cell PR:000025402 T cell receptor co-receptor CD8 CD8 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000771 eosinophil PR:000001254 C-C chemokine receptor type 1 CD191 (exact) insufficient_evidence none CD191/CCR1 not among the markers studied in PMID:38666394 (CCR3/CD193 is, but not CCR1); no other eosinophil-specific CD191 evidence found via targeted EuropePMC search. -CL:0000771 eosinophil PR:000001255 C-C chemokine receptor type 3 CD193 (exact) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 -CL:0000771 eosinophil PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 -CL:0000771 eosinophil PR:000001343 CD69 molecule CD69 (label) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 -CL:0000771 eosinophil PR:000005178 CD9 molecule CD9 (label) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 -CL:0000775 neutrophil PR:000001479 low affinity immunoglobulin gamma Fc region receptor II CD32 (broad) human europepmc_search Su K et al. 2007 (PMID:17312177; DOI:10.4049/jimmunol.178.5.3272) -- FcγRIIb (CD32B) expression profiling in human circulating leukocytes we found that FcgammaRIIb is expressed on the cell surface of circulating B lymphocytes, monocytes, neutrophils, myeloid dendritic cells (DCs), and at very low levels on plasmacytoid DCs from some donors https://europepmc.org/article/MED/17312177 -CL:0000775 neutrophil PR:000001879 leukosialin CD43 (related) insufficient_evidence none CD43 not found in any targeted EuropePMC search in a human-neutrophil-specific context ('CD43 leukosialin human neutrophil' returned unrelated papers). -CL:0000786 plasma cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000786 plasma cell PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000787 memory B cell PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) -- describes the plasmablast/plasma-cell transition boundary, not memory B cells directly, but confirms CD138 as a human B-lineage differentiation marker as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000787 memory B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) Mature B cells typically express both CD19 and CD20. archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000788 naive B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**N**: CD19+ CD27− CD38− CD24− IgD+"" [naive B cell gating entry, Table 1]" archive/2026-09_literature_narratives/b_cell_markers.md Martin VG et al. 2016 (PMID: 27994589; PMC5133252) """transitional (IgD+CD27−CD10+), and naïve (IgD+CD27−CD10−)""" Legacy human quote (Woodruff 2020 table) not verifiable; replaced by verified quote (literature/evidence.tsv EV00008). Mouse not yet assessed. 2026-09-28 -CL:0000788 naive B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) Mature B cells typically express both CD19 and CD20. archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies. archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) human m2_literature_report Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies. archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000814 mature NK T cell PR:000001874 KLRB1-like protein human m2_literature_report Lal KG et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) we defined iNKT cell subsets by the co-expression of TCR Vα24 and Vβ11 among CD3+ cells, and further through their expression of CD4 and CD161 archive/2026-09_literature_narratives/inkt_markers.md -CL:0000818 transitional stage B cell PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−) archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000818 transitional stage B cell PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−) archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000818 transitional stage B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none CD20 positivity on transitional B cells is not stated verbatim in archive/2026-09_literature_narratives/b_cell_markers.md -- the report only confirms CD20 on 'mature B cells' generally (Griffin & Rothstein 2012), not the transitional stage specifically. -CL:0000860 classical monocyte PR:000001199 C-C chemokine receptor type 2 CD192 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0000860 classical monocyte PR:000001002 CD19 molecule CD19 (label) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0000860 classical monocyte PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0000860 classical monocyte PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0000875 non-classical monocyte PR:000001206 CX3C chemokine receptor 1 insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0000875 non-classical monocyte PR:000001002 CD19 molecule CD19 (label) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0000875 non-classical monocyte PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0000875 non-classical monocyte PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000898 naive T cell PR:000001318 L-selectin CD62 (exact); CD62L (exact) human m2_literature_report Kamigaichi A et al. 2026 (PMID: 42047825; DOI: 10.1007/s00262-026-04357-4; PMC: PMC13125411) -- confirms CD62L used on human CD4+ T cells, though in a Th1 (not naive-T) context Th1 (CXCR3+CCR4−CCR6− CD62LlowCD4+ T cells) archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000898 naive T cell PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) insufficient_evidence none CD44 not mentioned anywhere in archive/2026-09_literature_narratives/t_cell_markers.md; not found via a targeted EuropePMC search either ('CD44 human naive T cell surface marker' returned unrelated tissue-resident-memory/B-cell papers). -CL:0000898 naive T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000898 naive T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000898 naive T cell PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000904 central memory CD4-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA− archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000904 central memory CD4-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA− archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000905 effector memory CD4-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7−/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000905 effector memory CD4-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7−/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000907 central memory CD8-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000907 central memory CD8-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000913 effector memory CD8-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000913 effector memory CD8-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md -CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells. archive/2026-09_literature_narratives/nk_cell_markers.md human Rebuffet L et al. 2024 (PMID: 38956378; PMC11291291) """human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells.""" PMID: 41898531; PMC13027196 (2026) """Because mice lack CD56, murine NK cell subsets are classified using alternative markers, particularly CD27 and Mac-1.""" CL term is human-specific; mouse not applicable. Human supported. Mouse contradicted: mouse NK cells are not classified by CD56 (mouse_quote), although a mouse ortholog exists (Ncam1, MGI:97281, Alliance of Genome Resources orthology). Biological/usage difference, not a missing reagent. 2026-09-29 -CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) CD56bright human NK cells express high levels of CD62L (l-selectin) and CD94 but absent or low levels of CD16 and KIRs archive/2026-09_literature_narratives/nk_cell_markers.md human Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """CD56bright human NK cells express high levels of CD62L (l-selectin) and CD94 but absent or low levels of CD16 and KIRs""" CL term is human-specific; mouse not applicable. Human supported (verified quote, reused). Mouse: not applicable as asked; the CL term is human-specific and mice have no CD56-bright NK subset (see the CD56 row). Note PR:000001483 itself is defined by the mouse Fcgr3 gene (see reports/cl_term_issues.md). 2026-09-29 -CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000002015 MHC class II histocompatibility antigen alpha chain DRA human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1) archive/2026-09_literature_narratives/nk_cell_markers.md unresolved PMID: 42450353; PMC13362507 (2026) """the proportion of HLA-DR+CD56bright cells ex vivo""" CL term is human-specific; mouse not applicable. Human NOT clearly supported: this quote reports HLA-DR+ CD56-bright cells, and the legacy quote (Rebuffet 2024, HLA-D genes in cluster NK3B) is about a different cluster. Mouse: not checked; PRO notes 'The mouse ortholog is called H2-Ea' (PR:000002015 definition, OLS4). 2026-09-29 -CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001319 SLAM family member 5 CD84 (exact) insufficient_evidence none No CD84-on-NK-cell evidence found in archive/2026-09_literature_narratives/nk_cell_markers.md or a targeted EuropePMC search ('CD84 human natural killer cell surface marker' -- top hits were CD84 in MDSCs/breast cancer/CLL, none NK-specific). unresolved CL term is human-specific; mouse not applicable. No human or mouse evidence found for CD84 on CD56-bright NK cells (legacy verdict was insufficient_evidence). 2026-09-29 -CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells. archive/2026-09_literature_narratives/nk_cell_markers.md -CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000002015 MHC class II histocompatibility antigen alpha chain DRA human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1) archive/2026-09_literature_narratives/nk_cell_markers.md -CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) In contrast, CD56dim NK cells are CD16hi and express more KIRs but less CD94 and CD62L; they predominate in PB archive/2026-09_literature_narratives/nk_cell_markers.md -CL:0000960 T3 B cell PR:000001318 L-selectin CD62 (exact); CD62L (exact) insufficient_evidence none CD62L not mentioned in the T3-transitional context in archive/2026-09_literature_narratives/b_cell_markers.md (only mentioned for DN2 B cells: 'lack of CXCR5 and CD62L expression', Sachinidis 2021, a different B cell subset). -CL:0000960 T3 B cell PR:000001338 complement receptor type 2 CD21 (exact) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells archive/2026-09_literature_narratives/b_cell_markers.md Martin VG et al. 2016 (PMID: 27994589; PMC5133252) """the gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells""" Legacy quote differed from the paper in capitalisation only; exact text recorded here. Mouse not yet assessed. 2026-09-28 -CL:0000960 T3 B cell PR:000001880 low affinity immunoglobulin epsilon Fc receptor CD23 (exact); CD23A (related) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells archive/2026-09_literature_narratives/b_cell_markers.md Martin VG et al. 2016 (PMID: 27994589; PMC5133252) """the gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells""" Legacy quote differed from the paper in capitalisation only; exact text recorded here. Mouse not yet assessed. 2026-09-28 -CL:0000970 unswitched memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**M**: CD19+ CD27+ CD38−/lo"" [memory B cell gating entry]" archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000972 class switched memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**M**: CD19+ CD27+ CD38−/lo"" [memory B cell gating entry]" archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000980 plasmablast PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**ASC**: CD19+ CD27+ CD38hi"" and ""**M**: CD19+ CD27+ CD38−/lo"" and" archive/2026-09_literature_narratives/b_cell_markers.md unresolved PMID: 42653236; PMC13513640 (2026) """Plasmablasts and Long-Lived Plasma Cells (CD19+CD20−IgD−CD27hiCD38hi/CD138+CD38+CD19−/Low)""" Human supported (the legacy Woodruff 2020 table quote could not be verified; no open-access full text). Mouse: no evidence found for CD38 on mouse plasmablasts; mouse studies gate plasmablasts on B220/CD138 instead. 2026-09-28 -CL:0000980 plasmablast PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**ASC**: CD19+ CD27+ CD38hi"" and ""**M**: CD19+ CD27+ CD38−/lo"" and" archive/2026-09_literature_narratives/b_cell_markers.md unresolved PMID: 42653236; PMC13513640 (2026) """Plasmablasts and Long-Lived Plasma Cells (CD19+CD20−IgD−CD27hiCD38hi/CD138+CD38+CD19−/Low)""" Human supported (legacy Woodruff 2020 quote not verifiable). Mouse: no evidence found for CD27 on mouse plasmablasts. 2026-09-28 -CL:0000980 plasmablast PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired archive/2026-09_literature_narratives/b_cell_markers.md unresolved Griffin DO & Rothstein TL 2012 (PMID: 22654880; PMC3360193) """as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired""" Human supported (verified quote, reused from the legacy check). Mouse: no evidence found for CD20 on mouse plasmablasts. 2026-09-28 -CL:0000980 plasmablast PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**CD138neg ASC**: CD138−"" and ""**CD138pos ASC**: CD138+"" [gating labels distinguishing" archive/2026-09_literature_narratives/b_cell_markers.md unresolved PMID: 41771939; PMC13066544 (2026) """short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)""" PMID: 42774878; PMC13594723 (2026) """plasmablasts as B220+CD138+""" CONTRADICTED in mouse: mouse plasmablasts are defined as CD138+ (mouse_quote). Human evidence conflicting: the human_quote defines plasmablasts as CD138++ in one scheme, contradicting 'lacks CD138'. Legacy human quote (Woodruff 2020 gating labels) could not be verified: treat the legacy 'human' verdict as insufficient_evidence. 2026-09-28 -CL:0000981 double negative memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Sachinidis A & Garyfallos A 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) Double negative (DN) B cells, also known as atypical memory B cells, constitute a B cell population that lacks expression of immunoglobulin D and CD27 memory marker. archive/2026-09_literature_narratives/b_cell_markers.md -CL:0000990 conventional dendritic cell PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123− archive/2026-09_literature_narratives/dc_markers.md -CL:0001058 plasmacytoid dendritic cell, human PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123− archive/2026-09_literature_narratives/dc_markers.md -CL:0001058 plasmacytoid dendritic cell, human PR:000001889 CD14 molecule CD14 (label) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DCs were defined as live, LIN(CD3, CD19, CD56)−CD14−HLA-DR+ cells. archive/2026-09_literature_narratives/dc_markers.md -CL:0001058 plasmacytoid dendritic cell, human PR:000001865 interleukin-3 receptor class 2 alpha chain CD123 (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) pDCs are CD11c− CD123+ cells best characterized for their type I interferon archive/2026-09_literature_narratives/dc_markers.md Guilliams M et al. 2016 (PMID: 27637149; PMC5040826) """CD123hiCD303hi (human) pDCs""" Legacy human quote (Rhodes 2019) not found in the paper; replaced by verified quote (literature/evidence.tsv EV00081). Mouse not yet assessed. 2026-09-28 -CL:0001065 innate lymphoid cell PR:000001002 CD19 molecule CD19 (label) human m2_literature_report Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696) Subsequently we gated out non‐relevant lineages using antibodies against CD3, CD4, TCRαβ, and TCRγδ (T cells), CD19 (B cells) CD14 (monocytes) FcRεR1a (mast cells), BDCA2 (pDCs), CD123 (pDCs, basophils), and CD34 (hematopoietic progenitors). archive/2026-09_literature_narratives/ilc_markers.md -CL:0001065 innate lymphoid cell PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) human m2_literature_report Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696) We gated for lymphocytes, excluded doublets and dead cells and selected CD45+CD3− cells archive/2026-09_literature_narratives/ilc_markers.md -CL:0002393 intermediate monocyte PR:000001002 CD19 molecule CD19 (label) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0002393 intermediate monocyte PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0002393 intermediate monocyte PR:000001199 C-C chemokine receptor type 2 CD192 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0002393 intermediate monocyte PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. -CL:0002394 CD141-positive myeloid dendritic cell PR:000002105 thrombomodulin CD141 (exact) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DC1 corresponds to the cross-presenting CD141/BDCA-3+ cDC1, which is best marked by CLEC9A archive/2026-09_literature_narratives/dc_markers.md -CL:0002399 CD1c-positive myeloid dendritic cell PR:000002027 T-cell surface glycoprotein CD1c CD1C (exact); CD1c (label) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DC2 and DC3 correspond to new subdivisions of the CD1C/BDCA-1+ cDC2 archive/2026-09_literature_narratives/dc_markers.md -CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) human species from PRO label 2026-09-28 -CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) human species from PRO label 2026-09-28 -CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) human species from PRO label 2026-09-28 -CL:0001078 group 3 innate lymphoid cell, human PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) human species from PRO label 2026-09-28 -CL:0001081 group 2 innate lymphoid cell, human PR:P01589 interleukin-2 receptor subunit alpha (human) CD25 (exact) human species from PRO label 2026-09-28 -CL:0001081 group 2 innate lymphoid cell, human PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) human species from PRO label 2026-09-28 -CL:0001081 group 2 innate lymphoid cell, human PR:P23771 trans-acting T-cell-specific transcription factor GATA-3 (human) human species from PRO label 2026-09-28 -CL:0001081 group 2 innate lymphoid cell, human PR:Q12918 killer cell lectin-like receptor subfamily B member 1 (human) CD161 (exact) human species from PRO label 2026-09-28 -CL:0001081 group 2 innate lymphoid cell, human PR:Q9Y5Y4 prostaglandin D2 receptor 2 (human) CD294 (exact) human species from PRO label 2026-09-28 -CL:4052055 mature NK T cell, human PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) human species from PRO label 2026-09-28 +cl_id cl_label pr_id pr_label cd_synonym species_support evidence_source citation quote source_ref species_scope human_status mouse_status human_citation human_quote mouse_citation mouse_quote counter_citation counter_quote note checked_on audit_batch +CL:0000623 natural killer cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303). archive/2026-09_literature_narratives/nk_cell_markers.md unresolved supported no_evidence_found Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303).""" Generic NK term. Human supported. Mouse: no evidence found (not contradicted). Europe PMC full-text queries (mouse NK1.1+/NKp46+ NK cells with CD14-/CD20- gating, 2026-10-05) found mouse NK gates on CD3/TCR and CD19, not CD14 or CD20. Dr. Diehl (meeting 2026-10-05) considers lacks-CD20 safe in mouse; expert opinion, not literature. 2026-10-05 nk_2026-10 +CL:0000623 natural killer cell PR:000001889 CD14 molecule CD14 (label) human m2_literature_report Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes archive/2026-09_literature_narratives/nk_cell_markers.md unresolved supported no_evidence_found Van Acker HH et al. 2017 (PMID: 28791027; PMC5522883) """there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes""" Generic NK term. Human supported. Mouse: no evidence found (not contradicted). Europe PMC full-text queries (mouse NK1.1+/NKp46+ NK cells with CD14-/CD20- gating, 2026-10-05) found mouse NK gates on CD3/TCR and CD19, not CD14 or CD20. Dr. Diehl was unsure about CD14 in mouse (meeting 2026-10-05). 