From 0debe25e4163c535d785f234eb89a42926fa3364 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Mon, 28 Sep 2026 19:42:37 -0400 Subject: [PATCH 1/3] feat: human/mouse marker validity columns and pilot on 3 CL terms (Dr. Diehl request) Extends reports/pro_marker_species_support.tsv in place; the 10 legacy columns and 77 legacy rows are unchanged (checked by script). - New columns: species_scope (human/mouse/both/unresolved), human_citation, human_quote, mouse_citation, mouse_quote, note, checked_on. Scope: the 87 directly asserted pairs on mapped CL terms; the 10 "(human)"-labelled pairs appended with species_scope = human, "species from PRO label". - Pilot: CL:0000623, CL:0000980, CL:0000938 (10 pairs). Every quote checked exactly against Europe PMC full text. 1 human (CD56-high: mouse NK cells are not classified by CD56), 9 unresolved (mostly no mouse evidence; CD138 contradicted in mouse and conflicting in human; HLA-DRA not clearly supported in human). - The 5 legacy human rows whose quotes did not verify: corrected in the new columns only (4 verified replacements; plasmablast CD138 is in the pilot). - pro-marker-species-support SKILL.md and reports/README describe the new schema; pro_species_support.py docstring points at curated_mappings.tsv. Co-Authored-By: Claude Opus 5.5 --- .../pro-marker-species-support/SKILL.md | 51 +++++- reports/README.md | 2 +- reports/pro_marker_species_support.tsv | 166 ++++++++++-------- src/soulcap_cl_mapping/pro_species_support.py | 4 +- 4 files changed, 133 insertions(+), 90 deletions(-) diff --git a/.claude/skills/pro-marker-species-support/SKILL.md b/.claude/skills/pro-marker-species-support/SKILL.md index ca5aa4b..a723250 100644 --- a/.claude/skills/pro-marker-species-support/SKILL.md +++ b/.claude/skills/pro-marker-species-support/SKILL.md @@ -118,21 +118,54 @@ own discipline here. ## Step 4 — write the row -Append to `reports/pro_marker_species_support.tsv` -(tab-separated, one row per pair): +`reports/pro_marker_species_support.tsv` has one row per directly asserted +(CL term, PRO marker) pair for every CL term in +`mappings/curated_mappings.tsv` (87 pairs as of 2026-09-28). The question is +Dr. Diehl's: **is each marker, as CL asserts it, valid in human, mouse, or +both?** + +**Never edit the first 10 (legacy) columns** of an existing row. They record +the original human-only check from issue #11. All new work goes in the 7 +columns after them. | Column | Meaning | |---|---| -| `cl_id`, `cl_label`, `pr_id`, `pr_label`, `cd_synonym` | From `get_scoped_pairs()` — don't hand-retype these, pull them programmatically to avoid transcription errors (a real bug caught during the first run: hand-typed PR labels didn't match `cl_pro_relationships.tsv`). | -| `species_support` | `human` / `mouse` / `both` / `insufficient_evidence`. | -| `evidence_source` | `m2_literature_report` / `citation_traversal` / `europepmc_search` / `none`. | -| `citation` | Author/year/PMID/DOI, plus a trailing `-- ` caveat clause when the quote's context doesn't exactly match the pair's cell type/subset (e.g. a naive-T marker's only evidence coming from a Treg paper) — say so rather than let the row imply a cleaner match than it is. | -| `quote` | The verbatim substring itself. | -| `source_ref` | `literature/evidence.tsv#` for M2 reuse (older rows cite `archive/2026-09_literature_narratives/.md`), an EuropePMC article URL for a fresh search, or `reports/citation_traversal//` for a traversal — or, for `insufficient_evidence`, a one-line note on what was tried. | +| `cl_id`, `cl_label`, `pr_id`, `pr_label`, `cd_synonym` | From `cl_pro_relationships.tsv` — pull them programmatically, don't retype them. | +| `species_support`, `evidence_source`, `citation`, `quote`, `source_ref` | **Legacy** (issue #11 human-only check). Read-only. | +| `species_scope` | `human`, `mouse`, `both` or `unresolved` (blank = not yet assessed). | +| `human_citation`, `human_quote` | Citation (author, year, PMID, PMCID) and an exact quote for the human side. | +| `mouse_citation`, `mouse_quote` | The same for mouse. | +| `note` | Free text explaining the verdict, e.g. "not tested in mouse, no reagent", "ortholog exists but not expressed", "contradicted in mouse", or "species from PRO label". | +| `checked_on` | Date the row was last assessed. | + +Rules for `species_scope`: + +- **Judge against the assertion as CL states it.