2026-10-05 nk_2026-10 +CL:0000624 CD4-positive, alpha-beta T cell PR:000025402 T cell receptor co-receptor CD8 CD8 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000624 CD4-positive, alpha-beta T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000625 CD8-positive, alpha-beta T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000625 CD8-positive, alpha-beta T cell PR:000025402 T cell receptor co-receptor CD8 CD8 (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000771 eosinophil PR:000001254 C-C chemokine receptor type 1 CD191 (exact) insufficient_evidence none CD191/CCR1 not among the markers studied in PMID:38666394 (CCR3/CD193 is, but not CCR1); no other eosinophil-specific CD191 evidence found via targeted EuropePMC search. +CL:0000771 eosinophil PR:000001255 C-C chemokine receptor type 3 CD193 (exact) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 +CL:0000771 eosinophil PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 +CL:0000771 eosinophil PR:000001343 CD69 molecule CD69 (label) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 +CL:0000771 eosinophil PR:000005178 CD9 molecule CD9 (label) human europepmc_search (Cytometry B) 2024 (PMID:38666394; DOI:10.1002/cyto.b.22174) -- flow cytometric immunophenotyping of eosinophilopoiesis in normal human bone marrow candidate markers that included EMR-1, Siglec-8, CCR3, CD9, CD11a, CD11b, CD11c, CD13, CD16, CD29, CD34, CD38, CD45, CD44, CD49d, CD49f, CD54, CD62L, CD69, CD117, CD125 (IL-5Rα), HLA-DR, using 10 parameter flow cytometry https://europepmc.org/article/MED/38666394 +CL:0000775 neutrophil PR:000001479 low affinity immunoglobulin gamma Fc region receptor II CD32 (broad) human europepmc_search Su K et al. 2007 (PMID:17312177; DOI:10.4049/jimmunol.178.5.3272) -- FcγRIIb (CD32B) expression profiling in human circulating leukocytes we found that FcgammaRIIb is expressed on the cell surface of circulating B lymphocytes, monocytes, neutrophils, myeloid dendritic cells (DCs), and at very low levels on plasmacytoid DCs from some donors https://europepmc.org/article/MED/17312177 +CL:0000775 neutrophil PR:000001879 leukosialin CD43 (related) insufficient_evidence none CD43 not found in any targeted EuropePMC search in a human-neutrophil-specific context ('CD43 leukosialin human neutrophil' returned unrelated papers). +CL:0000786 plasma cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000786 plasma cell PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000787 memory B cell PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) -- describes the plasmablast/plasma-cell transition boundary, not memory B cells directly, but confirms CD138 as a human B-lineage differentiation marker as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000787 memory B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) Mature B cells typically express both CD19 and CD20. archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000788 naive B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**N**: CD19+ CD27− CD38− CD24− IgD+"" [naive B cell gating entry, Table 1]" archive/2026-09_literature_narratives/b_cell_markers.md supported Martin VG et al. 2016 (PMID: 27994589; PMC5133252) """transitional (IgD+CD27−CD10+), and naïve (IgD+CD27−CD10−)""" Legacy human quote (Woodruff 2020 table) not verifiable; replaced by verified quote (literature/evidence.tsv EV00008). Mouse not yet assessed. 2026-09-28 +CL:0000788 naive B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) Mature B cells typically express both CD19 and CD20. archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell PR:000001004 CD4 molecule CD4 (label) human m2_literature_report Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies. archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) human m2_literature_report Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR monoclonal antibodies. archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000814 mature NK T cell PR:000001874 KLRB1-like protein human m2_literature_report Lal KG et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) we defined iNKT cell subsets by the co-expression of TCR Vα24 and Vβ11 among CD3+ cells, and further through their expression of CD4 and CD161 archive/2026-09_literature_narratives/inkt_markers.md +CL:0000818 transitional stage B cell PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−) archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000818 transitional stage B cell PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−) archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000818 transitional stage B cell PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none CD20 positivity on transitional B cells is not stated verbatim in archive/2026-09_literature_narratives/b_cell_markers.md -- the report only confirms CD20 on 'mature B cells' generally (Griffin & Rothstein 2012), not the transitional stage specifically. +CL:0000860 classical monocyte PR:000001199 C-C chemokine receptor type 2 CD192 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0000860 classical monocyte PR:000001002 CD19 molecule CD19 (label) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0000860 classical monocyte PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0000860 classical monocyte PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0000875 non-classical monocyte PR:000001206 CX3C chemokine receptor 1 insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0000875 non-classical monocyte PR:000001002 CD19 molecule CD19 (label) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0000875 non-classical monocyte PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0000875 non-classical monocyte PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000898 naive T cell PR:000001318 L-selectin CD62 (exact); CD62L (exact) human m2_literature_report Kamigaichi A et al. 2026 (PMID: 42047825; DOI: 10.1007/s00262-026-04357-4; PMC: PMC13125411) -- confirms CD62L used on human CD4+ T cells, though in a Th1 (not naive-T) context Th1 (CXCR3+CCR4−CCR6− CD62LlowCD4+ T cells) archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000898 naive T cell PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) insufficient_evidence none CD44 not mentioned anywhere in archive/2026-09_literature_narratives/t_cell_markers.md; not found via a targeted EuropePMC search either ('CD44 human naive T cell surface marker' returned unrelated tissue-resident-memory/B-cell papers). +CL:0000898 naive T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000898 naive T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000898 naive T cell PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) human m2_literature_report Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) -- confirms CD25/CD127 as human T cell markers, though in a Treg (not naive-T) context; naive T cells are CD25-low/CD127-high, the inverse pattern from Treg In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate Tregs from effector T cells, which usually express high levels of CD127 archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000904 central memory CD4-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA− archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000904 central memory CD4-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7+/CD45RA− archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000905 effector memory CD4-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7−/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000905 effector memory CD4-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) CD3+/CD8−/CD4+/CCR7−/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000907 central memory CD8-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000907 central memory CD8-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Central Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000913 effector memory CD8-positive, alpha-beta T cell PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000913 effector memory CD8-positive, alpha-beta T cell PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) human m2_literature_report Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) -- CD8 Naive gating string quoted verbatim; the CD8 Effector Memory string was not separately captured in this M2 report, but the same CD45RA/CCR7 panel is applied orthogonally to CD4 and CD8 per the paper's design CD3+/CD8+/CD4−/CCR7+/CD45RA+ archive/2026-09_literature_narratives/t_cell_markers.md +CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells. archive/2026-09_literature_narratives/nk_cell_markers.md human supported not_applicable Rebuffet L et al. 2024 (PMID: 38956378; PMC11291291) """human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells.""" Kim Y et al. 2026 (PMID: 41898531; PMC13027196) """Because mice lack CD56, murine NK cell subsets are classified using alternative markers, particularly CD27 and Mac-1.""" CL term is human-specific; mouse not applicable. Human supported. CD56/NCAM1 is a human-only NK marker: the mouse quote shows mouse NK subsets are not classified by CD56, although a mouse ortholog exists (Ncam1, MGI:97281). 2026-10-05 nk_2026-10 +CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) CD56bright human NK cells express high levels of CD62L (l-selectin) and CD94 but absent or low levels of CD16 and KIRs archive/2026-09_literature_narratives/nk_cell_markers.md human supported not_applicable Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """CD56bright human NK cells express high levels of CD62L (l-selectin) and CD94 but absent or low levels of CD16 and KIRs""" CL term is human-specific; mouse not applicable. Human supported. PR:000001483 itself is defined by the mouse Fcgr3 gene (see reports/cl_term_issues.md). 2026-10-05 nk_2026-10 +CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000002015 MHC class II histocompatibility antigen alpha chain DRA human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1) archive/2026-09_literature_narratives/nk_cell_markers.md unresolved contradicted not_applicable Erokhina SA et al. 2018 (PMID: 29363179; PMC8063572) """We have observed that HLA-DR expression in freshly isolated circulating NK cells was mostly associated with less differentiated CD56brightCD57− cells, although in some individuals it could also be found in terminally differentiated CD57+ cells.""" Evans JH et al. 2011 (PMID: 21491418; PMC3549558) """In contrast, only 2–5.5% (median 3.5%) of fresh NK cells ex vivo expressed HLA-DR""" CL term is human-specific; mouse not applicable. CONTRADICTED in human: most resting NK cells are HLA-DR− (counter_quote), but an HLA-DR+ subset exists ex vivo and is concentrated in CD56bright cells (human_quote). Neither definition source supports 'lacks HLA-DRA': PMID:19796267 never mentions HLA-DR; PMID:22343568 mentions HLA-DR on NK cells only as an activation marker. HLA-DRA is human-only (PRO: mouse ortholog H2-Ea). See reports/nk_hladr_conflicts_2026-10.tsv. 2026-10-05 nk_2026-10 +CL:0000938 CD16-negative, CD56-bright natural killer cell, human PR:000001319 SLAM family member 5 CD84 (exact) insufficient_evidence none No CD84-on-NK-cell evidence found in archive/2026-09_literature_narratives/nk_cell_markers.md or a targeted EuropePMC search ('CD84 human natural killer cell surface marker' -- top hits were CD84 in MDSCs/breast cancer/CLL, none NK-specific). unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. No human evidence found for CD84 on CD56bright NK cells (Europe PMC 'CD84 AND CD56bright', 2026-10-05; legacy check also insufficient_evidence). 2026-10-05 nk_2026-10 +CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells. archive/2026-09_literature_narratives/nk_cell_markers.md human supported not_applicable Rebuffet L et al. 2024 (PMID: 38956378; PMC11291291) """human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells.""" CL term is human-specific; mouse not applicable. Human supported (CD56dim). CD56 is a human-only NK marker. 2026-10-05 nk_2026-10 +CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000002015 MHC class II histocompatibility antigen alpha chain DRA human m2_literature_report Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) -- indirect: HLA-D family expression shown on an adaptive NK subset (NK3B), not stated specifically for CD56bright/CD56dim Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1) archive/2026-09_literature_narratives/nk_cell_markers.md unresolved contradicted not_applicable Erokhina SA et al. 2018 (PMID: 29363179; PMC8063572) """However, in some individuals CD56dimCD57+HLA-DR+ cells were observed, which comprise terminally differentiated but at the same time activated NK cells.""" Erokhina SA et al. 2018 (PMID: 29363179; PMC8063572) """The proportion of HLA-DR-positive cells in peripheral blood was much higher in CD56bright cells than in CD56dim cells for the most part of the volunteers""" CL term is human-specific; mouse not applicable. CONTRADICTED in human for a subset: HLA-DR+ CD56dim cells occur in some individuals (human_quote), though HLA-DR+ cells are mostly CD56bright (counter_quote). Same definition sources as CL:0000938; neither supports 'lacks HLA-DRA'. See reports/nk_hladr_conflicts_2026-10.tsv. 2026-10-05 nk_2026-10 +CL:0000939 CD16-positive, CD56-dim natural killer cell, human PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) human m2_literature_report Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) In contrast, CD56dim NK cells are CD16hi and express more KIRs but less CD94 and CD62L; they predominate in PB archive/2026-09_literature_narratives/nk_cell_markers.md human supported not_applicable Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """In contrast, CD56dim NK cells are CD16hi and express more KIRs but less CD94 and CD62L""" CL term is human-specific; mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:0000960 T3 B cell PR:000001318 L-selectin CD62 (exact); CD62L (exact) insufficient_evidence none CD62L not mentioned in the T3-transitional context in archive/2026-09_literature_narratives/b_cell_markers.md (only mentioned for DN2 B cells: 'lack of CXCR5 and CD62L expression', Sachinidis 2021, a different B cell subset). +CL:0000960 T3 B cell PR:000001338 complement receptor type 2 CD21 (exact) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells archive/2026-09_literature_narratives/b_cell_markers.md supported Martin VG et al. 2016 (PMID: 27994589; PMC5133252) """the gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells""" Legacy quote differed from the paper in capitalisation only; exact text recorded here. Mouse not yet assessed. 2026-09-28 +CL:0000960 T3 B cell PR:000001880 low affinity immunoglobulin epsilon Fc receptor CD23 (exact); CD23A (related) human m2_literature_report Martin VG et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells archive/2026-09_literature_narratives/b_cell_markers.md supported Martin VG et al. 2016 (PMID: 27994589; PMC5133252) """the gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells""" Legacy quote differed from the paper in capitalisation only; exact text recorded here. Mouse not yet assessed. 2026-09-28 +CL:0000970 unswitched memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**M**: CD19+ CD27+ CD38−/lo"" [memory B cell gating entry]" archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000972 class switched memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**M**: CD19+ CD27+ CD38−/lo"" [memory B cell gating entry]" archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000980 plasmablast PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**ASC**: CD19+ CD27+ CD38hi"" and ""**M**: CD19+ CD27+ CD38−/lo"" and" archive/2026-09_literature_narratives/b_cell_markers.md unresolved supported no_evidence_found Georgopoulos C et al. 2026 (PMID: 42653236; PMC13513640) """Plasmablasts and Long-Lived Plasma Cells (CD19+CD20−IgD−CD27hiCD38hi/CD138+CD38+CD19−/Low)""" Generic term. Human supported. Mouse: no evidence found; mouse studies gate plasmablasts on B220/CD138 instead. Candidate to move to a mammal/human-specific child (reports/plasmablast_marker_audit_2026-10.md). 2026-10-05 nk_2026-10 +CL:0000980 plasmablast PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**ASC**: CD19+ CD27+ CD38hi"" and ""**M**: CD19+ CD27+ CD38−/lo"" and" archive/2026-09_literature_narratives/b_cell_markers.md unresolved supported no_evidence_found Georgopoulos C et al. 2026 (PMID: 42653236; PMC13513640) """Plasmablasts and Long-Lived Plasma Cells (CD19+CD20−IgD−CD27hiCD38hi/CD138+CD38+CD19−/Low)""" Generic term. Human supported. Mouse: no evidence found. Dr. Diehl: strip CD27 from the generic term (meeting 2026-10-05). 2026-10-05 nk_2026-10 +CL:0000980 plasmablast PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) human m2_literature_report Griffin DO & Rothstein TL 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired archive/2026-09_literature_narratives/b_cell_markers.md unresolved supported no_evidence_found Griffin DO & Rothstein TL 2012 (PMID: 22654880; PMC3360193) """as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 remains, as CD38/CD138 is acquired""" Generic term. Human supported. Mouse: no evidence found. 2026-10-05 nk_2026-10 +CL:0000980 plasmablast PR:000001935 syndecan-1 CD138 (exact) human m2_literature_report Woodruff MC et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) """**CD138neg ASC**: CD138−"" and ""**CD138pos ASC**: CD138+"" [gating labels distinguishing" archive/2026-09_literature_narratives/b_cell_markers.md unresolved contradicted contradicted Jamaluddin J et al. 2026 (PMID: 41771939; PMC13066544) """short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)""" Marques RF et al. 2026 (PMID: 42774878; PMC13594723) """plasmablasts as B220+CD138+""" Generic term. CONTRADICTED in both species: mouse plasmablasts are defined as CD138+; one human scheme defines plasmablasts as CD138++. Legacy human quote (Woodruff 2020) not verifiable. No supporting quote found for 'lacks CD138'. 2026-10-05 nk_2026-10 +CL:0000981 double negative memory B cell PR:000001963 CD27 molecule CD27 (label); CD27L (exact) human m2_literature_report Sachinidis A & Garyfallos A 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) Double negative (DN) B cells, also known as atypical memory B cells, constitute a B cell population that lacks expression of immunoglobulin D and CD27 memory marker. archive/2026-09_literature_narratives/b_cell_markers.md +CL:0000990 conventional dendritic cell PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123− archive/2026-09_literature_narratives/dc_markers.md +CL:0001058 plasmacytoid dendritic cell, human PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123− archive/2026-09_literature_narratives/dc_markers.md +CL:0001058 plasmacytoid dendritic cell, human PR:000001889 CD14 molecule CD14 (label) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DCs were defined as live, LIN(CD3, CD19, CD56)−CD14−HLA-DR+ cells. archive/2026-09_literature_narratives/dc_markers.md +CL:0001058 plasmacytoid dendritic cell, human PR:000001865 interleukin-3 receptor class 2 alpha chain CD123 (exact) human m2_literature_report Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) pDCs are CD11c− CD123+ cells best characterized for their type I interferon archive/2026-09_literature_narratives/dc_markers.md supported Guilliams M et al. 2016 (PMID: 27637149; PMC5040826) """CD123hiCD303hi (human) pDCs""" Legacy human quote (Rhodes 2019) not found in the paper; replaced by verified quote (literature/evidence.tsv EV00081). Mouse not yet assessed. 2026-09-28 +CL:0001065 innate lymphoid cell PR:000001002 CD19 molecule CD19 (label) human m2_literature_report Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696) Subsequently we gated out non‐relevant lineages using antibodies against CD3, CD4, TCRαβ, and TCRγδ (T cells), CD19 (B cells) CD14 (monocytes) FcRεR1a (mast cells), BDCA2 (pDCs), CD123 (pDCs, basophils), and CD34 (hematopoietic progenitors). archive/2026-09_literature_narratives/ilc_markers.md +CL:0001065 innate lymphoid cell PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) human m2_literature_report Krabbendam L et al. 2021 (PMID:33300130; DOI:10.1002/eji.202048696) We gated for lymphocytes, excluded doublets and dead cells and selected CD45+CD3− cells archive/2026-09_literature_narratives/ilc_markers.md +CL:0002393 intermediate monocyte PR:000001002 CD19 molecule CD19 (label) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0002393 intermediate monocyte PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0002393 intermediate monocyte PR:000001199 C-C chemokine receptor type 2 CD192 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0002393 intermediate monocyte PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) insufficient_evidence none No verbatim sentence naming this marker on monocytes was found. The canonical human/mouse monocyte nomenclature paper this repo already cites for issue #12 (Ziegler-Heitbrock L et al. 2010, PMID:20628149, DOI:10.1182/blood-2010-02-258558) explicitly covers both species at the classification-scheme level ('defines 3 types of monocytes ... in human and in mouse blood') but its abstract does not name this marker specifically; full text would be needed to confirm. Targeted EuropePMC searches for this marker in a monocyte context returned only tangential recent disease-cohort papers, not clean definitional statements. +CL:0002394 CD141-positive myeloid dendritic cell PR:000002105 thrombomodulin CD141 (exact) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DC1 corresponds to the cross-presenting CD141/BDCA-3+ cDC1, which is best marked by CLEC9A archive/2026-09_literature_narratives/dc_markers.md +CL:0002399 CD1c-positive myeloid dendritic cell PR:000002027 T-cell surface glycoprotein CD1c CD1C (exact); CD1c (label) human m2_literature_report Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) DC2 and DC3 correspond to new subdivisions of the CD1C/BDCA-1+ cDC2 archive/2026-09_literature_narratives/dc_markers.md +CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) human not_applicable species from PRO label 2026-09-28 +CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) human not_applicable species from PRO label 2026-09-28 +CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) human not_applicable species from PRO label 2026-09-28 +CL:0001078 group 3 innate lymphoid cell, human PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) human not_applicable species from PRO label 2026-09-28 +CL:0001081 group 2 innate lymphoid cell, human PR:P01589 interleukin-2 receptor subunit alpha (human) CD25 (exact) human not_applicable species from PRO label 2026-09-28 +CL:0001081 group 2 innate lymphoid cell, human PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) human not_applicable species from PRO label 2026-09-28 +CL:0001081 group 2 innate lymphoid cell, human PR:P23771 trans-acting T-cell-specific transcription factor GATA-3 (human) human not_applicable species from PRO label 2026-09-28 +CL:0001081 group 2 innate lymphoid cell, human PR:Q12918 killer cell lectin-like receptor subfamily B member 1 (human) CD161 (exact) human not_applicable species from PRO label 2026-09-28 +CL:0001081 group 2 innate lymphoid cell, human PR:Q9Y5Y4 prostaglandin D2 receptor 2 (human) CD294 (exact) human not_applicable species from PRO label 2026-09-28 +CL:4052055 mature NK T cell, human PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) human not_applicable species from PRO label 2026-09-28 +CL:0000937 pre-natural killer cell PR:000001003 CD34 molecule CD34 (label) unresolved supported no_evidence_found Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """stage 2 cells (Lin−CD34+CD117+CD94−CD16−) constitutively express CD122 (albeit below the level of detection by flow cytometry)""" Generic term. Human: supported if CL 'pre-NK' corresponds to human stage 2 (Lin−CD34+CD117+); that correspondence is an interpretation. Mouse: no statement on CD34 for mouse pre-NKP/rNKP found (Fathman 2011 abstract). 2026-10-05 nk_2026-10 +CL:0000937 pre-natural killer cell PR:000001381 interleukin-2 receptor subunit beta CD122 (exact) human supported contradicted Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """stage 2 cells (Lin−CD34+CD117+CD94−CD16−) constitutively express CD122 (albeit below the level of detection by flow cytometry)""" Fathman JW et al. 2011 (PMID: 21931117; PMC3217348) """Unlike the rNKP, the pre-NKP does not express IL-2Rβ (CD122), yet it is lineage committed toward the NK cell fate""" Generic term. Human: stage 2 cells express CD122 but 'below the level of detection by flow cytometry'. Mouse CONTRADICTED for the earliest stage: the pre-NKP lacks CD122 (only the later rNKP has it). CD122+ is therefore stage-specific in mouse. 2026-10-05 nk_2026-10 +CL:0000937 pre-natural killer cell PR:000002065 mast/stem cell growth factor receptor CD117 (exact) unresolved supported no_evidence_found Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """stage 2 cells (Lin−CD34+CD117+CD94−CD16−) constitutively express CD122 (albeit below the level of detection by flow cytometry)""" Generic term. Human supported (stage 2, see CD34 row). Mouse: no statement on CD117 for mouse pre-NKP/rNKP found. 2026-10-05 nk_2026-10 +CL:0001077 ILC1, human PR:Q9UL17 T-box transcription factor TBX21 (human) human supported not_applicable Riggan L et al. 2019 (PMID: 31500958; PMC6823149) """While single cell sequencing studies have identified a rare human T-bet+ putative ILC1 population in human tonsils""" CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Human supported (T-bet+ putative ILC1, rare). 2026-10-05 nk_2026-10 +CL:0001077 ILC1, human PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) human supported not_applicable Riggan L et al. 2019 (PMID: 31500958; PMC6823149) """current gating strategies used to identify human ILC1 (Lin-IL-7Rα+NKp44- CRTH2-CD117-)""" CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Human supported as the standard gate, but Riggan 2019 argues the Lin−CD56−IL-7Rα+ definition may be too restrictive (putative IL-7Rα− human ILC1 in liver). Flag for expert review. 2026-10-05 nk_2026-10 +CL:0002338 CD56-positive, CD161-positive immature natural killer cell, human PR:000001003 CD34 molecule CD34 (label) human supported not_applicable Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """In contrast, human stage 3 cells (Lin−CD34−CD117+CD94−CD16−) lacked T cell and DC developmental potential.""" CL term is human-specific; mouse not applicable. Human supported (stage 3 is CD34−CD117+). CL definition cites PMID:12457618, a mouse NK progenitor review, for this human term. 2026-10-05 nk_2026-10 +CL:0002338 CD56-positive, CD161-positive immature natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human supported not_applicable Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """Within the stage 3/ILC3 population in human SLTs, there is marked heterogeneity with regards to the expression of numerous surface markers, including CD7, CD56, CD62L, HLA-DR, and NKp44""" CL term is human-specific; mouse not applicable. Human supported: stage 3 is heterogeneous for CD56, so CD56+ and CD56− stage 3 cells exist. 2026-10-05 nk_2026-10 +CL:0002338 CD56-positive, CD161-positive immature natural killer cell, human PR:000001381 interleukin-2 receptor subunit beta CD122 (exact) unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. No stage-3-specific statement on CD122 found (Scoville 2017 says stage 2 expresses CD122 below flow detection). 2026-10-05 nk_2026-10 +CL:0002338 CD56-positive, CD161-positive immature natural killer cell, human PR:000001874 KLRB1-like protein unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. No stage-3-specific statement on CD161 found (Scoville 2017 only says human NK cells 'can also express' CD161). 2026-10-05 nk_2026-10 +CL:0002338 CD56-positive, CD161-positive immature natural killer cell, human PR:000002065 mast/stem cell growth factor receptor CD117 (exact) human supported not_applicable Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """In contrast, human stage 3 cells (Lin−CD34−CD117+CD94−CD16−) lacked T cell and DC developmental potential.""" CL term is human-specific; mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:0002344 CD56-negative, CD161-positive immature natural killer cell, human PR:000001003 CD34 molecule CD34 (label) human supported not_applicable Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """In contrast, human stage 3 cells (Lin−CD34−CD117+CD94−CD16−) lacked T cell and DC developmental potential.""" CL term is human-specific; mouse not applicable. Human supported. CL definition cites PMID:12457618, a mouse NK progenitor review, for this human term. 2026-10-05 nk_2026-10 +CL:0002344 CD56-negative, CD161-positive immature natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human supported not_applicable Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """Within the stage 3/ILC3 population in human SLTs, there is marked heterogeneity with regards to the expression of numerous surface markers, including CD7, CD56, CD62L, HLA-DR, and NKp44""" CL term is human-specific; mouse not applicable. Human supported: stage 3 is heterogeneous for CD56. 2026-10-05 nk_2026-10 +CL:0002344 CD56-negative, CD161-positive immature natural killer cell, human PR:000001381 interleukin-2 receptor subunit beta CD122 (exact) unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. No stage-3-specific statement on CD122 found. 2026-10-05 nk_2026-10 +CL:0002344 CD56-negative, CD161-positive immature natural killer cell, human PR:000001874 KLRB1-like protein unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. No stage-3-specific statement on CD161 found. 2026-10-05 nk_2026-10 +CL:0002344 CD56-negative, CD161-positive immature natural killer cell, human PR:000002065 mast/stem cell growth factor receptor CD117 (exact) human supported not_applicable Scoville SD et al. 2017 (PMID: 28396671; PMC5366880) """In contrast, human stage 3 cells (Lin−CD34−CD117+CD94−CD16−) lacked T cell and DC developmental potential.""" CL term is human-specific; mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:0002343 decidual natural killer cell, human PR:000001024 neural cell adhesion molecule 1 CD56 (exact) human supported not_applicable Koopman LA et al. 2003 (PMID: 14568979; PMC2194228) """The resemblance of dNK cells to the CD56bright pNK subset, at least in terms of their CD56bright CD16neg phenotype""" CL term is human-specific; mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:0002343 decidual natural killer cell, human PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) human supported not_applicable Koopman LA et al. 2003 (PMID: 14568979; PMC2194228) """The resemblance of dNK cells to the CD56bright pNK subset, at least in terms of their CD56bright CD16neg phenotype""" CL term is human-specific; mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:0002343 decidual natural killer cell, human PR:000009766 galectin-1 unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. Galectin-1 expression by dNK is supported (Koopman 2003: 'two secreted proteins, galectin-1 and progestagen-associated protein 14, ... were selectively expressed in dNK cells'), but the source calls it secreted, so 'has plasma membrane part' is not supported. Candidate relation change to 'expresses'. 2026-10-05 nk_2026-10 +CL:4052051 uterine natural killer cell 1, human PR:O95971 CD160 antigen (human) CD160 (label) unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Lack of CD160 on uNK1 is implied by the subset scheme but no explicit negative statement found (Vento-Tormo 2018, Whettlock 2022 full text). 2026-10-05 nk_2026-10 +CL:4052051 uterine natural killer cell 1, human PR:P38570 integrin alpha-E (human) CD103 (exact) unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Lack of CD103 implied by the gating (Whettlock 2022: subsets 'defined by their expression of CD39 and CD103'), no explicit statement. 2026-10-05 nk_2026-10 +CL:4052051 uterine natural killer cell 1, human PR:P49961 ectonucleoside triphosphate diphosphohydrolase 1 (human) CD39 (related) human supported not_applicable Vento-Tormo R et al. 2018 (PMID: 30429548; PMC7612850) """dNK1 cells express CD39 (also known as ENTPD1), CYP26A1 and B4GALNT1""" CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:4052051 uterine natural killer cell 1, human PR:P56199 integrin alpha-1 (human) CD49 (exact); CD49a (exact) human supported not_applicable Vento-Tormo R et al. 2018 (PMID: 30429548; PMC7612850) """We identified three main dNK subsets (dNK1, dNK2 and dNK3), which all co-express the tissue-resident markers CD49A (also known as ITGA1) and CD9""" CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:4052052 uterine natural killer cell 2, human PR:O95971 CD160 antigen (human) CD160 (label) unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Implied only; no explicit statement found. 2026-10-05 nk_2026-10 +CL:4052052 uterine natural killer cell 2, human PR:P38570 integrin alpha-E (human) CD103 (exact) unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Implied only; no explicit statement found. 2026-10-05 nk_2026-10 +CL:4052052 uterine natural killer cell 2, human PR:P49961 ectonucleoside triphosphate diphosphohydrolase 1 (human) CD39 (related) human supported not_applicable Whettlock EM et al. 2022 (PMID: 35784314; PMC9245422) """KIR+CD39− (mostly representing uNK2)""" CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:4052052 uterine natural killer cell 2, human PR:P56199 integrin alpha-1 (human) CD49 (exact); CD49a (exact) human supported not_applicable Vento-Tormo R et al. 2018 (PMID: 30429548; PMC7612850) """We identified three main dNK subsets (dNK1, dNK2 and dNK3), which all co-express the tissue-resident markers CD49A (also known as ITGA1) and CD9""" CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:4052053 uterine natural killer cell 3, human PR:P49961 ectonucleoside triphosphate diphosphohydrolase 1 (human) CD39 (related) unresolved no_evidence_found not_applicable CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Lack of CD39 on uNK3 implied (Vento-Tormo 2018 names CD39 as a dNK1 marker), no explicit statement. 2026-10-05 nk_2026-10 +CL:4052053 uterine natural killer cell 3, human PR:O95971 CD160 antigen (human) CD160 (label) human supported not_applicable Vento-Tormo R et al. 2018 (PMID: 30429548; PMC7612850) """dNK3 cells express CD160, KLRB1 and CD103 (also known as ITGAE)""" CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:4052053 uterine natural killer cell 3, human PR:P38570 integrin alpha-E (human) CD103 (exact) human supported not_applicable Vento-Tormo R et al. 2018 (PMID: 30429548; PMC7612850) """dNK3 cells express CD160, KLRB1 and CD103 (also known as ITGAE)""" CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:4052053 uterine natural killer cell 3, human PR:P56199 integrin alpha-1 (human) CD49 (exact); CD49a (exact) human supported not_applicable Vento-Tormo R et al. 2018 (PMID: 30429548; PMC7612850) """We identified three main dNK subsets (dNK1, dNK2 and dNK3), which all co-express the tissue-resident markers CD49A (also known as ITGA1) and CD9""" CL term is human-specific; mouse not applicable. PRO term is the human protein (species in PRO label); mouse not applicable. Human supported. 2026-10-05 nk_2026-10 +CL:0002345 CD27-low, CD11b-low immature natural killer cell, mouse PR:000001008 integrin alpha-2 CD49 (exact); CD49B (related); CD49b (exact) unresolved not_applicable contradicted Riggan L et al. 2019 (PMID: 31500958; PMC6823149) """Collective reports have demonstrated that iNK cells in mouse bone marrow and periphery can express Ly49 receptors, CD49a, CD90, TRAIL, CD69, and Eomes, and lack CD49b expression""" CL term is mouse-specific; human not applicable. CONTRADICTED in mouse: immature NK cells are reported to lack CD49b (DX5 antigen), while this term asserts DX5-positive. No supporting quote found (the definition source PMID:19949422 abstract does not mention DX5). 2026-10-05 nk_2026-10 +CL:0002345 CD27-low, CD11b-low immature natural killer cell, mouse PR:000002977 killer cell lectin-like receptor subfamily B member 1C CD161 (exact); CD161c (exact) mouse not_applicable supported Qin J et al. 2024 (PMID: 39628473; PMC11611892) """C57BL/6 and SJL mice use NK1.1 for identification, whereas BALB/c mice, due to allelic variations, rely on CD49b and NKp46 in the absence of NK1.1 responsiveness""" CL term is mouse-specific; human not applicable. Mouse supported. NK1.1 is strain-restricted (not usable in BALB/c). 2026-10-05 nk_2026-10 +CL:0002345 CD27-low, CD11b-low immature natural killer cell, mouse PR:000009616 T-cell surface glycoprotein YE1/48 unresolved not_applicable no_evidence_found CL term is mouse-specific; human not applicable. Riggan 2019 says mouse iNK cells 'can express Ly49 receptors' (family level); no statement found for the single Ly49 protein CL chose (PR:000009616). 2026-10-05 nk_2026-10 +CL:0002345 CD27-low, CD11b-low immature natural killer cell, mouse PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported (CD11b low). 2026-10-05 nk_2026-10 +CL:0002345 CD27-low, CD11b-low immature natural killer cell, mouse PR:000001963 CD27 molecule CD27 (label); CD27L (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported (CD27 low). 2026-10-05 nk_2026-10 +CL:0002346 Dx5-negative, NK1.1-positive immature natural killer cell, mouse PR:000001008 integrin alpha-2 CD49 (exact); CD49B (related); CD49b (exact) mouse not_applicable supported Riggan L et al. 2019 (PMID: 31500958; PMC6823149) """Collective reports have demonstrated that iNK cells in mouse bone marrow and periphery can express Ly49 receptors, CD49a, CD90, TRAIL, CD69, and Eomes, and lack CD49b expression""" CL term is mouse-specific; human not applicable. Mouse supported, but Riggan 2019 notes that DX5(CD49b)−NK1.1+ cells overlap with ILC1, so this term may not be a clean immature-NK class. 2026-10-05 nk_2026-10 +CL:0002346 Dx5-negative, NK1.1-positive immature natural killer cell, mouse PR:000002977 killer cell lectin-like receptor subfamily B member 1C CD161 (exact); CD161c (exact) mouse not_applicable supported Qin J et al. 2024 (PMID: 39628473; PMC11611892) """C57BL/6 and SJL mice use NK1.1 for identification, whereas BALB/c mice, due to allelic variations, rely on CD49b and NKp46 in the absence of NK1.1 responsiveness""" CL term is mouse-specific; human not applicable. Mouse supported. NK1.1 is strain-restricted (not usable in BALB/c). 2026-10-05 nk_2026-10 +CL:0002347 CD27-high, CD11b-high natural killer cell, mouse PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported. 2026-10-05 nk_2026-10 +CL:0002347 CD27-high, CD11b-high natural killer cell, mouse PR:000001963 CD27 molecule CD27 (label); CD27L (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported. 2026-10-05 nk_2026-10 +CL:0002348 CD27-low, CD11b-high natural killer cell, mouse PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported. CL definition cites PMID:1994922, an unrelated 1991 paper (Liang MH, pulmonary venoocclusive disease); probably a typo for PMID:19949422 (Andrews DM 2010), which sibling terms cite. 2026-10-05 nk_2026-10 +CL:0002348 CD27-low, CD11b-high natural killer cell, mouse PR:000001963 CD27 molecule CD27 (label); CD27L (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported. CL definition cites PMID:1994922, an unrelated 1991 paper (Liang MH, pulmonary venoocclusive disease); probably a typo for PMID:19949422 (Andrews DM 2010), which sibling terms cite. 2026-10-05 nk_2026-10 +CL:0002349 CD27-high, CD11b-low natural killer cell, mouse PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported. CL definition cites PMID:1994922, an unrelated 1991 paper (Liang MH, pulmonary venoocclusive disease); probably a typo for PMID:19949422 (Andrews DM 2010), which sibling terms cite. 2026-10-05 nk_2026-10 +CL:0002349 CD27-high, CD11b-low natural killer cell, mouse PR:000001963 CD27 molecule CD27 (label); CD27L (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported. CL definition cites PMID:1994922, an unrelated 1991 paper (Liang MH, pulmonary venoocclusive disease); probably a typo for PMID:19949422 (Andrews DM 2010), which sibling terms cite. 2026-10-05 nk_2026-10 +CL:0002426 CD11b-positive, CD27-positive natural killer cell, mouse PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported. Overlaps CL:0002347 (CD27-high, CD11b-high) — possible duplicate class. 2026-10-05 nk_2026-10 +CL:0002426 CD11b-positive, CD27-positive natural killer cell, mouse PR:000001963 CD27 molecule CD27 (label); CD27L (exact) mouse not_applicable supported Chiossone L et al. 2009 (PMID: 19234143) """Surface density of CD27 and CD11b subdivides mouse natural killer (NK) cells into 4 subsets: CD11b(low)CD27(low), CD11b(low)CD27(high), CD11b(high)CD27(high), and CD11b(high)CD27(low).""" CL term is mouse-specific; human not applicable. Mouse supported. See CD11b row. 2026-10-05 nk_2026-10 +CL:0002438 NK1.1-positive natural killer cell, mouse PR:000002977 killer cell lectin-like receptor subfamily B member 1C CD161 (exact); CD161c (exact) mouse not_applicable supported Qin J et al. 2024 (PMID: 39628473; PMC11611892) """C57BL/6 and SJL mice use NK1.1 for identification, whereas BALB/c mice, due to allelic variations, rely on CD49b and NKp46 in the absence of NK1.1 responsiveness""" CL term is mouse-specific; human not applicable. Mouse supported. NK1.1 is strain-restricted (not usable in BALB/c). 2026-10-05 nk_2026-10 +CL:0002439 NKGA2-positive natural killer cell, mouse PR:000002023 NKG2-A/NKG2-B type II integral membrane protein CD159 (exact); CD159a (exact) mouse not_applicable supported Shreeve N et al. 2021 (PMID: 33887202; PMC8211638) """Most murine and human peripheral NK cells display a bi-modal expression pattern for NKG2A.""" CL term is mouse-specific; human not applicable. Mouse supported. CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 +CL:0002440 Ly49D-positive natural killer cell, mouse PR:000009619 killer cell lectin-like receptor 4 mouse not_applicable supported Piersma SJ et al. 2025 (PMID: 40085489; PMC11908779) """The Klra4 gene appears intact and Ly49D+ NK cells expressed Ly49D at normal levels""" CL term is mouse-specific; human not applicable. Mouse supported. CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 +CL:0002441 CD94-positive natural killer cell, mouse PR:000001402 killer cell lectin-like receptor subfamily D member 1 CD94 (exact) unresolved not_applicable no_evidence_found CL term is mouse-specific; human not applicable. No explicit statement on a CD94+ vs CD94− mouse NK subset found (Europe PMC full-text queries, 2026-10-05). CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 +CL:0002442 CD94-negative, Ly49CI-negative natural killer cell, mouse PR:000001402 killer cell lectin-like receptor subfamily D member 1 CD94 (exact) unresolved not_applicable no_evidence_found CL term is mouse-specific; human not applicable. No explicit CD94− mouse NK statement found. CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). Unlike its siblings, its parent is CL:0000623, not CL:0002438. 2026-10-05 nk_2026-10 +CL:0002442 CD94-negative, Ly49CI-negative natural killer cell, mouse PR:000009618 killer cell lectin-like receptor 3 mouse not_applicable supported Patil ND et al. 2022 (PMID: 35911713; PMC9329629) """whereas their double negative (Ly49C/I-NKG2A-) counterparts are expected to be hypo-reactive""" CL term is mouse-specific; human not applicable. Mouse supported (Ly49C/I−). CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 +CL:0002443 Ly49CI-positive natural killer cell, mouse PR:000009618 killer cell lectin-like receptor 3 mouse not_applicable supported Patil ND et al. 2022 (PMID: 35911713; PMC9329629) """Ly49C/I+ NK cells contained more IFNγ-producers than the double negative subset.""" CL term is mouse-specific; human not applicable. Mouse supported. CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 +CL:0002444 Ly49H-positive natural killer cell, mouse PR:000009623 killer cell lectin-like receptor 8 mouse not_applicable supported Sun JC et al. 2009 (PMID: 19136945; PMC2674434) """Because Ly49H+ cells constitute ~50% of total NK cells in a naïve B6 mouse""" CL term is mouse-specific; human not applicable. Mouse supported (~50% Ly49H+). CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 +CL:0002445 Ly49D-negative natural killer cell, mouse PR:000009619 killer cell lectin-like receptor 4 unresolved not_applicable no_evidence_found CL term is mouse-specific; human not applicable. Ly49D+ cells are a subset (Piersma 2025), implying a Ly49D− subset, but no explicit statement found. CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 +CL:0002446 Ly49CI-negative natural killer cell, mouse PR:000009618 killer cell lectin-like receptor 3 mouse not_applicable supported Patil ND et al. 2022 (PMID: 35911713; PMC9329629) """whereas their double negative (Ly49C/I-NKG2A-) counterparts are expected to be hypo-reactive""" CL term is mouse-specific; human not applicable. Mouse supported. CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 +CL:0002447 CD94-negative natural killer cell, mouse PR:000001402 killer cell lectin-like receptor subfamily D member 1 CD94 (exact) unresolved not_applicable no_evidence_found CL term is mouse-specific; human not applicable. No explicit CD94− mouse NK statement found. CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 +CL:0002448 Ly49H-negative natural killer cell, mouse PR:000009623 killer cell lectin-like receptor 8 mouse not_applicable supported Sun JC et al. 2009 (PMID: 19136945; PMC2674434) """Because Ly49H+ cells constitute ~50% of total NK cells in a naïve B6 mouse""" CL term is mouse-specific; human not applicable. Mouse supported (~50% Ly49H+, so ~50% Ly49H−). CL definition reads 'A NK1.1-positive T cell', but the term is an NK cell (parent CL:0002438). 2026-10-05 nk_2026-10 From 47f15c4bf46aa2b967bd6a538b0bc174a3402580 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 5 Oct 2026 19:48:04 -0400 Subject: [PATCH 02/11] =?UTF-8?q?docs:=20draft=20CL=20issues=20for=20revie?= =?UTF-8?q?w=20and=20Prot=C3=A9g=C3=A9=20NCAM1=20repro=20note=20(Dr.=20Die?= =?UTF-8?q?hl,=202026-10-05)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Task B of the 2026-10-05 meeting plan. Nothing filed. - gaps.tsv: 9 appended rows (existing rows untouched). 7 draft_for_review (B1 lacks HLA-DRA on CL:0000938; B3a plasmablast lacks CD138; B3b plasmablast markers to a human child; B6a DX5+ on CL:0002345; B6b PMID:1994922 typo; B6c "NK1.1-positive T cell" definitions; B6d galectin-1 relation) and 2 on_hold pending Dr. Diehl (B2 opposing HLA-DR definition not found in CL; B6e pre-NK markers). - gap-issue-filing skill: never file draft_for_review / on_hold rows. - docs/protege_ncam1_query_repro.md: expected classes from Ubergraph, NCAM1/CD56 are PRO synonyms not labels, high/low-amount sub-properties and PR:P13591 as likely causes, what to record. Co-Authored-By: Claude Opus 5.5 --- .claude/skills/gap-issue-filing/SKILL.md | 9 ++- docs/README.md | 1 + docs/protege_ncam1_query_repro.md | 71 ++++++++++++++++++++++++ reports/gaps.tsv | 9 +++ 4 files changed, 87 insertions(+), 3 deletions(-) create mode 100644 docs/protege_ncam1_query_repro.md diff --git a/.claude/skills/gap-issue-filing/SKILL.md b/.claude/skills/gap-issue-filing/SKILL.md index e56a65b..a42feae 100644 --- a/.claude/skills/gap-issue-filing/SKILL.md +++ b/.claude/skills/gap-issue-filing/SKILL.md @@ -23,8 +23,11 @@ how many logged gaps still lack a tracking issue. - `reports/gaps.tsv` — the source rows. Columns: `soulcap_abbreviation`, `soulcap_full_name`, `gap_type`, `description`, `related_cl_ids`, - `evidence`, `status` (`open` / `filed_as_issue`), `repo_issue`, - `date_logged`. + `evidence`, `status` (`open` / `filed_as_issue` / `draft_for_review` / + `on_hold`), `repo_issue`, `date_logged`. `draft_for_review` rows are CL + issue drafts waiting for Alex (and sometimes Dr. Diehl) to approve them; + change them to `open` only after that approval. `on_hold` rows wait on an + open question named in their description. Never file either directly. - `.github/ISSUE_TEMPLATE/mapping_gap.yml` — the template whose fields map directly onto `gaps.tsv` columns: `soulcap_abbreviation` → title, `gap_type` → the dropdown, `description` + `related_cl_ids` + `evidence` → the @@ -38,7 +41,7 @@ how many logged gaps still lack a tracking issue. ## Step 1 — find what's actually unfiled Read `reports/gaps.tsv` and list every row where `status` is `open` (not -`filed_as_issue`). Note two rows sharing a `soulcap_abbreviation` group (e.g. +`filed_as_issue`, `draft_for_review` or `on_hold`). Note two rows sharing a `soulcap_abbreviation` group (e.g. `NK1 / NK3`) file as **one** issue, matching how the row itself is structured — don't split a single row into multiple issues. diff --git a/docs/README.md b/docs/README.md index 94bf95e..e3d4b91 100644 --- a/docs/README.md +++ b/docs/README.md @@ -9,6 +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 | +| [protege_ncam1_query_repro.md](protege_ncam1_query_repro.md) | Repro note for the Protégé NCAM1 (CD56) query that returned too few classes (Dr. Diehl, 2026-10-05): expected classes, likely causes, what to record | | [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) diff --git a/docs/protege_ncam1_query_repro.md b/docs/protege_ncam1_query_repro.md new file mode 100644 index 0000000..0b7b01b --- /dev/null +++ b/docs/protege_ncam1_query_repro.md @@ -0,0 +1,71 @@ +# Protégé query for NCAM1 (CD56) returns too few classes: repro note + +Dr. Diehl reported on 5 October 2026 that a Protégé DL query for +`has plasma membrane part some NCAM1` did not return a cell type that has that +axiom, even after running the reasoner. **Not filed against CL** until it is +reproduced. This note lists what the query should return according to +Ubergraph, the likely causes, and what to check. + +## What the query should return + +Ubergraph (queried 2026-10-05) has these **positive** NCAM1 axioms on CL +terms. "Lacks" axioms (`CL:4030046`) should *not* be returned and are left out. + +| CL term | Relation | PRO term | +|---|---|---| +| `CL:0000570` parafollicular cell | has plasma membrane part (`RO:0002104`) | `PR:000001024` | +| `CL:0002338` CD56-positive, CD161-positive immature natural killer cell, human | has plasma membrane part (`RO:0002104`) | `PR:000001024` | +| `CL:0000938` CD16-negative, CD56-bright natural killer cell, human | has high plasma membrane amount (`RO:0015015`) | `PR:000001024` | +| `CL:0002343` decidual natural killer cell, human | has high plasma membrane amount (`RO:0015015`) | `PR:000001024` | +| `CL:0000939` CD16-positive, CD56-dim natural killer cell, human | has low plasma membrane amount (`RO:0015016`) | `PR:000001024` | +| `CL:0001073` CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human | has plasma membrane part (`RO:0002104`) | `PR:P13591` (human) | +| `CL:0001074` CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human | has plasma membrane part (`RO:0002104`) | `PR:P13591` (human) | +| `CL:4052055` mature NK T cell, human | has plasma membrane part (`RO:0002104`) | `PR:P13591` (human) | + +Subclasses of these terms should also be returned. + +## Names of the protein + +| Identifier | Label | Notes | +|---|---|---| +| `PR:000001024` | neural cell adhesion molecule 1 | Exact synonyms: CD56, NCAM1, N-CAM-1, NCAM-1. Related synonym: NCAM | +| `PR:P13591` | neural cell adhesion molecule 1 (human) | A subclass of `PR:000001024` in PRO (Ubergraph) | +| UniProtKB:P13591 | — | The human UniProt entry behind `PR:P13591` | + +"NCAM1" and "CD56" are **synonyms**, not labels. If Protégé renders entities +by label, the query has to name the class as `'neural cell adhesion molecule 1'`. + +## Likely causes, to test one at a time + +1. **The relation used.** The CD56-bright, CD56-dim and decidual NK terms + don't use `has plasma membrane part`. They use `has high` / `has low plasma + membrane amount`. In Ubergraph these two are sub-properties of `has plasma + membrane part`, so a reasoner should return them. But it can only do that if + the loaded file contains those sub-property axioms (from the RO import). If + the missing class is one of these three, this is the likely cause. +2. **The protein term used.** `CL:0001073`, `CL:0001074` and `CL:4052055` use + the human protein `PR:P13591`, not `PR:000001024`. The query only returns + them if the loaded file says `PR:P13591` is a subclass of `PR:000001024`. + PRO says so, but CL's PRO import may not include that link. +3. **The name typed.** Typing `NCAM1` or `CD56` may resolve to nothing, or to a + different entity, if Protégé is rendering by label (see above). +4. **Protégé settings.** Check that the DL query has "Subclasses" ticked (not + only "Direct subclasses") and that the reasoner was synchronised *after* + the file finished loading. +5. **Reasoner.** Record which reasoner was used (ELK, HermiT, …) and its + version. Some reasoners handle anonymous class-expression queries + differently; this hasn't been checked here. + +## What to record when reproducing + +- CL file and version (for example `cl-edit.owl` at commit X, or `cl.owl` + release date), and whether imports were loaded. +- The exact query text, copied from Protégé. +- Reasoner name and version, and whether it was synchronised. +- Expected class (from the table above) vs. what was returned. +- Results of the same query with `'neural cell adhesion molecule 1'`, with + `PR_000001024` by IRI, and with `has high plasma membrane amount some …`. + +If the difference comes from cause 1 or 2 (a missing import axiom), that is a +CL import issue worth filing. If it comes from cause 3 or 4, nothing needs to +be filed. diff --git a/reports/gaps.tsv b/reports/gaps.tsv index 806ea23..ff99698 100644 --- a/reports/gaps.tsv +++ b/reports/gaps.tsv @@ -16,3 +16,12 @@ CD56+ T cell family (13 rows) various CD56+ T cell subsets cl_axiom_gap SOULCAP Tcm / Tem / Temra (general, no CD4/CD8 split) and all TCRgd-specific Tnaive/Tcm/Tem/Temra rows various cl_axiom_gap CL has no generic central/effector memory T cell term spanning both CD4 and CD8 (only CD4-specific and CD8-specific versions exist), and no gamma-delta-specific differentiation-state terms at all. ~13 rows Broad-matched to the nearest available parent (CL:0000084 T cell, or CL:0000798 gamma-delta T cell) with this gap noted. CL:0000084; CL:0000798 reports/candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree open (not yet filed) 2026-07-24 CD8+ Temra / CD8+ TCRab Temra CD8+ CD45RA+ effector memory T cell cl_axiom_gap CL:4030002 (effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated) appears to be CD4-specific only; no CD8+ counterpart with the same "terminally differentiated" qualifier was found — only the non-TEMRA-specific CL:0000913 (effector memory CD8-positive, alpha-beta T cell). Possible asymmetry in CL's own hierarchy; needs a second look before concluding it's a genuine omission rather than differently-named. CL:4030002; CL:0000913 reports/candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree open (not yet filed) 2026-07-24 (26 rows, various abbreviations) (no Full Name in sheet) sheet_data_issue 26 rows in the T cell branch have a completely empty Full Name field, so no name-based match can be attempted (Conv TCRab family, T helper, T cytotoxic, Tfh, CD4 PanT helper/Treg, ConT Treg-like/Tfh-like, Th1/2/9/17-like, Vg9/Vd1/Vd2/Vd3 subsets). Additionally, Th1-like/Th2-like/Th9-like/Th17-like each appear TWICE in the sheet: one copy (parented under "CD4 ConT") has iNKT-style TCRVa24-Ja18/CD1d-a-GalCer markers that look copy-pasted from an unrelated row; the other (no parent) has the correct Th-subset chemokine receptor panel (CD183/CD185/CD194/CD196). Likely a genuine sheet data bug, not two intentional variants. Cannot be fixed here — requires correction in the Google Sheet master. CL:0000912 (T helper, once named); CL:0000910 (T cytotoxic, once named) reports/candidate_cl_mappings_narrative.md#rows-with-no-full-name-in-the-sheet--not-mapped open (not yet filed) 2026-07-24 +NK2 Natural Killer Cell 2 cl_marker_conflict [Draft B1] Remove or disable 'lacks_plasma_membrane_part HLA-DRA' (PR:000002015) on CL:0000938 until a source is found (Dr. Diehl, 2026-10-05). Neither definition source supports it: PMID:19796267 never mentions HLA-DR; PMID:22343568 mentions HLA-DR on NK cells only as an activation marker. Human evidence: most resting NK cells are HLA-DR− (Evans 2011, PMID:21491418), but an HLA-DR+ subset exists ex vivo, mostly CD56bright (Erokhina 2018, PMID:29363179). HLA-DRA is human-only (PRO: mouse ortholog H2-Ea). Proposed labels: gap. CL:0000938 reports/nk_hladr_conflicts_2026-10.tsv; reports/nk_marker_audit_2026-10.md#hla-dra-on-the-cd16-negative-nk-class; reports/pro_marker_species_support.tsv draft_for_review (not yet filed) 2026-10-05 +CTNK / NK1 / NK3 Cytotoxic Natural Killer Cell / Natural Killer Cell 1 / 3 cl_marker_conflict [Draft B2, on hold] Dr. Diehl described two NK definitions for the same cell, one HLA-DR+ and one HLA-DR−. No CL term asserts HLA-DR+ NK (Ubergraph, 2026-10-05). What exists: CL:0000939 (CD56-dim) ALSO asserts 'lacks HLA-DRA', with the same two unsupporting definition sources as CL:0000938; HLA-DR+ CD56dim cells occur 'in some individuals' (Erokhina 2018, PMID:29363179). Hold until Dr. Diehl confirms which term he meant; if CL:0000939, merge with B1 as one issue covering both IDs. Proposed labels: gap, evidence needed. CL:0000938; CL:0000939 reports/nk_hladr_conflicts_2026-10.tsv; reports/nk_marker_audit_2026-10.md#open-questions-for-alex-and-dr-diehl on_hold (not yet filed) 2026-10-05 +PB Plasmablast cl_marker_conflict [Draft B3a] Drop 'lacks_plasma_membrane_part syndecan-1 (CD138)' (PR:000001935) from CL:0000980 plasmablast. Contradicted in mouse ('plasmablasts as B220+CD138+', PMID:42774878) and in one human scheme ('short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)', PMID:41771939). The definition source (PMC2673126, Jackson 2009) does not mention CD138. Also remove 'CD138-negative' from the text definition. Proposed labels: gap. CL:0000980 reports/plasmablast_marker_audit_2026-10.md; reports/pro_marker_species_support.tsv; reports/cl_term_issues.md#plasmablast-lacks-cd138--cl0000980-pr000001935-syndecan-1 draft_for_review (not yet filed) 2026-10-05 +PB Plasmablast cl_axiom_gap [Draft B3b] Move the remaining plasmablast markers (CD38 high, CD27 high, lacks CD20) from generic CL:0000980 to a new child 'plasmablast, human' (in taxon Homo sapiens), leaving the generic term markerless (Dr. Diehl, 2026-10-05). All three are supported in human and have no mouse evidence, so a mammal-level child isn't supported yet. Optional: 'plasmablast, mouse' with CD138+. Note for discussion, not this issue: plasmablast is already mammal-only through mature B cell → B cell, CD19-positive → CL:0001200 (in taxon Mammalia). Proposed labels: gap, new term request. CL:0000980; CL:0000785; CL:0001200 reports/plasmablast_marker_audit_2026-10.md; reports/pro_marker_species_support.tsv draft_for_review (not yet filed) 2026-10-05 +(none: mouse CL term) (no SOULCAP row) cl_marker_conflict [Draft B6a] CL:0002345 'CD27-low, CD11b-low immature natural killer cell, mouse' asserts DX5 (integrin alpha-2 / CD49b, PR:000001008) positive. Mouse immature NK cells are reported to 'lack CD49b expression' (Riggan 2019, PMID:31500958); sibling CL:0002346 is DX5-negative. No supporting quote found (definition source PMID:19949422 abstract doesn't mention DX5). Proposed labels: gap, evidence needed. CL:0002345 reports/nk_marker_audit_2026-10.md#other-findings-issue-candidates; reports/pro_marker_species_support.tsv draft_for_review (not yet filed) 2026-10-05 +(none: mouse CL terms) (no SOULCAP row) cl_axiom_gap [Draft B6b] CL:0002348 and CL:0002349 cite PMID:1994922 in their definitions. That PMID is an unrelated 1991 paper (Liang MH, pulmonary venoocclusive disease). Probably a typo for PMID:19949422 (Andrews DM 2010, mouse NK ontogeny), which CL:0002345 and CL:0002347 cite. Proposed labels: gap. CL:0002348; CL:0002349 reports/nk_marker_audit_2026-10.md#other-findings-issue-candidates draft_for_review (not yet filed) 2026-10-05 +(none: mouse CL terms) (no SOULCAP row) cl_axiom_gap [Draft B6c] The definitions of 10 mouse NK terms (CL:0002439 to CL:0002448) read 'A NK1.1-positive T cell that is …', but the terms are natural killer cells (parent CL:0002438 NK1.1-positive natural killer cell, mouse). Proposed fix: 'A NK1.1-positive natural killer cell that is …'. Proposed labels: gap. CL:0002439; CL:0002440; CL:0002441; CL:0002442; CL:0002443; CL:0002444; CL:0002445; CL:0002446; CL:0002447; CL:0002448 reports/nk_marker_audit_2026-10.md#other-findings-issue-candidates draft_for_review (not yet filed) 2026-10-05 +(none: no SOULCAP decidual NK row) (no SOULCAP row) cl_axiom_gap [Draft B6d] CL:0002343 'decidual natural killer cell, human' asserts galectin-1 (PR:000009766) as 'has plasma membrane part'. Its definition source describes galectin-1 as one of 'two secreted proteins … selectively expressed in dNK cells' (Koopman 2003, PMID:14568979). Expression is supported; plasma membrane localisation isn't. Proposed fix: use 'expresses' (RO:0002292). Proposed labels: gap. CL:0002343 reports/nk_marker_audit_2026-10.md#other-findings-issue-candidates; reports/pro_marker_species_support.tsv draft_for_review (not yet filed) 2026-10-05 +(none: no SOULCAP pre-NK row) (no SOULCAP row) cl_marker_conflict [Draft B6e, on hold] CL:0000937 pre-natural killer cell (generic) asserts CD34, CD122 and CD117 positive. In mouse, the earliest pre-NKP 'does not express IL-2Rβ (CD122)' (Fathman 2011, PMID:21931117). In human, the markers fit stage 2 cells. Hold until Dr. Diehl decides whether these markers move to a human child (as for plasmablast). Proposed labels: gap, evidence needed. CL:0000937 reports/nk_marker_audit_2026-10.md#open-questions-for-alex-and-dr-diehl; reports/pro_marker_species_support.tsv on_hold (not yet filed) 2026-10-05 From d1d0a2cddf809a5735b1e13adff66d361936bea3 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 5 Oct 2026 19:54:30 -0400 Subject: [PATCH 03/11] chore: force LF on mappings/*.tsv so the benchmark reserve hashes match on Windows core.autocrlf=true checked these files out with CRLF, so test_benchmark_reserve failed locally although the committed content matched the frozen hashes. Co-Authored-By: Claude Opus 5.5 --- .gitattributes | 2 ++ CLAUDE.md | 1 + 2 files changed, 3 insertions(+) create mode 100644 .gitattributes diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..cb3cea1 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# The benchmark reserve test hashes these files; keep LF on every OS. +mappings/*.tsv text eol=lf diff --git a/CLAUDE.md b/CLAUDE.md index 742e102..040a618 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -75,6 +75,7 @@ AST in `marker_syntax.py`, compiled/evaluated by `phenotype.py`. | `pyproject.toml` | Project metadata, deps, and the CLI entry points. | | `.mcp.json` | MCP servers available in this project (see below). | | `.env` | `ASTA_API_KEY=...` (gitignored; required for the Asta MCP server). | +| `.gitattributes` | Forces LF line endings on `mappings/*.tsv`, whose hashes `tests/test_benchmark_reserve.py` checks (Windows `core.autocrlf` would otherwise break it). | When you create a new artifact, put it in the established location and link it from here and the README so locations stay consistent. Do not scatter From 9a80c8ed75ad27805c4ec1ea42954bb9dcf388ea Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 5 Oct 2026 19:56:40 -0400 Subject: [PATCH 04/11] docs: review doc for Dr. Diehl; widen HLA-DRA draft, close B2, withdraw CD56 draft - docs/diehl_review_2026-10.md: batch 1 (B1 HLA-DRA on CL:0000938 and CL:0000939, B3a plasmablast lacks CD138 with quotes, B3b plasmablast child with both human and mammal options), batch 2 (B6a-d), on-hold items. Nothing filed. - gaps.tsv: B1 now one issue for both NK terms; B2 not_a_cl_issue (the conflict was in Dr. Diehl's old spreadsheet); old "add CD56 to CL:0000623" row withdrawn (generic NK keeps only lack statements). - cl_term_issues.md, audit report and gap-issue-filing skill updated to match (withdrawn / not_a_cl_issue are closed statuses). Co-Authored-By: Claude Opus 5.5 --- .claude/skills/gap-issue-filing/SKILL.md | 4 +- docs/README.md | 1 + docs/diehl_review_2026-10.md | 165 +++++++++++++++++++++++ reports/cl_term_issues.md | 2 +- reports/gaps.tsv | 6 +- reports/nk_marker_audit_2026-10.md | 12 +- 6 files changed, 179 insertions(+), 11 deletions(-) create mode 100644 docs/diehl_review_2026-10.md diff --git a/.claude/skills/gap-issue-filing/SKILL.md b/.claude/skills/gap-issue-filing/SKILL.md index a42feae..6c9621d 100644 --- a/.claude/skills/gap-issue-filing/SKILL.md +++ b/.claude/skills/gap-issue-filing/SKILL.md @@ -28,6 +28,8 @@ how many logged gaps still lack a tracking issue. issue drafts waiting for Alex (and sometimes Dr. Diehl) to approve them; change them to `open` only after that approval. `on_hold` rows wait on an open question named in their description. Never file either directly. + `withdrawn` (the proposal was dropped) and `not_a_cl_issue` (the problem + turned out not to be in CL) are closed: never file them. - `.github/ISSUE_TEMPLATE/mapping_gap.yml` — the template whose fields map directly onto `gaps.tsv` columns: `soulcap_abbreviation` → title, `gap_type` → the dropdown, `description` + `related_cl_ids` + `evidence` → the @@ -41,7 +43,7 @@ how many logged gaps still lack a tracking issue. ## Step 1 — find what's actually unfiled Read `reports/gaps.tsv` and list every row where `status` is `open` (not -`filed_as_issue`, `draft_for_review` or `on_hold`). Note two rows sharing a `soulcap_abbreviation` group (e.g. +`filed_as_issue`, `draft_for_review`, `on_hold`, `withdrawn` or `not_a_cl_issue`). Note two rows sharing a `soulcap_abbreviation` group (e.g. `NK1 / NK3`) file as **one** issue, matching how the row itself is structured — don't split a single row into multiple issues. diff --git a/docs/README.md b/docs/README.md index e3d4b91..f7df7c8 100644 --- a/docs/README.md +++ b/docs/README.md @@ -9,6 +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 | +| [diehl_review_2026-10.md](diehl_review_2026-10.md) | CL issue drafts from the October 2026 NK and plasmablast audit, for Dr. Diehl to approve before anything is filed | | [protege_ncam1_query_repro.md](protege_ncam1_query_repro.md) | Repro note for the Protégé NCAM1 (CD56) query that returned too few classes (Dr. Diehl, 2026-10-05): expected classes, likely causes, what to record | | [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 | diff --git a/docs/diehl_review_2026-10.md b/docs/diehl_review_2026-10.md new file mode 100644 index 0000000..7e2e4f8 --- /dev/null +++ b/docs/diehl_review_2026-10.md @@ -0,0 +1,165 @@ +# CL issue drafts for review — October 2026 + +For Dr. Diehl, before anything is handed to David's team. Nothing has been +filed yet. Each section is one proposed GitHub issue against CL. Please mark +each one **file**, **change** or **drop**. + +Every quote below was checked word for word against the paper's Europe PMC +full text. Full detail is in +[reports/nk_marker_audit_2026-10.md](../reports/nk_marker_audit_2026-10.md), +[reports/plasmablast_marker_audit_2026-10.md](../reports/plasmablast_marker_audit_2026-10.md) +and the draft rows at the end of [reports/gaps.tsv](../reports/gaps.tsv). + +**The HLA-DR positive vs negative conflict** you described was in your old +curation spreadsheet, not in CL, so it isn't a CL issue. In CL, both +NK subset terms say "lacks HLA-DRA", and B1 below covers both. + +--- + +## Batch 1: NK and plasmablast + +### B1. Remove "lacks HLA-DRA" from the CD56-bright and CD56-dim NK terms + +**CL IDs:** `CL:0000938` CD16-negative, CD56-bright natural killer cell, human; +`CL:0000939` CD16-positive, CD56-dim natural killer cell, human + +**Change:** remove (or disable) `lacks_plasma_membrane_part` `PR:000002015` +(HLA-DRA) on both terms until a source is found. **One issue for both +terms**, because they share the same axiom, the same two definition sources +and the same evidence. + +**Why:** neither definition source supports it. PMID:19796267 never mentions +HLA-DR. PMID:22343568 mentions it on NK cells only as an activation marker: + +> "The similar use of HLA-DR to track activated NK cells is a possibility that +> has been less well explored, but that might be equally fruitful." +> — Maecker HT et al. 2012 (PMID:22343568) + +Resting NK cells are mostly HLA-DR negative, but not all: + +> "In contrast, only 2–5.5% (median 3.5%) of fresh NK cells ex vivo expressed +> HLA-DR" — Evans JH et al. 2011 (PMID:21491418) + +> "We have observed that HLA-DR expression in freshly isolated circulating NK +> cells was mostly associated with less differentiated CD56brightCD57− cells, +> although in some individuals it could also be found in terminally +> differentiated CD57+ cells." — Erokhina SA et al. 2018 (PMID:29363179) + +**Confidence:** high that the axiom has no source; medium that it is wrong, +since HLA-DR+ cells are a minority (more so for CD56-dim). Attach +[nk_hladr_conflicts_2026-10.tsv](../reports/nk_hladr_conflicts_2026-10.tsv). + +### B3a. Drop "lacks CD138" from plasmablast + +**CL ID:** `CL:0000980` plasmablast + +**Change:** remove `lacks_plasma_membrane_part` `PR:000001935` (syndecan-1 / +CD138) and "CD138-negative" from the text definition. + +**Why:** contradicted in mouse and in one human scheme, and the definition +source (Jackson SM et al. 2009, PMID:19059880) does not mention CD138. + +> "plasmablasts as B220+CD138+" — Marques RF et al. 2026 (PMID:42774878), mouse + +> "short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)" +> — Jamaluddin J et al. 2026 (PMID:41771939), human + +**Confidence:** high for mouse; medium for human, where some schemes do treat +plasmablasts as CD138-low. No quote supporting "lacks CD138" was found. + +### B3b. Move plasmablast markers to a species-specific child + +**CL ID:** `CL:0000980` plasmablast (generic term keeps no markers) + +**Markers to move:** CD38 high, CD27 high, lacks CD20 (with B3a, CD138 is +dropped). + +> "Plasmablasts and Long-Lived Plasma Cells +> (CD19+CD20−IgD−CD27hiCD38hi/CD138+CD38+CD19−/Low)" +> — Georgopoulos C et al. 2026 (PMID:42653236), human + +> "as B cells differentiate to become plasmablasts and plasma cells, CD20 is +> lost but CD19 remains, as CD38/CD138 is acquired" +> — Griffin DO & Rothstein TL 2012 (PMID:22654880), human + +**Two options. Your choice:** + +| | Option 1: "plasmablast, human" | Option 2: mammal-level child | +|---|---|---| +| Taxon | in taxon Homo sapiens | in taxon Mammalia | +| Evidence | All three markers supported in human | Same human quotes; **no mouse evidence found** for CD38, CD27 or CD20 on mouse plasmablasts (mouse studies gate on B220/CD138) | +| Fits | What the literature shows today | What was discussed on 5 October | + +**Note for either option:** plasmablast is *already* mammal-only. Its parent +"mature B cell" sits under "B cell, CD19-positive", whose parent +`CL:0001200` is `in taxon Mammalia`. So stripping markers from the generic +term alone won't make it usable for zebrafish; the mature B cell link would +also have to change. Do you want that raised as a separate issue? + +**Confidence:** high on the evidence; the choice between options is yours. + +--- + +## Batch 2: smaller CL fixes found during the audit + +### B6a. DX5-positive on an immature mouse NK term + +**CL ID:** `CL:0002345` CD27-low, CD11b-low immature natural killer cell, mouse + +**Change:** review or remove the DX5 (CD49b, `PR:000001008`) positive axiom. +Its sibling `CL:0002346` is DX5-negative. + +> "Collective reports have demonstrated that iNK cells in mouse bone marrow +> and periphery can express Ly49 receptors, CD49a, CD90, TRAIL, CD69, and +> Eomes, and lack CD49b expression" — Riggan L et al. 2019 (PMID:31500958) + +**Confidence:** medium. One review statement; the definition source's +abstract (PMID:19949422) doesn't mention DX5, and its full text isn't open +access. + +### B6b. Wrong PMID in two definitions + +**CL IDs:** `CL:0002348` CD27-low, CD11b-high natural killer cell, mouse; +`CL:0002349` CD27-high, CD11b-low natural killer cell, mouse + +**Change:** both cite PMID:1994922, which is an unrelated 1991 paper (Liang +MH, pulmonary venoocclusive disease). Probably a typo for PMID:19949422 +(Andrews DM 2010, mouse NK ontogeny), which `CL:0002345` and `CL:0002347` cite. + +**Confidence:** high that the PMID is wrong; medium that 19949422 is the +intended one. + +### B6c. "NK1.1-positive T cell" in 10 NK definitions + +**CL IDs:** `CL:0002439` to `CL:0002448` (Ly49, CD94 and NKG2A subsets of +NK cells, mouse) + +**Change:** their definitions read "A NK1.1-positive T cell that is …", but +they are NK cells (parent `CL:0002438` NK1.1-positive natural killer cell, +mouse). Change to "A NK1.1-positive natural killer cell that is …". + +**Confidence:** high (wording error, no literature needed). + +### B6d. Galectin-1 on decidual NK: wrong relation + +**CL ID:** `CL:0002343` decidual natural killer cell, human + +**Change:** galectin-1 (`PR:000009766`) is asserted as `has plasma membrane +part`. Use `expresses` instead. + +> "two secreted proteins, galectin-1 and progestagen-associated protein 14, +> known to have immunomodulatory functions, were selectively expressed in dNK +> cells" — Koopman LA et al. 2003 (PMID:14568979), the definition source + +**Confidence:** medium. Expression is clearly supported; membrane +localisation just isn't shown. + +--- + +## Still on hold + +- **Pre-NK markers** (`CL:0000937`, CD34/CD117/CD122). In mouse, the earliest + pre-NK "does not express IL-2Rβ (CD122)" (Fathman JW et al. 2011, + PMID:21931117). Should these move to a human child, as for plasmablast? +- **Withdrawn:** our old draft to *add* CD56 to generic NK (`CL:0000623`). + It conflicts with your rule that generic NK terms keep only lack statements. diff --git a/reports/cl_term_issues.md b/reports/cl_term_issues.md index 3b927e4..ef385fb 100644 --- a/reports/cl_term_issues.md +++ b/reports/cl_term_issues.md @@ -81,7 +81,7 @@ cells. **Repo issue:** not yet filed **Reference:** SOULCAP `NK` row ([data/marker_combinations.csv](../data/marker_combinations.csv), regenerate via `uv run soulcap-sync`); literature in [archive/2026-09_literature_narratives/nk_cell_markers.md](../archive/2026-09_literature_narratives/nk_cell_markers.md) -**Status:** Drafted during Milestone 4 candidate mapping work — not yet filed as a repo issue +**Status:** Drafted during Milestone 4 candidate mapping work — **withdrawn 2026-10-05**. It conflicts with Dr. Diehl's rule that generic NK terms keep only lack statements; CD56 belongs on the human-specific children, which already assert it (see [nk_marker_audit_2026-10.md](nk_marker_audit_2026-10.md#ncam1--cd56)). Kept for the record. #### CL:0000623 — "natural killer cell" diff --git a/reports/gaps.tsv b/reports/gaps.tsv index ff99698..a6572c1 100644 --- a/reports/gaps.tsv +++ b/reports/gaps.tsv @@ -1,5 +1,5 @@ soulcap_abbreviation soulcap_full_name gap_type description related_cl_ids evidence status repo_issue date_logged -NK Natural Killer Cell cl_axiom_gap CL:0000623 asserts only negative exclusion markers (CD14-/CD19-/CD3-/CD20-); the field-standard defining positive marker CD56 is absent from its own axioms, though present on its child terms. CL:0000623 reports/cl_pro_relationships.md; archive/2026-09_literature_narratives/nk_cell_markers.md; reports/cl_term_issues.md#natural-killer-cell-missing-cd56-marker-axiom--cl0000623 open (not yet filed) 2026-07-22 +NK Natural Killer Cell cl_axiom_gap [Withdrawn 2026-10-05] CL:0000623 asserts only negative exclusion markers (CD14-/CD19-/CD3-/CD20-); the field-standard defining positive marker CD56 is absent from its own axioms, though present on its child terms. WITHDRAWN: conflicts with Dr. Diehl's rule (meeting 2026-10-05) that generic NK terms keep only lack statements; CD56/NCAM1 is a human-only NK marker and belongs on human-specific children, where CL already asserts it (reports/nk_marker_audit_2026-10.md#ncam1--cd56). CL:0000623 reports/cl_pro_relationships.md; archive/2026-09_literature_narratives/nk_cell_markers.md; reports/cl_term_issues.md#natural-killer-cell-missing-cd56-marker-axiom--cl0000623 withdrawn (not yet filed) 2026-07-22 NK1 / NK3 Natural Killer Cell 1 / Natural Killer Cell 3 cl_axiom_gap CL:0000939 (CD16-positive, CD56-dim NK cell, human) does not distinguish CD57-negative (NK1) from CD57-positive (NK3) substates; both SOULCAP rows currently map to the same CL term at Broad match type. CL:0000939 reports/candidate_cl_mappings_narrative.md#ctnk--nk1--nk3--cytotoxic-natural-killer-cell-cd16-positive open (not yet filed) 2026-07-22 ILC1 Innate Lymphoid Cell 1 cl_axiom_gap No human-specific "group 1 innate lymphoid cell" CL term exists, unlike group 2 (CL:0001081) and group 3 (CL:0001078); confirmed by direct OLS4 search returning zero hits for the human-qualified query. CL:0001067 reports/cl_term_issues.md#missing-human-specific-group-1-innate-lymphoid-cell-term filed_as_issue https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/14 2026-07-23 Transitional Transitional B cell no_reasonable_cl_match SOULCAP row has all four marker columns (Required/Ideal exclusion, Required/Ideal phenotypic markers) completely empty in the master sheet — there is no marker definition to match against at all, so no CL candidate can be derived from markers. Distinct from the more specific "T3" (Transitional B cell 3) row, which does have marker data. (none) reports/candidate_cl_mappings_batch.tsv (note column); data/marker_combinations.csv open (not yet filed) 2026-07-24 @@ -16,8 +16,8 @@ CD56+ T cell family (13 rows) various CD56+ T cell subsets cl_axiom_gap SOULCAP Tcm / Tem / Temra (general, no CD4/CD8 split) and all TCRgd-specific Tnaive/Tcm/Tem/Temra rows various cl_axiom_gap CL has no generic central/effector memory T cell term spanning both CD4 and CD8 (only CD4-specific and CD8-specific versions exist), and no gamma-delta-specific differentiation-state terms at all. ~13 rows Broad-matched to the nearest available parent (CL:0000084 T cell, or CL:0000798 gamma-delta T cell) with this gap noted. CL:0000084; CL:0000798 reports/candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree open (not yet filed) 2026-07-24 CD8+ Temra / CD8+ TCRab Temra CD8+ CD45RA+ effector memory T cell cl_axiom_gap CL:4030002 (effector memory CD45RA-positive, alpha-beta T cell, terminally differentiated) appears to be CD4-specific only; no CD8+ counterpart with the same "terminally differentiated" qualifier was found — only the non-TEMRA-specific CL:0000913 (effector memory CD8-positive, alpha-beta T cell). Possible asymmetry in CL's own hierarchy; needs a second look before concluding it's a genuine omission rather than differently-named. CL:4030002; CL:0000913 reports/candidate_cl_mappings_narrative.md#naive--central-memory--effector-memory--temra-tree open (not yet filed) 2026-07-24 (26 rows, various abbreviations) (no Full Name in sheet) sheet_data_issue 26 rows in the T cell branch have a completely empty Full Name field, so no name-based match can be attempted (Conv TCRab family, T helper, T cytotoxic, Tfh, CD4 PanT helper/Treg, ConT Treg-like/Tfh-like, Th1/2/9/17-like, Vg9/Vd1/Vd2/Vd3 subsets). Additionally, Th1-like/Th2-like/Th9-like/Th17-like each appear TWICE in the sheet: one copy (parented under "CD4 ConT") has iNKT-style TCRVa24-Ja18/CD1d-a-GalCer markers that look copy-pasted from an unrelated row; the other (no parent) has the correct Th-subset chemokine receptor panel (CD183/CD185/CD194/CD196). Likely a genuine sheet data bug, not two intentional variants. Cannot be fixed here — requires correction in the Google Sheet master. CL:0000912 (T helper, once named); CL:0000910 (T cytotoxic, once named) reports/candidate_cl_mappings_narrative.md#rows-with-no-full-name-in-the-sheet--not-mapped open (not yet filed) 2026-07-24 -NK2 Natural Killer Cell 2 cl_marker_conflict [Draft B1] Remove or disable 'lacks_plasma_membrane_part HLA-DRA' (PR:000002015) on CL:0000938 until a source is found (Dr. Diehl, 2026-10-05). Neither definition source supports it: PMID:19796267 never mentions HLA-DR; PMID:22343568 mentions HLA-DR on NK cells only as an activation marker. Human evidence: most resting NK cells are HLA-DR− (Evans 2011, PMID:21491418), but an HLA-DR+ subset exists ex vivo, mostly CD56bright (Erokhina 2018, PMID:29363179). HLA-DRA is human-only (PRO: mouse ortholog H2-Ea). Proposed labels: gap. CL:0000938 reports/nk_hladr_conflicts_2026-10.tsv; reports/nk_marker_audit_2026-10.md#hla-dra-on-the-cd16-negative-nk-class; reports/pro_marker_species_support.tsv draft_for_review (not yet filed) 2026-10-05 -CTNK / NK1 / NK3 Cytotoxic Natural Killer Cell / Natural Killer Cell 1 / 3 cl_marker_conflict [Draft B2, on hold] Dr. Diehl described two NK definitions for the same cell, one HLA-DR+ and one HLA-DR−. No CL term asserts HLA-DR+ NK (Ubergraph, 2026-10-05). What exists: CL:0000939 (CD56-dim) ALSO asserts 'lacks HLA-DRA', with the same two unsupporting definition sources as CL:0000938; HLA-DR+ CD56dim cells occur 'in some individuals' (Erokhina 2018, PMID:29363179). Hold until Dr. Diehl confirms which term he meant; if CL:0000939, merge with B1 as one issue covering both IDs. Proposed labels: gap, evidence needed. CL:0000938; CL:0000939 reports/nk_hladr_conflicts_2026-10.tsv; reports/nk_marker_audit_2026-10.md#open-questions-for-alex-and-dr-diehl on_hold (not yet filed) 2026-10-05 +NK2 / CTNK / NK1 / NK3 Natural Killer Cell 2 / Cytotoxic Natural Killer Cell / Natural Killer Cell 1 / 3 cl_marker_conflict [Draft B1] One issue for both terms: remove or disable 'lacks_plasma_membrane_part HLA-DRA' (PR:000002015) on CL:0000938 (CD16-negative, CD56-bright NK, human) and CL:0000939 (CD16-positive, CD56-dim NK, human) until a source is found (Dr. Diehl, 2026-10-05). One issue because both share the same axiom, the same two definition sources and the same evidence. Neither source supports it: PMID:19796267 never mentions HLA-DR; PMID:22343568 mentions HLA-DR on NK cells only as an activation marker. Human evidence: most resting NK cells are HLA-DR− (Evans 2011, PMID:21491418), but an HLA-DR+ subset exists ex vivo, mostly CD56bright and in some individuals CD56dim (Erokhina 2018, PMID:29363179). HLA-DRA is human-only (PRO: mouse ortholog H2-Ea). Proposed labels: gap. CL:0000938; CL:0000939 reports/nk_hladr_conflicts_2026-10.tsv; reports/nk_marker_audit_2026-10.md#hla-dra-on-the-cd16-negative-nk-class; reports/pro_marker_species_support.tsv draft_for_review (not yet filed) 2026-10-05 +CTNK / NK1 / NK3 Cytotoxic Natural Killer Cell / Natural Killer Cell 1 / 3 cl_marker_conflict [B2, not a CL issue] Dr. Diehl described two NK definitions for the same cell, one HLA-DR+ and one HLA-DR−. No CL term asserts HLA-DR+ NK (Ubergraph, 2026-10-05). What exists: CL:0000939 (CD56-dim) ALSO asserts 'lacks HLA-DRA', with the same two unsupporting definition sources as CL:0000938; HLA-DR+ CD56dim cells occur 'in some individuals' (Erokhina 2018, PMID:29363179). Hold until Dr. Diehl confirms which term he meant; if CL:0000939, merge with B1 as one issue covering both IDs. Proposed labels: gap, evidence needed. RESOLVED 2026-10-05 (Alex): the HLA-DR positive vs negative conflict Dr. Diehl described was in his own old curation spreadsheet, not in CL. Nothing to file; CL:0000939 is covered by B1. CL:0000938; CL:0000939 reports/nk_hladr_conflicts_2026-10.tsv; reports/nk_marker_audit_2026-10.md#open-questions-for-alex-and-dr-diehl not_a_cl_issue (not yet filed) 2026-10-05 PB Plasmablast cl_marker_conflict [Draft B3a] Drop 'lacks_plasma_membrane_part syndecan-1 (CD138)' (PR:000001935) from CL:0000980 plasmablast. Contradicted in mouse ('plasmablasts as B220+CD138+', PMID:42774878) and in one human scheme ('short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)', PMID:41771939). The definition source (PMC2673126, Jackson 2009) does not mention CD138. Also remove 'CD138-negative' from the text definition. Proposed labels: gap. CL:0000980 reports/plasmablast_marker_audit_2026-10.md; reports/pro_marker_species_support.tsv; reports/cl_term_issues.md#plasmablast-lacks-cd138--cl0000980-pr000001935-syndecan-1 draft_for_review (not yet filed) 2026-10-05 PB Plasmablast cl_axiom_gap [Draft B3b] Move the remaining plasmablast markers (CD38 high, CD27 high, lacks CD20) from generic CL:0000980 to a new child 'plasmablast, human' (in taxon Homo sapiens), leaving the generic term markerless (Dr. Diehl, 2026-10-05). All three are supported in human and have no mouse evidence, so a mammal-level child isn't supported yet. Optional: 'plasmablast, mouse' with CD138+. Note for discussion, not this issue: plasmablast is already mammal-only through mature B cell → B cell, CD19-positive → CL:0001200 (in taxon Mammalia). Proposed labels: gap, new term request. CL:0000980; CL:0000785; CL:0001200 reports/plasmablast_marker_audit_2026-10.md; reports/pro_marker_species_support.tsv draft_for_review (not yet filed) 2026-10-05 (none: mouse CL term) (no SOULCAP row) cl_marker_conflict [Draft B6a] CL:0002345 'CD27-low, CD11b-low immature natural killer cell, mouse' asserts DX5 (integrin alpha-2 / CD49b, PR:000001008) positive. Mouse immature NK cells are reported to 'lack CD49b expression' (Riggan 2019, PMID:31500958); sibling CL:0002346 is DX5-negative. No supporting quote found (definition source PMID:19949422 abstract doesn't mention DX5). Proposed labels: gap, evidence needed. CL:0002345 reports/nk_marker_audit_2026-10.md#other-findings-issue-candidates; reports/pro_marker_species_support.tsv draft_for_review (not yet filed) 2026-10-05 diff --git a/reports/nk_marker_audit_2026-10.md b/reports/nk_marker_audit_2026-10.md index 5f03c00..7faa2c1 100644 --- a/reports/nk_marker_audit_2026-10.md +++ b/reports/nk_marker_audit_2026-10.md @@ -85,8 +85,8 @@ PMID:41898531). This conflicts with an earlier draft in this repo: the unfiled `NK` row in [gaps.tsv](gaps.tsv) and the "Natural killer cell missing CD56 marker axiom" entry in [cl_term_issues.md](cl_term_issues.md) propose *adding* CD56 to -generic `CL:0000623`. Under Dr. Diehl's rule, that proposal should be -withdrawn. +generic `CL:0000623`. That proposal conflicts with Dr. Diehl's rule and was +**withdrawn** on 2026-10-05. ### Terms that mix human-only and mouse-only markers @@ -120,9 +120,9 @@ opinion. ## Open questions for Alex and Dr. Diehl 1. **Which term has the HLA-DR-positive definition?** Nothing in current CL - matches. Could it be a different resource, an older CL release, or - `CL:0000939` (which is also "lacks")? If it's the latter, the proposed - issue becomes "drop 'lacks HLA-DRA' from both CD56-bright and CD56-dim". + matches. **Resolved 2026-10-05:** the conflict was in Dr. Diehl's own old + curation spreadsheet, not in CL. The HLA-DRA issue draft now covers both + `CL:0000938` and `CL:0000939`. 2. **CD14 in mouse NK:** `no_evidence_found`, not contradicted. Is that good enough to keep the axiom on generic `CL:0000623`, or do you want a mouse source before it stays? @@ -132,7 +132,7 @@ opinion. human child, as with plasmablast? 4. **ILC1, human (`CL:0001077`) IL-7Rα:** this is the standard gate, but Riggan 2019 argues it may miss IL-7Rα-negative human ILC1. Keep as is? -5. **Withdraw the old "add CD56 to `CL:0000623`" draft?** (See NCAM1 above.) +5. ~~Withdraw the old "add CD56 to `CL:0000623`" draft?~~ Withdrawn 2026-10-05. ## Reproducing From 3794b8eac335defe37230f18bd4547c84fa74283 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 5 Oct 2026 20:00:04 -0400 Subject: [PATCH 05/11] docs: group 1 ILC parallel human/mouse hierarchy proposal (Task C, design only) - Before/after trees for the 37-term CL:0001067 subtree (Ubergraph 2026-10-05; parents match CL 2026-03-26). ILC1 and NK kept apart under group 1; NK gets generic, human and mouse branches. - 6 new grouping terms (natural killer cell / immature NK / mature NK, each ", human" and ", mouse") plus 3 optional (uterine NK, human; group 1 ILC, human / mouse, the latter matching issue #14). - 15 re-parentings incl. CL:0002442 under CL:0002438; 4 terms with unclear species and 5 questions flagged for Alex and Dr. Diehl. - TSV lists every term: assignment, current/proposed parents, new term needed, reason. Co-Authored-By: Claude Opus 5.5 --- docs/README.md | 1 + docs/group1_ilc_species_hierarchy_proposal.md | 182 ++++++++++++++++++ .../group1_ilc_species_hierarchy_proposal.tsv | 47 +++++ 3 files changed, 230 insertions(+) create mode 100644 docs/group1_ilc_species_hierarchy_proposal.md create mode 100644 docs/group1_ilc_species_hierarchy_proposal.tsv diff --git a/docs/README.md b/docs/README.md index f7df7c8..7acc549 100644 --- a/docs/README.md +++ b/docs/README.md @@ -10,6 +10,7 @@ pages hold the full detail. | [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 | | [diehl_review_2026-10.md](diehl_review_2026-10.md) | CL issue drafts from the October 2026 NK and plasmablast audit, for Dr. Diehl to approve before anything is filed | +| [group1_ilc_species_hierarchy_proposal.md](group1_ilc_species_hierarchy_proposal.md) | Design proposal for a parallel human / mouse hierarchy under group 1 ILC and NK cell (Dr. Diehl, 2026-10-05): before/after trees, new grouping terms, terms to decide. Per-term changes in the matching [.tsv](group1_ilc_species_hierarchy_proposal.tsv) | | [protege_ncam1_query_repro.md](protege_ncam1_query_repro.md) | Repro note for the Protégé NCAM1 (CD56) query that returned too few classes (Dr. Diehl, 2026-10-05): expected classes, likely causes, what to record | | [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 | diff --git a/docs/group1_ilc_species_hierarchy_proposal.md b/docs/group1_ilc_species_hierarchy_proposal.md new file mode 100644 index 0000000..13abf97 --- /dev/null +++ b/docs/group1_ilc_species_hierarchy_proposal.md @@ -0,0 +1,182 @@ +# Group 1 ILC: parallel human / mouse hierarchy (proposal) + +Design only. Nothing here changes CL. Dr. Diehl asked for the **hierarchy +first** (meeting 2026-10-05); definitions and sources for the new terms are a +second pass. Every term, its current parent and its proposed parent are listed +in [group1_ilc_species_hierarchy_proposal.tsv](group1_ilc_species_hierarchy_proposal.tsv). + +**Source:** the subtree of `CL:0001067` group 1 innate lymphoid cell, pulled from +Ubergraph on 2026-10-05 (37 terms). The parents match the local CL release of +2026-03-26 exactly. `in taxon` values are as asserted. Terms without one inherit +it from a parent. + +## Constraints from the meeting + +- **ILC1 is not group 1.** ILC2/ILC3 are used as synonyms of group 2/group 3, + but group 1 contains two things: ILC1 (non-cytotoxic) and NK cells + (cytotoxic). The proposal keeps `CL:0001068` ILC1 and `CL:0000623` natural + killer cell as separate children of group 1. +- Keep the ", human" / ", mouse" label convention and `in taxon` axioms + (Homo sapiens `NCBITaxon:9606`, Mus musculus `NCBITaxon:10090`). + Hsap/Mmus-style labels are only a possible future option, not proposed here. +- Terms not marked as species-specific stay in the generic hierarchy. +- Pattern to follow: group 2 ILC already has "group 2 innate lymphoid cell, + human" (`CL:0001081`) and "…, mouse" (`CL:0002089`) side by side. Group 3 + has only the human one (`CL:0001078`). + +## Before (current CL) + +`[Hs]` = in taxon Homo sapiens, `[Mm]` = in taxon Mus musculus (asserted on the +term). `(+)` = the term has more than one parent. + +``` +group 1 innate lymphoid cell CL:0001067 +├── ILC1 CL:0001068 +│ └── ILC1, human CL:0001077 [Hs] +└── natural killer cell CL:0000623 + ├── pre-natural killer cell CL:0000937 + ├── immature natural killer cell CL:0000823 (+ immature innate lymphoid cell) + │ ├── CD56-positive, CD161-positive immature NK cell, human CL:0002338 [Hs] + │ ├── CD56-negative, CD161-positive immature NK cell, human CL:0002344 [Hs] + │ ├── CD27-low, CD11b-low immature NK cell, mouse CL:0002345 [Mm] + │ └── Dx5-negative, NK1.1-positive immature NK cell, mouse CL:0002346 [Mm] + ├── mature natural killer cell CL:0000824 + │ ├── CD16-negative, CD56-bright NK cell, human CL:0000938 [Hs] + │ ├── CD16-positive, CD56-dim NK cell, human CL:0000939 [Hs] + │ ├── decidual natural killer cell, human CL:0002343 [Hs] (+ uterine NK, extraembryonic cell) + │ ├── CD27-high, CD11b-high NK cell, mouse CL:0002347 [Mm] + │ ├── CD27-low, CD11b-high NK cell, mouse CL:0002348 [Mm] + │ ├── CD27-high, CD11b-low NK cell, mouse CL:0002349 [Mm] + │ └── NK1.1-positive NK cell, mouse CL:0002438 [Mm] + │ └── 11 Ly49 / CD94 / NKG2A / CD11b-CD27 subsets, mouse + │ (CL:0002426, CL:0002439–0002441, CL:0002443–0002449) + ├── CD94-negative, Ly49CI-negative NK cell, mouse CL:0002442 [Mm] + ├── cycling natural killer cell CL:4033071 + ├── liver-resident natural killer cell CL:4047101 + │ └── hepatic pit cell CL:2000054 + └── uterine natural killer cell CL:4052028 + ├── uterine natural killer cell 1 / 2 / 3, human CL:4052051–4052053 [Hs] + └── decidual natural killer cell, human CL:0002343 [Hs] +``` + +Human and mouse terms are interleaved under the same generic parents, and +there is no node that collects "all human NK" or "all mouse NK". + +## After (proposed) + +`NEW:n` = proposed new grouping term (IDs to be assigned by CL). Species terms +sit under their developmental parent *and* their species branch. + +``` +group 1 innate lymphoid cell CL:0001067 +├── ILC1 CL:0001068 +│ └── ILC1, human CL:0001077 +├── [optional] group 1 innate lymphoid cell, human NEW:8 ── parent of CL:0001077 and NEW:1 +├── [optional] group 1 innate lymphoid cell, mouse NEW:9 ── parent of NEW:2 +└── natural killer cell CL:0000623 + │ + │ generic branch (no species) + ├── pre-natural killer cell CL:0000937 + ├── immature natural killer cell CL:0000823 + │ ├── immature natural killer cell, human NEW:3 + │ └── immature natural killer cell, mouse NEW:4 + ├── mature natural killer cell CL:0000824 + │ ├── mature natural killer cell, human NEW:5 + │ └── mature natural killer cell, mouse NEW:6 + ├── cycling natural killer cell CL:4033071 + ├── liver-resident natural killer cell CL:4047101 + │ └── hepatic pit cell CL:2000054 + ├── uterine natural killer cell CL:4052028 + │ └── [optional] uterine natural killer cell, human NEW:7 + │ + │ human branch + ├── natural killer cell, human NEW:1 [Hs] + │ ├── immature natural killer cell, human NEW:3 [Hs] + │ │ ├── CL:0002338 CD56-positive, CD161-positive immature NK cell, human + │ │ └── CL:0002344 CD56-negative, CD161-positive immature NK cell, human + │ ├── mature natural killer cell, human NEW:5 [Hs] + │ │ ├── CL:0000938 CD16-negative, CD56-bright NK cell, human + │ │ ├── CL:0000939 CD16-positive, CD56-dim NK cell, human + │ │ └── CL:0002343 decidual natural killer cell, human (+ NEW:7 or CL:4052028) + │ └── [optional] uterine natural killer cell, human NEW:7 [Hs] + │ ├── CL:4052051 / CL:4052052 / CL:4052053 uterine NK 1 / 2 / 3, human + │ └── CL:0002343 decidual natural killer cell, human + │ + │ mouse branch + └── natural killer cell, mouse NEW:2 [Mm] + ├── immature natural killer cell, mouse NEW:4 [Mm] + │ ├── CL:0002345 CD27-low, CD11b-low immature NK cell, mouse + │ └── CL:0002346 Dx5-negative, NK1.1-positive immature NK cell, mouse + └── mature natural killer cell, mouse NEW:6 [Mm] + ├── CL:0002347 / CL:0002348 / CL:0002349 CD27/CD11b subsets, mouse + └── CL:0002438 NK1.1-positive NK cell, mouse + ├── 11 existing subsets (unchanged) + └── CL:0002442 CD94-negative, Ly49CI-negative NK cell, mouse (moved here) +``` + +NEW:3–NEW:6 appear twice in the drawing because each has two parents: the +generic stage and the species branch. + +## New grouping terms + +| ID | Label | Parents | Why | +|---|---|---|---| +| NEW:1 | natural killer cell, human | `CL:0000623` | The human branch under NK; collects every human NK term. | +| NEW:2 | natural killer cell, mouse | `CL:0000623` | The mouse branch under NK. | +| NEW:3 | immature natural killer cell, human | `CL:0000823`, NEW:1 | Human/mouse pair for immature NK; parent of `CL:0002338`, `CL:0002344`. | +| NEW:4 | immature natural killer cell, mouse | `CL:0000823`, NEW:2 | Parent of `CL:0002345`, `CL:0002346`. | +| NEW:5 | mature natural killer cell, human | `CL:0000824`, NEW:1 | Dr. Diehl's example pair; parent of `CL:0000938`, `CL:0000939`, `CL:0002343`. | +| NEW:6 | mature natural killer cell, mouse | `CL:0000824`, NEW:2 | Parent of `CL:0002347`–`CL:0002349` and `CL:0002438`. | +| NEW:7 | uterine natural killer cell, human *(optional)* | `CL:4052028`, NEW:1 | All 4 current uterine/decidual NK subtypes are human. | +| NEW:8 | group 1 innate lymphoid cell, human *(optional)* | `CL:0001067` | Matches group 2/3; this is what repo issue #14 already asks for. | +| NEW:9 | group 1 innate lymphoid cell, mouse *(optional)* | `CL:0001067` | Mouse counterpart of NEW:8. CL has no "ILC1, mouse" term yet. | + +Six terms are needed for the structure Dr. Diehl described (NEW:1–6). The +other three are optional. + +**One modelling choice for David's team:** NEW:3–NEW:6 need two parents each. They can be +asserted by hand, or the species grouping terms can be given logical +definitions (for example "natural killer cell and in taxon some Homo sapiens") +so the reasoner places them. This proposal doesn't depend on which is used. + +## Existing terms that move + +| Term | From | To | +|---|---|---| +| `CL:0000938`, `CL:0000939` | mature NK `CL:0000824` | NEW:5 | +| `CL:0002343` | mature NK; uterine NK; extraembryonic cell | NEW:5; NEW:7 (or uterine NK); extraembryonic cell | +| `CL:0002338`, `CL:0002344` | immature NK `CL:0000823` | NEW:3 | +| `CL:0002345`, `CL:0002346` | immature NK `CL:0000823` | NEW:4 | +| `CL:0002347`, `CL:0002348`, `CL:0002349`, `CL:0002438` | mature NK `CL:0000824` | NEW:6 | +| `CL:4052051`–`CL:4052053` | uterine NK `CL:4052028` | NEW:7 (only if adopted) | +| `CL:0002442` | natural killer cell `CL:0000623` | `CL:0002438` NK1.1-positive NK cell, mouse (its definition says NK1.1-positive; all its siblings are there) | + +Nothing else moves: the 11 subsets under `CL:0002438` go along with it, and all +generic terms stay where they are. + +## For Alex and Dr. Diehl to decide + +**Species unclear (left generic for now):** + +| Term | Why it's unclear | +|---|---| +| `CL:4047101` liver-resident natural killer cell | Label is generic, but the definition gives human markers ("In humans this cell type is distinguished … by CD49a or CD69"). Dr. Diehl named it as generic; the human-marker sentences could later move to a human child. | +| `CL:4052028` uterine natural killer cell | Label is generic, but the definition describes changes over the menstrual cycle, which mice don't have. | +| `CL:4033071` cycling natural killer cell | No species stated; the definition source wasn't checked. | +| `CL:2000054` hepatic pit cell | "Liver specific" NK cell; no species in label or definition. | + +**Other questions:** + +1. Adopt the optional NEW:7 (uterine, human) and NEW:8/9 (group 1 ILC, human/mouse)? + NEW:8 would close repo issue #14. +2. `CL:0002349` CD27-high, CD11b-low NK cell, mouse sits under *mature* NK, but + in Chiossone 2009 (PMID:19234143) CD11b-low CD27-high is the second of four + maturation stages. Should it move to immature NK, mouse (NEW:4)? +3. `CL:0002426` CD11b-positive, CD27-positive NK cell, mouse may duplicate + `CL:0002347` CD27-high, CD11b-high NK cell, mouse. Merge? +4. `CL:0002346` Dx5-negative, NK1.1-positive immature NK cell, mouse: these + cells overlap with ILC1 (Riggan 2019, PMID:31500958). Keep it under NK? +5. `pro-NK cell` (`CL:0000825`) sits under lymphoid lineage-restricted progenitor + rather than group 1, and the human ILC precursors (`CL:0001072`–`CL:0001076`) + sit under immature innate lymphoid cell. Both are out of scope here. Should + they be included in a later pass? diff --git a/docs/group1_ilc_species_hierarchy_proposal.tsv b/docs/group1_ilc_species_hierarchy_proposal.tsv new file mode 100644 index 0000000..94fee33 --- /dev/null +++ b/docs/group1_ilc_species_hierarchy_proposal.tsv @@ -0,0 +1,47 @@ +term_id label species_assignment current_in_taxon current_parents proposed_parents new_term_needed change reason +CL:0000623 natural killer cell generic CL:0001067 group 1 innate lymphoid cell CL:0001067 group 1 innate lymphoid cell no none Generic NK; keeps only lack statements. +CL:0000823 immature natural killer cell generic CL:0000623 natural killer cell; CL:0001082 immature innate lymphoid cell CL:0000623 natural killer cell; CL:0001082 immature innate lymphoid cell no none Generic developmental stage; its species children move under NEW:3 / NEW:4. Keeps its second parent CL:0001082 immature innate lymphoid cell. +CL:0000824 mature natural killer cell generic CL:0000623 natural killer cell CL:0000623 natural killer cell no none Generic developmental stage; its species children move under NEW:5 / NEW:6. +CL:0000937 pre-natural killer cell generic CL:0000623 natural killer cell CL:0000623 natural killer cell no none Stays generic (Dr. Diehl). Its markers fit human stage 2; see the on-hold item in docs/diehl_review_2026-10.md. +CL:0000938 CD16-negative, CD56-bright natural killer cell, human human NCBITaxon:9606 Homo sapiens CL:0000824 mature natural killer cell NEW:5 mature natural killer cell, human no re-parent Human mature NK subset. +CL:0000939 CD16-positive, CD56-dim natural killer cell, human human NCBITaxon:9606 Homo sapiens CL:0000824 mature natural killer cell NEW:5 mature natural killer cell, human no re-parent Human mature NK subset. +CL:0001067 group 1 innate lymphoid cell generic CL:0001065 innate lymphoid cell CL:0001065 innate lymphoid cell no none Top of the hierarchy (Dr. Diehl). Not the same as ILC1. +CL:0001068 ILC1 generic CL:0001067 group 1 innate lymphoid cell CL:0001067 group 1 innate lymphoid cell no none Non-cytotoxic group 1 ILC. Not a synonym of group 1, and not NK. +CL:0001077 ILC1, human human NCBITaxon:9606 Homo sapiens CL:0001068 ILC1 CL:0001068 ILC1 no none Already split. Would also go under NEW:8 if that is adopted. +CL:0002338 CD56-positive, CD161-positive immature natural killer cell, human human NCBITaxon:9606 Homo sapiens CL:0000823 immature natural killer cell NEW:3 immature natural killer cell, human no re-parent Human immature NK (stage 3-like). +CL:0002343 decidual natural killer cell, human human NCBITaxon:9606 Homo sapiens CL:0000349 extraembryonic cell; CL:0000824 mature natural killer cell; CL:4052028 uterine natural killer cell NEW:5 mature natural killer cell, human; NEW:7 uterine natural killer cell, human (if adopted, else CL:4052028); CL:0000349 extraembryonic cell no re-parent Human; keeps its extraembryonic cell parent. +CL:0002344 CD56-negative, CD161-positive immature natural killer cell, human human NCBITaxon:9606 Homo sapiens CL:0000823 immature natural killer cell NEW:3 immature natural killer cell, human no re-parent Human immature NK (stage 3-like). +CL:0002345 CD27-low, CD11b-low immature natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000823 immature natural killer cell NEW:4 immature natural killer cell, mouse no re-parent Mouse immature NK. +CL:0002346 Dx5-negative, NK1.1-positive immature natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000823 immature natural killer cell NEW:4 immature natural killer cell, mouse no re-parent Mouse immature NK. DX5-negative NK1.1-positive cells overlap with ILC1 (Riggan 2019, PMID:31500958). +CL:0002347 CD27-high, CD11b-high natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000824 mature natural killer cell NEW:6 mature natural killer cell, mouse no re-parent Mouse CD27/CD11b subset. +CL:0002348 CD27-low, CD11b-high natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000824 mature natural killer cell NEW:6 mature natural killer cell, mouse no re-parent Mouse CD27/CD11b subset. +CL:0002349 CD27-high, CD11b-low natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000824 mature natural killer cell NEW:6 mature natural killer cell, mouse no re-parent Mouse CD27/CD11b subset. CD11b-low CD27-high is an earlier maturation stage in Chiossone 2009 (PMID:19234143), yet the term sits under mature NK. Check the placement. +CL:0002426 CD11b-positive, CD27-positive natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). Possible duplicate of CL:0002347. +CL:0002438 NK1.1-positive natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000824 mature natural killer cell NEW:6 mature natural killer cell, mouse no re-parent Mouse NK1.1+ NK; its 11 descendants move with it. +CL:0002439 NKGA2-positive natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:0002440 Ly49D-positive natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:0002441 CD94-positive natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:0002442 CD94-negative, Ly49CI-negative natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000623 natural killer cell CL:0002438 NK1.1-positive natural killer cell, mouse no re-parent The only Ly49/CD94 subset not under CL:0002438, although its definition says NK1.1-positive. Re-parent (it then falls under NEW:2 through CL:0002438). +CL:0002443 Ly49CI-positive natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:0002444 Ly49H-positive natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:0002445 Ly49D-negative natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:0002446 Ly49CI-negative natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:0002447 CD94-negative natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:0002448 Ly49H-negative natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:0002449 CD94-positive Ly49CI-positive natural killer cell, mouse mouse CL:0002441 CD94-positive natural killer cell, mouse; CL:0002443 Ly49CI-positive natural killer cell, mouse CL:0002441 CD94-positive natural killer cell, mouse; CL:0002443 Ly49CI-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). +CL:2000054 hepatic pit cell unclear CL:4047101 liver-resident natural killer cell CL:4047101 liver-resident natural killer cell no none 'Liver specific' NK cell with no species in the label or definition. Stays generic under liver-resident NK. +CL:4033071 cycling natural killer cell unclear CL:0000623 natural killer cell CL:0000623 natural killer cell no none Generic label; the definition source (PMID:34062119) was not checked for species. Stays generic unless you decide otherwise. +CL:4047101 liver-resident natural killer cell unclear CL:0000623 natural killer cell CL:0000623 natural killer cell no none Generic label, but the definition gives human markers ('In humans this cell type is distinguished ...'). Stays generic (Dr. Diehl's example); the human marker sentences could later move to a human child. +CL:4052028 uterine natural killer cell unclear CL:0000623 natural killer cell CL:0000623 natural killer cell no none Generic label, but the definition describes changes over the menstrual cycle, which mice don't have. Stays generic; the wording may need to change. +CL:4052051 uterine natural killer cell 1, human human NCBITaxon:9606 Homo sapiens CL:4052028 uterine natural killer cell NEW:7 uterine natural killer cell, human (if adopted, else unchanged) no re-parent Human uterine NK subset. +CL:4052052 uterine natural killer cell 2, human human NCBITaxon:9606 Homo sapiens CL:4052028 uterine natural killer cell NEW:7 uterine natural killer cell, human (if adopted, else unchanged) no re-parent Human uterine NK subset. +CL:4052053 uterine natural killer cell 3, human human NCBITaxon:9606 Homo sapiens CL:4052028 uterine natural killer cell NEW:7 uterine natural killer cell, human (if adopted, else unchanged) no re-parent Human uterine NK subset. +NEW:1 natural killer cell, human human CL:0000623 natural killer cell yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) Human branch under NK: groups every human NK term (Dr. Diehl, 2026-10-05). +NEW:2 natural killer cell, mouse mouse CL:0000623 natural killer cell yes new grouping term (in taxon NCBITaxon:10090 Mus musculus) Mouse branch under NK: groups every mouse NK term. +NEW:3 immature natural killer cell, human human CL:0000823 immature natural killer cell; NEW:1 natural killer cell, human yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) Parallel pair for immature NK; groups CL:0002338 and CL:0002344. +NEW:4 immature natural killer cell, mouse mouse CL:0000823 immature natural killer cell; NEW:2 natural killer cell, mouse yes new grouping term (in taxon NCBITaxon:10090 Mus musculus) Parallel pair for immature NK; groups CL:0002345 and CL:0002346. +NEW:5 mature natural killer cell, human human CL:0000824 mature natural killer cell; NEW:1 natural killer cell, human yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) Dr. Diehl's example pair; groups CL:0000938, CL:0000939 and CL:0002343. +NEW:6 mature natural killer cell, mouse mouse CL:0000824 mature natural killer cell; NEW:2 natural killer cell, mouse yes new grouping term (in taxon NCBITaxon:10090 Mus musculus) Dr. Diehl's example pair; groups CL:0002347, CL:0002348, CL:0002349 and CL:0002438 with its subtree. +NEW:7 uterine natural killer cell, human human CL:4052028 uterine natural killer cell; NEW:1 natural killer cell, human yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) OPTIONAL. Groups uNK1-3 and decidual NK, which are all human; the generic uterine NK term stays for other species. Decide. +NEW:8 group 1 innate lymphoid cell, human human CL:0001067 group 1 innate lymphoid cell yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) OPTIONAL. Same request as repo issue #14 (no human group 1 term, unlike group 2 and 3). Would be the parent of CL:0001077 ILC1, human and NEW:1. Decide. +NEW:9 group 1 innate lymphoid cell, mouse mouse CL:0001067 group 1 innate lymphoid cell yes new grouping term (in taxon NCBITaxon:10090 Mus musculus) OPTIONAL. Mouse counterpart of NEW:8 and parent of NEW:2. CL has no 'ILC1, mouse' term to put under it. Decide. From ba7d29de62c484d6c40e1cdc665d8023f1a80606 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 5 Oct 2026 20:27:08 -0400 Subject: [PATCH 06/11] =?UTF-8?q?docs:=20Task=20C=20follow-ups=20=E2=80=94?= =?UTF-8?q?=20existing-term=20check,=20defaults,=20decisions=20list?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Proposal: "Why a parallel hierarchy"; none of NEW:1-9 exists in CL incl. obsolete terms (52 label variants vs CL 2026-03-26 and Ubergraph); NEW:7 and NEW:8 (issue #14) recommended, NEW:9 optional; logical definitions with in_taxon as the suggested two-parent default. - Recommended defaults for the four unclear-species terms with sources: mice have uNK (Shreeve 2021); hepatic pit cell first described in rat (Wisse 1976, PMID:991252); cycling NK source is human PBMC (Hao 2021). - CL:0002349 note kept with the exact Chiossone 2009 four-stage quote and Andrews 2010 (both abstracts; Chiossone full text not accessible). - gaps.tsv: draft C1, liver-resident NK human sentences to a human child. - diehl_review_2026-10.md: numbered "Decisions needed" list up top. Co-Authored-By: Claude Opus 5.5 --- docs/diehl_review_2026-10.md | 34 +++++ docs/group1_ilc_species_hierarchy_proposal.md | 118 ++++++++++++------ .../group1_ilc_species_hierarchy_proposal.tsv | 22 ++-- reports/gaps.tsv | 1 + 4 files changed, 129 insertions(+), 46 deletions(-) diff --git a/docs/diehl_review_2026-10.md b/docs/diehl_review_2026-10.md index 7e2e4f8..281ebf5 100644 --- a/docs/diehl_review_2026-10.md +++ b/docs/diehl_review_2026-10.md @@ -10,6 +10,40 @@ full text. Full detail is in [reports/plasmablast_marker_audit_2026-10.md](../reports/plasmablast_marker_audit_2026-10.md) and the draft rows at the end of [reports/gaps.tsv](../reports/gaps.tsv). +## Decisions needed from Dr. Diehl + +Issue drafts (details below): + +1. **B1** HLA-DRA on the CD56-bright and CD56-dim NK terms: file, change or drop? +2. **B3a** plasmablast "lacks CD138": file, change or drop? +3. **B3b** plasmablast child: Option 1 "plasmablast, human" or Option 2 a + mammal-level child? And should the mature B cell → Mammalia link be raised + as its own issue? +4. **Batch 2** (B6a DX5 on `CL:0002345`, B6b wrong PMID, B6c "T cell" + wording, B6d galectin-1 relation): file, change or drop, each. +5. **Pre-NK** (`CL:0000937`, on hold): move CD34/CD117/CD122 to a human child? + +Group 1 ILC hierarchy (details in +[group1_ilc_species_hierarchy_proposal.md](group1_ilc_species_hierarchy_proposal.md)): + +6. **Terms with unclear species.** Accept the recommended defaults? + - Keep uterine NK, liver-resident NK, hepatic pit cell and cycling NK generic. + - Make the uterine NK definition species-neutral. + - Move liver-resident NK's human sentences to a human child (draft C1 in + `gaps.tsv`). +7. **New grouping terms.** NEW:7 "uterine natural killer cell, human" and + NEW:8 "group 1 innate lymphoid cell, human" (issue #14) are recommended. + NEW:9 "group 1 innate lymphoid cell, mouse" is optional. Which do you want? +8. **Two parents.** Logical definitions with `in taxon` (suggested default), or + hand-asserted parents? +9. **`CL:0002349`** CD27-high, CD11b-low NK cell, mouse: move from mature to + immature NK, mouse? +10. **`CL:0002426`**: merge with `CL:0002347`, which it may duplicate? +11. **`CL:0002346`** Dx5-negative, NK1.1-positive immature NK cell, mouse: + keep under NK despite its overlap with ILC1? + +--- + **The HLA-DR positive vs negative conflict** you described was in your old curation spreadsheet, not in CL, so it isn't a CL issue. In CL, both NK subset terms say "lacks HLA-DRA", and B1 below covers both. diff --git a/docs/group1_ilc_species_hierarchy_proposal.md b/docs/group1_ilc_species_hierarchy_proposal.md index 13abf97..46d146c 100644 --- a/docs/group1_ilc_species_hierarchy_proposal.md +++ b/docs/group1_ilc_species_hierarchy_proposal.md @@ -5,6 +5,16 @@ first** (meeting 2026-10-05); definitions and sources for the new terms are a second pass. Every term, its current parent and its proposed parent are listed in [group1_ilc_species_hierarchy_proposal.tsv](group1_ilc_species_hierarchy_proposal.tsv). +## Why a parallel hierarchy + +Grouping all human NK terms under one node and all mouse NK terms under +another makes species-specific terms easy to find, instead of having them +interleaved under the same generic parents. It also lines SOULCAP's human +cell types up against a human-only branch of CL. The generic terms stay free of +species markers, so zebrafish and other non-mammal users can still use them. +The cost is extra grouping terms (6 required, 2 recommended, 1 optional) and more terms with +two parents, which makes the hierarchy more complex to maintain. + **Source:** the subtree of `CL:0001067` group 1 innate lymphoid cell, pulled from Ubergraph on 2026-10-05 (37 terms). The parents match the local CL release of 2026-03-26 exactly. `in taxon` values are as asserted. Terms without one inherit @@ -71,7 +81,7 @@ sit under their developmental parent *and* their species branch. group 1 innate lymphoid cell CL:0001067 ├── ILC1 CL:0001068 │ └── ILC1, human CL:0001077 -├── [optional] group 1 innate lymphoid cell, human NEW:8 ── parent of CL:0001077 and NEW:1 +├── [recommended] group 1 innate lymphoid cell, human NEW:8 ── parent of CL:0001077 and NEW:1 ├── [optional] group 1 innate lymphoid cell, mouse NEW:9 ── parent of NEW:2 └── natural killer cell CL:0000623 │ @@ -87,7 +97,7 @@ group 1 innate lymphoid cell CL:0001067 ├── liver-resident natural killer cell CL:4047101 │ └── hepatic pit cell CL:2000054 ├── uterine natural killer cell CL:4052028 - │ └── [optional] uterine natural killer cell, human NEW:7 + │ └── [recommended] uterine natural killer cell, human NEW:7 │ │ human branch ├── natural killer cell, human NEW:1 [Hs] @@ -98,7 +108,7 @@ group 1 innate lymphoid cell CL:0001067 │ │ ├── CL:0000938 CD16-negative, CD56-bright NK cell, human │ │ ├── CL:0000939 CD16-positive, CD56-dim NK cell, human │ │ └── CL:0002343 decidual natural killer cell, human (+ NEW:7 or CL:4052028) - │ └── [optional] uterine natural killer cell, human NEW:7 [Hs] + │ └── [recommended] uterine natural killer cell, human NEW:7 [Hs] │ ├── CL:4052051 / CL:4052052 / CL:4052053 uterine NK 1 / 2 / 3, human │ └── CL:0002343 decidual natural killer cell, human │ @@ -127,17 +137,40 @@ generic stage and the species branch. | NEW:4 | immature natural killer cell, mouse | `CL:0000823`, NEW:2 | Parent of `CL:0002345`, `CL:0002346`. | | NEW:5 | mature natural killer cell, human | `CL:0000824`, NEW:1 | Dr. Diehl's example pair; parent of `CL:0000938`, `CL:0000939`, `CL:0002343`. | | NEW:6 | mature natural killer cell, mouse | `CL:0000824`, NEW:2 | Parent of `CL:0002347`–`CL:0002349` and `CL:0002438`. | -| NEW:7 | uterine natural killer cell, human *(optional)* | `CL:4052028`, NEW:1 | All 4 current uterine/decidual NK subtypes are human. | -| NEW:8 | group 1 innate lymphoid cell, human *(optional)* | `CL:0001067` | Matches group 2/3; this is what repo issue #14 already asks for. | +| NEW:7 | uterine natural killer cell, human *(recommended)* | `CL:4052028`, NEW:1 | All 4 current uterine/decidual NK subtypes are human; takes the menstrual-cycle wording from `CL:4052028`. | +| NEW:8 | group 1 innate lymphoid cell, human *(recommended)* | `CL:0001067` | Matches group 2/3; requested in [repo issue #14](https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/14). | | NEW:9 | group 1 innate lymphoid cell, mouse *(optional)* | `CL:0001067` | Mouse counterpart of NEW:8. CL has no "ILC1, mouse" term yet. | -Six terms are needed for the structure Dr. Diehl described (NEW:1–6). The -other three are optional. - -**One modelling choice for David's team:** NEW:3–NEW:6 need two parents each. They can be -asserted by hand, or the species grouping terms can be given logical -definitions (for example "natural killer cell and in taxon some Homo sapiens") -so the reasoner places them. This proposal doesn't depend on which is used. +Six terms are needed for the structure Dr. Diehl described (NEW:1–6). +**NEW:7 and NEW:8 are recommended**: +- NEW:7 gives the human-only menstrual-cycle wording a home (see uterine NK below). +- NEW:8 is the term [repo issue #14](https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/14) asks for. + +NEW:9 is optional, for Dr. Diehl to decide. + +**None of these terms exists in CL already**, obsolete terms included. Checked +on 2026-10-05 against 52 variants of the nine labels: +- "…, human", "human …", "… human", the same with "NK cell", and for group 1 + also "group 1 ILC, …" and "human/mouse ILC1". +- Matched against every label and synonym (exact, related, broad, narrow) in + the local CL release of 2026-03-26, which includes its 272 obsolete terms. +- Also matched against Ubergraph: the labels and synonyms of all + innate lymphoid cell descendants, and of all 199 deprecated CL terms. + +The only near-hit was `CL:0001077` "ILC1, human". It is ILC1, not group 1, so +it is not a match for NEW:8. The OLS4 search API was returning incomplete +results that day, so it wasn't used. + +**Two parents (question for Dr. Diehl):** NEW:3–NEW:6 and the terms under them +need both a developmental parent and a species parent. There are two ways to +do this: +- **Logical definitions (suggested default):** give each species grouping term + a definition such as "natural killer cell and in taxon some Homo sapiens" and + let the reasoner place terms under it. Every term that carries an `in taxon` + axiom then lands in the right branch automatically, and new terms can't be + forgotten. +- **Hand-asserted parents:** simpler to read in the source file, but every new + species term needs both parents added by hand. ## Existing terms that move @@ -148,7 +181,7 @@ so the reasoner places them. This proposal doesn't depend on which is used. | `CL:0002338`, `CL:0002344` | immature NK `CL:0000823` | NEW:3 | | `CL:0002345`, `CL:0002346` | immature NK `CL:0000823` | NEW:4 | | `CL:0002347`, `CL:0002348`, `CL:0002349`, `CL:0002438` | mature NK `CL:0000824` | NEW:6 | -| `CL:4052051`–`CL:4052053` | uterine NK `CL:4052028` | NEW:7 (only if adopted) | +| `CL:4052051`–`CL:4052053` | uterine NK `CL:4052028` | NEW:7 (recommended) | | `CL:0002442` | natural killer cell `CL:0000623` | `CL:0002438` NK1.1-positive NK cell, mouse (its definition says NK1.1-positive; all its siblings are there) | Nothing else moves: the 11 subsets under `CL:0002438` go along with it, and all @@ -156,27 +189,42 @@ generic terms stay where they are. ## For Alex and Dr. Diehl to decide -**Species unclear (left generic for now):** +### Terms with unclear species: recommended defaults -| Term | Why it's unclear | -|---|---| -| `CL:4047101` liver-resident natural killer cell | Label is generic, but the definition gives human markers ("In humans this cell type is distinguished … by CD49a or CD69"). Dr. Diehl named it as generic; the human-marker sentences could later move to a human child. | -| `CL:4052028` uterine natural killer cell | Label is generic, but the definition describes changes over the menstrual cycle, which mice don't have. | -| `CL:4033071` cycling natural killer cell | No species stated; the definition source wasn't checked. | -| `CL:2000054` hepatic pit cell | "Liver specific" NK cell; no species in label or definition. | - -**Other questions:** - -1. Adopt the optional NEW:7 (uterine, human) and NEW:8/9 (group 1 ILC, human/mouse)? - NEW:8 would close repo issue #14. -2. `CL:0002349` CD27-high, CD11b-low NK cell, mouse sits under *mature* NK, but - in Chiossone 2009 (PMID:19234143) CD11b-low CD27-high is the second of four - maturation stages. Should it move to immature NK, mouse (NEW:4)? -3. `CL:0002426` CD11b-positive, CD27-positive NK cell, mouse may duplicate +| Term | Evidence | Recommended default | +|---|---|---| +| `CL:4052028` uterine natural killer cell | Mice have uterine NK cells too: "The conserved CD94/NKG2A inhibitory receptor is expressed by nearly all human and ∼50% of mouse uterine natural killer (uNK) cells." (Shreeve N et al. 2021, PMID:33887202). But the current definition describes changes over the menstrual cycle, which is human wording. | **Keep generic.** Rewrite its definition to be species-neutral and move the menstrual-cycle wording to NEW:7 "uterine natural killer cell, human" (recommended). | +| `CL:4047101` liver-resident natural killer cell | Generic label; the definition adds human markers ("In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression"). | **Keep generic.** A separate draft (`gaps.tsv`, status `draft_for_review`) proposes moving the human-marker sentences to a human child term. | +| `CL:2000054` hepatic pit cell | First described in rat: "The pit cell: description of a new type of cell occurring in rat liver sinusoids and peripheral blood." (Wisse E et al. 1976, PMID:991252, title). CL's definition cites a later review (Wisse E et al. 1997, PMID:9408963) that names no species. | **Keep generic** under liver-resident NK. It isn't human- or mouse-specific, and the original species is rat. | +| `CL:4033071` cycling natural killer cell | The only definition source is a human study: "a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs)", in which "a small population of NK cells expressing proliferation and cell-cycle genes (NK_proliferation), consistently increased upon vaccination" (Hao Y et al. 2021, PMID:34062119). | **Keep generic.** A cycling state isn't species-specific, even though the source is human. Note the human source in the definition. | + +### Other questions + +1. **NEW:7 and NEW:8 are recommended. Adopt them?** NEW:8 would close + [repo issue #14](https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/14). + NEW:9 (group 1 ILC, mouse) is optional. +2. **Two parents:** logical definitions with `in taxon` (suggested default) or + hand-asserted parents? See [New grouping terms](#new-grouping-terms). +3. **`CL:0002349` CD27-high, CD11b-low NK cell, mouse** sits under *mature* + NK, but two sources place this phenotype early in maturation: + > "The results of these various experiments collectively support a 4-stage + > model of NK-cell maturation CD11b(low)CD27(low) --> CD11b(low)CD27(high) + > --> CD11b(high)CD27(high) --> CD11b(high)CD27(low)." + > — Chiossone L et al. 2009 (PMID:19234143), abstract + + > "Neonatal NK cells in the bone marrow, spleen and lung exist as immature + > CD27(+)/CD11B(lo) cells." — Andrews DM et al. 2010 (PMID:19949422), abstract + + Both quotes are checked against the Europe PMC abstracts. **Chiossone's + full text could not be checked:** it isn't in PMC, the publisher's page + blocks automated access, and the Undermind connector was unreachable. The + note is kept on the strength of the two abstracts. Should `CL:0002349` move + to immature NK, mouse (NEW:4)? +4. **`CL:0002426`** CD11b-positive, CD27-positive NK cell, mouse may duplicate `CL:0002347` CD27-high, CD11b-high NK cell, mouse. Merge? -4. `CL:0002346` Dx5-negative, NK1.1-positive immature NK cell, mouse: these - cells overlap with ILC1 (Riggan 2019, PMID:31500958). Keep it under NK? -5. `pro-NK cell` (`CL:0000825`) sits under lymphoid lineage-restricted progenitor - rather than group 1, and the human ILC precursors (`CL:0001072`–`CL:0001076`) - sit under immature innate lymphoid cell. Both are out of scope here. Should - they be included in a later pass? +5. **`CL:0002346`** Dx5-negative, NK1.1-positive immature NK cell, mouse: + these cells overlap with ILC1 (Riggan 2019, PMID:31500958). Keep it under NK? +6. `pro-NK cell` (`CL:0000825`) sits under lymphoid lineage-restricted + progenitor rather than group 1, and the human ILC precursors + (`CL:0001072`–`CL:0001076`) sit under immature innate lymphoid cell. Both + are out of scope here. Include them in a later pass? diff --git a/docs/group1_ilc_species_hierarchy_proposal.tsv b/docs/group1_ilc_species_hierarchy_proposal.tsv index 94fee33..8a7e746 100644 --- a/docs/group1_ilc_species_hierarchy_proposal.tsv +++ b/docs/group1_ilc_species_hierarchy_proposal.tsv @@ -15,7 +15,7 @@ CL:0002345 CD27-low, CD11b-low immature natural killer cell, mouse mouse NCBITax CL:0002346 Dx5-negative, NK1.1-positive immature natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000823 immature natural killer cell NEW:4 immature natural killer cell, mouse no re-parent Mouse immature NK. DX5-negative NK1.1-positive cells overlap with ILC1 (Riggan 2019, PMID:31500958). CL:0002347 CD27-high, CD11b-high natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000824 mature natural killer cell NEW:6 mature natural killer cell, mouse no re-parent Mouse CD27/CD11b subset. CL:0002348 CD27-low, CD11b-high natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000824 mature natural killer cell NEW:6 mature natural killer cell, mouse no re-parent Mouse CD27/CD11b subset. -CL:0002349 CD27-high, CD11b-low natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000824 mature natural killer cell NEW:6 mature natural killer cell, mouse no re-parent Mouse CD27/CD11b subset. CD11b-low CD27-high is an earlier maturation stage in Chiossone 2009 (PMID:19234143), yet the term sits under mature NK. Check the placement. +CL:0002349 CD27-high, CD11b-low natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000824 mature natural killer cell NEW:6 mature natural killer cell, mouse no re-parent Mouse CD27/CD11b subset. CD11b-low CD27-high is the second of four maturation stages (Chiossone 2009, PMID:19234143, abstract; full text not accessible) and immature in neonates (Andrews 2010, PMID:19949422), yet the term sits under mature NK. Question for Dr. Diehl: move to NEW:4? CL:0002426 CD11b-positive, CD27-positive natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). Possible duplicate of CL:0002347. CL:0002438 NK1.1-positive natural killer cell, mouse mouse NCBITaxon:10090 Mus musculus CL:0000824 mature natural killer cell NEW:6 mature natural killer cell, mouse no re-parent Mouse NK1.1+ NK; its 11 descendants move with it. CL:0002439 NKGA2-positive natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). @@ -29,19 +29,19 @@ CL:0002446 Ly49CI-negative natural killer cell, mouse mouse CL:0002438 NK1.1-po CL:0002447 CD94-negative natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). CL:0002448 Ly49H-negative natural killer cell, mouse mouse CL:0002438 NK1.1-positive natural killer cell, mouse CL:0002438 NK1.1-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). CL:0002449 CD94-positive Ly49CI-positive natural killer cell, mouse mouse CL:0002441 CD94-positive natural killer cell, mouse; CL:0002443 Ly49CI-positive natural killer cell, mouse CL:0002441 CD94-positive natural killer cell, mouse; CL:0002443 Ly49CI-positive natural killer cell, mouse no none Stays under its current mouse parent (mouse taxon inherited). -CL:2000054 hepatic pit cell unclear CL:4047101 liver-resident natural killer cell CL:4047101 liver-resident natural killer cell no none 'Liver specific' NK cell with no species in the label or definition. Stays generic under liver-resident NK. -CL:4033071 cycling natural killer cell unclear CL:0000623 natural killer cell CL:0000623 natural killer cell no none Generic label; the definition source (PMID:34062119) was not checked for species. Stays generic unless you decide otherwise. -CL:4047101 liver-resident natural killer cell unclear CL:0000623 natural killer cell CL:0000623 natural killer cell no none Generic label, but the definition gives human markers ('In humans this cell type is distinguished ...'). Stays generic (Dr. Diehl's example); the human marker sentences could later move to a human child. -CL:4052028 uterine natural killer cell unclear CL:0000623 natural killer cell CL:0000623 natural killer cell no none Generic label, but the definition describes changes over the menstrual cycle, which mice don't have. Stays generic; the wording may need to change. -CL:4052051 uterine natural killer cell 1, human human NCBITaxon:9606 Homo sapiens CL:4052028 uterine natural killer cell NEW:7 uterine natural killer cell, human (if adopted, else unchanged) no re-parent Human uterine NK subset. -CL:4052052 uterine natural killer cell 2, human human NCBITaxon:9606 Homo sapiens CL:4052028 uterine natural killer cell NEW:7 uterine natural killer cell, human (if adopted, else unchanged) no re-parent Human uterine NK subset. -CL:4052053 uterine natural killer cell 3, human human NCBITaxon:9606 Homo sapiens CL:4052028 uterine natural killer cell NEW:7 uterine natural killer cell, human (if adopted, else unchanged) no re-parent Human uterine NK subset. +CL:2000054 hepatic pit cell generic CL:4047101 liver-resident natural killer cell CL:4047101 liver-resident natural killer cell no none Recommended default: keep generic under liver-resident NK. First described in rat (Wisse 1976, PMID:991252); CL cites a later review naming no species. +CL:4033071 cycling natural killer cell generic CL:0000623 natural killer cell CL:0000623 natural killer cell no none Recommended default: keep generic. The only definition source (Hao 2021, PMID:34062119) is a human PBMC study, but a cycling state is not species-specific. +CL:4047101 liver-resident natural killer cell generic CL:0000623 natural killer cell CL:0000623 natural killer cell no none Recommended default: keep generic (Dr. Diehl's example). Separate gaps.tsv draft proposes moving the human-marker sentences of the definition to a human child term. +CL:4052028 uterine natural killer cell generic CL:0000623 natural killer cell CL:0000623 natural killer cell no none Recommended default: keep generic (mice have uterine NK cells, Shreeve 2021, PMID:33887202). Make the definition species-neutral and move the menstrual-cycle wording to NEW:7. +CL:4052051 uterine natural killer cell 1, human human NCBITaxon:9606 Homo sapiens CL:4052028 uterine natural killer cell NEW:7 uterine natural killer cell, human (recommended) no re-parent Human uterine NK subset. +CL:4052052 uterine natural killer cell 2, human human NCBITaxon:9606 Homo sapiens CL:4052028 uterine natural killer cell NEW:7 uterine natural killer cell, human (recommended) no re-parent Human uterine NK subset. +CL:4052053 uterine natural killer cell 3, human human NCBITaxon:9606 Homo sapiens CL:4052028 uterine natural killer cell NEW:7 uterine natural killer cell, human (recommended) no re-parent Human uterine NK subset. NEW:1 natural killer cell, human human CL:0000623 natural killer cell yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) Human branch under NK: groups every human NK term (Dr. Diehl, 2026-10-05). NEW:2 natural killer cell, mouse mouse CL:0000623 natural killer cell yes new grouping term (in taxon NCBITaxon:10090 Mus musculus) Mouse branch under NK: groups every mouse NK term. NEW:3 immature natural killer cell, human human CL:0000823 immature natural killer cell; NEW:1 natural killer cell, human yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) Parallel pair for immature NK; groups CL:0002338 and CL:0002344. NEW:4 immature natural killer cell, mouse mouse CL:0000823 immature natural killer cell; NEW:2 natural killer cell, mouse yes new grouping term (in taxon NCBITaxon:10090 Mus musculus) Parallel pair for immature NK; groups CL:0002345 and CL:0002346. NEW:5 mature natural killer cell, human human CL:0000824 mature natural killer cell; NEW:1 natural killer cell, human yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) Dr. Diehl's example pair; groups CL:0000938, CL:0000939 and CL:0002343. NEW:6 mature natural killer cell, mouse mouse CL:0000824 mature natural killer cell; NEW:2 natural killer cell, mouse yes new grouping term (in taxon NCBITaxon:10090 Mus musculus) Dr. Diehl's example pair; groups CL:0002347, CL:0002348, CL:0002349 and CL:0002438 with its subtree. -NEW:7 uterine natural killer cell, human human CL:4052028 uterine natural killer cell; NEW:1 natural killer cell, human yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) OPTIONAL. Groups uNK1-3 and decidual NK, which are all human; the generic uterine NK term stays for other species. Decide. -NEW:8 group 1 innate lymphoid cell, human human CL:0001067 group 1 innate lymphoid cell yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) OPTIONAL. Same request as repo issue #14 (no human group 1 term, unlike group 2 and 3). Would be the parent of CL:0001077 ILC1, human and NEW:1. Decide. -NEW:9 group 1 innate lymphoid cell, mouse mouse CL:0001067 group 1 innate lymphoid cell yes new grouping term (in taxon NCBITaxon:10090 Mus musculus) OPTIONAL. Mouse counterpart of NEW:8 and parent of NEW:2. CL has no 'ILC1, mouse' term to put under it. Decide. +NEW:7 uterine natural killer cell, human human CL:4052028 uterine natural killer cell; NEW:1 natural killer cell, human yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) RECOMMENDED. Groups uNK1-3 and decidual NK (all human) and takes the menstrual-cycle wording from CL:4052028; the generic term stays for other species (mice have uNK cells, Shreeve 2021, PMID:33887202). +NEW:8 group 1 innate lymphoid cell, human human CL:0001067 group 1 innate lymphoid cell yes new grouping term (in taxon NCBITaxon:9606 Homo sapiens) RECOMMENDED. Requested in repo issue #14 (https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/14); matches group 2 and 3. Parent of CL:0001077 ILC1, human and NEW:1. +NEW:9 group 1 innate lymphoid cell, mouse mouse CL:0001067 group 1 innate lymphoid cell yes new grouping term (in taxon NCBITaxon:10090 Mus musculus) OPTIONAL (Dr. Diehl to decide). Mouse counterpart of NEW:8 and parent of NEW:2. CL has no 'ILC1, mouse' term to put under it. diff --git a/reports/gaps.tsv b/reports/gaps.tsv index a6572c1..99cf750 100644 --- a/reports/gaps.tsv +++ b/reports/gaps.tsv @@ -25,3 +25,4 @@ PB Plasmablast cl_axiom_gap [Draft B3b] Move the remaining plasmablast markers ( (none: mouse CL terms) (no SOULCAP row) cl_axiom_gap [Draft B6c] The definitions of 10 mouse NK terms (CL:0002439 to CL:0002448) read 'A NK1.1-positive T cell that is …', but the terms are natural killer cells (parent CL:0002438 NK1.1-positive natural killer cell, mouse). Proposed fix: 'A NK1.1-positive natural killer cell that is …'. Proposed labels: gap. CL:0002439; CL:0002440; CL:0002441; CL:0002442; CL:0002443; CL:0002444; CL:0002445; CL:0002446; CL:0002447; CL:0002448 reports/nk_marker_audit_2026-10.md#other-findings-issue-candidates draft_for_review (not yet filed) 2026-10-05 (none: no SOULCAP decidual NK row) (no SOULCAP row) cl_axiom_gap [Draft B6d] CL:0002343 'decidual natural killer cell, human' asserts galectin-1 (PR:000009766) as 'has plasma membrane part'. Its definition source describes galectin-1 as one of 'two secreted proteins … selectively expressed in dNK cells' (Koopman 2003, PMID:14568979). Expression is supported; plasma membrane localisation isn't. Proposed fix: use 'expresses' (RO:0002292). Proposed labels: gap. CL:0002343 reports/nk_marker_audit_2026-10.md#other-findings-issue-candidates; reports/pro_marker_species_support.tsv draft_for_review (not yet filed) 2026-10-05 (none: no SOULCAP pre-NK row) (no SOULCAP row) cl_marker_conflict [Draft B6e, on hold] CL:0000937 pre-natural killer cell (generic) asserts CD34, CD122 and CD117 positive. In mouse, the earliest pre-NKP 'does not express IL-2Rβ (CD122)' (Fathman 2011, PMID:21931117). In human, the markers fit stage 2 cells. Hold until Dr. Diehl decides whether these markers move to a human child (as for plasmablast). Proposed labels: gap, evidence needed. CL:0000937 reports/nk_marker_audit_2026-10.md#open-questions-for-alex-and-dr-diehl; reports/pro_marker_species_support.tsv on_hold (not yet filed) 2026-10-05 +(none: no SOULCAP liver NK row) (no SOULCAP row) cl_axiom_gap [Draft C1] Keep CL:4047101 'liver-resident natural killer cell' generic (Dr. Diehl, 2026-10-05) but move the human-specific sentences of its definition ('In humans this cell type is distinguished from circulating natural killer cells by CD49a or CD69 gene expression. Liver-resident natural killer cells have also been shown to express CCR5, EOMES, KLRB1, GZMK, and CXCR6 in humans.') to a new child term 'liver-resident natural killer cell, human' (in taxon Homo sapiens), placed under NEW:1 natural killer cell, human in the group 1 ILC proposal. The generic definition keeps only 'A natural killer cell resident to the liver, located in the hepatic sinusoids.' Sources for the human child: the PMIDs already cited by CL:4047101 (to be checked per sentence). Proposed labels: gap, new term request. CL:4047101 docs/group1_ilc_species_hierarchy_proposal.md#terms-with-unclear-species-recommended-defaults; docs/group1_ilc_species_hierarchy_proposal.tsv draft_for_review (not yet filed) 2026-10-05 From d8e76ff361e17763ba260a0c7be7271f3a06de54 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 5 Oct 2026 20:33:34 -0400 Subject: [PATCH 07/11] feat: audit keeps contradicted, no evidence and not applicable apart (Task E) - pro_species_support: SPECIES_STATUSES, HUMAN_ONLY_MARKERS (HLA-DRA, NCAM1), not_applicable_reason(), species_status() (a blank becomes not_applicable when the term/protein is limited to the other species or a human-only marker is on the mouse side; never overrides a recorded value) and species_scope(). - soulcap-audit: per-species status + basis on every species row; summary counts human/mouse statuses; only "contradicted" raises a finding (species_marker_contradicted); unknown values are flagged; dashboard shows Human / Mouse badges and defines the vocabulary. - Regenerated audit_* (6 contradicted findings). The matcher evaluation shows stale_or_unverified: its source fingerprints predate later commits to cl_match.py / marker_resolution.py as well as this audit.py change. - Tests for the helpers, the audit behaviour and the curated TSV (vocabulary, quotes behind verdicts, no failure where a species can't apply). mapping-audit and pro-marker-species-support skills updated. - marker_validation.md is grammar-only (no evidence statuses); unchanged. Co-Authored-By: Claude Opus 5.5 --- .claude/skills/mapping-audit/SKILL.md | 20 +- .../pro-marker-species-support/SKILL.md | 9 + reports/README.md | 2 +- reports/audit_dashboard.html | 4 +- reports/audit_data.json | 3582 ++++++++++++++++- reports/audit_summary.md | 17 +- src/README.md | 2 +- src/soulcap_cl_mapping/audit.py | 47 +- src/soulcap_cl_mapping/audit_dashboard.html | 2 +- src/soulcap_cl_mapping/pro_species_support.py | 60 + tests/test_audit.py | 93 + tests/test_pro_species_support.py | 105 + 12 files changed, 3729 insertions(+), 214 deletions(-) diff --git a/.claude/skills/mapping-audit/SKILL.md b/.claude/skills/mapping-audit/SKILL.md index de15c83..3e31cdc 100644 --- a/.claude/skills/mapping-audit/SKILL.md +++ b/.claude/skills/mapping-audit/SKILL.md @@ -71,10 +71,22 @@ is to question it, not just print it — for each row, ask: fixes changes the term's markers/definition/label out from under a mapping made before the fix landed. 3. **Does literature actually back a species-specific claim the mapping - relies on?** Cross-check against `reports/pro_marker_species_support.tsv` - — if a mapping leans on a marker that TSV records as - `insufficient_evidence` or a different species than SOULCAP's row assumes, - that's a real finding, not noise. + relies on?** Cross-check against `reports/pro_marker_species_support.tsv`, + using `human_status` (SOULCAP rows are human). The four values mean + different things, so report them separately and never merge them: + - `contradicted`: a real finding. Evidence goes against the CL assertion + (`soulcap-audit` raises `species_marker_contradicted`). + - `no_evidence_found`: searched, nothing found. Note it as an evidence gap, + **not** a contradiction. + - `not_applicable`: the species question doesn't apply (term or protein + limited to the other species, or a human-only marker such as HLA-DRA or + NCAM1/CD56 on the mouse side). **Never a failure.** + - blank / `not_assessed`: not checked yet; say so. + + Use `pro_species_support.species_status(row, "human")` to read a row: it + fills a blank with `not_applicable` when a rule applies and never + overrides a recorded value. The legacy `species_support` column + (`insufficient_evidence` etc.) is superseded by these columns. 4. **Was it marked `uncertain` for a reason that's since been resolved (or gotten worse)?** Re-read the `note` field and check whether the ambiguity it describes is still accurate. diff --git a/.claude/skills/pro-marker-species-support/SKILL.md b/.claude/skills/pro-marker-species-support/SKILL.md index 502d701..6cb6ade 100644 --- a/.claude/skills/pro-marker-species-support/SKILL.md +++ b/.claude/skills/pro-marker-species-support/SKILL.md @@ -158,6 +158,15 @@ Keep these four apart; they mean different things: | `not_applicable` | The species question doesn't apply: the CL term is limited to the other species (", human" / ", mouse"), the PRO term is the other species' protein, or the marker is human-only. Human-only markers so far: HLA-DRA (mouse ortholog H2-Ea is a different protein) and NCAM1/CD56 for NK cells. | | *(blank)* | Not assessed. | +The same vocabulary is in code: `pro_species_support.SPECIES_STATUSES`, +`HUMAN_ONLY_MARKERS`, `not_applicable_reason()`, `species_status()` and +`species_scope()`. `soulcap-audit` uses them. It reports `contradicted` rows +as findings and counts every status per species in `audit_summary.md`. Add +a new human-only marker to `HUMAN_ONLY_MARKERS` (with a test), not only to a +note. `tests/test_pro_species_support.py` checks that every recorded value is +in the vocabulary, that `supported`/`contradicted` have a quote, and that a +species which can't apply is never marked anything but `not_applicable`. + Derive `species_scope` from them: `both` if both are `supported`; `human` if human is `supported` and mouse is `not_applicable` or `contradicted` (likewise `mouse`); otherwise `unresolved`. diff --git a/reports/README.md b/reports/README.md index f8a62d4..8060d00 100644 --- a/reports/README.md +++ b/reports/README.md @@ -23,7 +23,7 @@ literature evidence in [literature/](../literature/), and planning documents in | File | What it is | Produced by | Type | |---|---|---|---| -| [audit_dashboard.html](audit_dashboard.html) | Offline, filterable dashboard of entities, proposals, findings, marker coverage, gaps and provenance | `uv run soulcap-audit` | Generated | +| [audit_dashboard.html](audit_dashboard.html) | Offline, filterable dashboard of entities, proposals, findings, marker coverage, gaps, provenance and species evidence (human and mouse status per CL marker: `supported`, `contradicted`, `no_evidence_found`, `not_applicable`, `not_assessed`; only `contradicted` raises a finding) | `uv run soulcap-audit` | Generated | | [audit_summary.md](audit_summary.md) | Text summary of the same audit | `uv run soulcap-audit` | Generated | | [audit_data.json](audit_data.json) | Data behind the dashboard | `uv run soulcap-audit` | Generated | | [matcher_evaluation.md](matcher_evaluation.md), [matcher_evaluation.tsv](matcher_evaluation.tsv), [matcher_evaluation.json](matcher_evaluation.json) | How well the matcher retrieves the proposed CL targets (provisional agreement, not accuracy) | `uv run soulcap-evaluate` | Generated | diff --git a/reports/audit_dashboard.html b/reports/audit_dashboard.html index f54a5a1..5166441 100644 --- a/reports/audit_dashboard.html +++ b/reports/audit_dashboard.html @@ -28,7 +28,7 @@

How to interpret this audit

    Markdown summaryDownload audit JSON

    Generated by soulcap-audit. Re-run the command to refresh this snapshot. No external scripts, fonts, or services are used.

    - +