** For a negative pair + ("lacks CD14"), evidence that the marker is absent in a species *supports* + it. +- `both` only when **both** species have an exact quote supporting the + assertion. +- `human` / `mouse` when that species is supported and the other is + contradicted by a quote (e.g. mouse NK cells are not classified by CD56). +- `unresolved` whenever a species has no evidence, only "not tested", or + conflicting evidence. Explain which in `note`. **Never treat "not tested in + mouse" as human-only.** +- Pairs whose PRO label is species-qualified, e.g. "(human)", get + `species_scope = human` and the note "species from PRO label". +- An existing mouse ortholog (Alliance of Genome Resources / MGI) is **not** + evidence that a marker works in mouse. It may go in `note` with its record + ID; mouse support needs literature. +- Every quote is checked word for word against the paper's Europe PMC full + text (as `soulcap-evidence verify` does) before it is written. If none can + be verified, leave the quote blank and say so in `note`. + +Evidence sources, in order: references in `literature/reviews/` (Dr. Diehl's +first); verified rows of `literature/evidence.tsv`; then open-access +literature via `soulcap-europepmc` / Europe PMC full text. ## Step 5 — flag real findings -If a `species_support` result is genuinely surprising (e.g. a marker CL +If a `species_scope` result is genuinely surprising (e.g. a marker CL implicitly treats as pan-species turns out to only have mouse evidence, or a whole marker cluster comes back `insufficient_evidence` the way monocyte subset markers did), log it the same way other literature/CL gaps from this diff --git a/reports/README.md b/reports/README.md index 7ba589c..9467844 100644 --- a/reports/README.md +++ b/reports/README.md @@ -60,7 +60,7 @@ These are generated, but they are inputs to other code and need network access |---|---|---|---| | [gaps.tsv](gaps.tsv) | Cases with no good CL match, CL/marker conflicts, CL axiom gaps, or sheet data problems. Filed as GitHub issues by the `gap-issue-filing` skill | Hand-maintained | Curated | | [cl_term_issues.md](cl_term_issues.md) | Proposed Cell Ontology corrections found during mapping | Hand-maintained | Curated | -| [pro_marker_species_support.tsv](pro_marker_species_support.tsv) | Whether literature supports each CL PRO marker as human, mouse, or both (issue #11) | `pro-marker-species-support` skill, quotes verified verbatim | Curated | +| [pro_marker_species_support.tsv](pro_marker_species_support.tsv) | For every directly asserted PRO marker on a mapped CL term (87 pairs): is the assertion valid in human, mouse, or both? The first 10 columns are the original human-only check (issue #11, read-only); `species_scope`, `human_*`/`mouse_*` citation and quote, `note` and `checked_on` hold the human/mouse assessment (Dr. Diehl's request, 2026-09-28; pilot on 3 CL terms so far) | `pro-marker-species-support` skill; every quote checked against the paper's full text | Curated | ## Not tracked diff --git a/reports/pro_marker_species_support.tsv b/reports/pro_marker_species_support.tsv index f787118..987fafa 100644 --- a/reports/pro_marker_species_support.tsv +++ b/reports/pro_marker_species_support.tsv @@ -1,78 +1,88 @@ -cl_id cl_label pr_id pr_label cd_synonym species_support evidence_source citation quote source_ref -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 -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 -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 -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 -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 -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 -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). -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 -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 -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 -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 -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 -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 -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 -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_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.""" 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. 2026-09-28 +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 unresolved 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""" 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). 2026-09-28 +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""" 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). 2026-09-28 +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 human or mouse evidence found for CD84 on CD56-bright NK cells (legacy verdict was insufficient_evidence). 2026-09-28 +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 diff --git a/src/soulcap_cl_mapping/pro_species_support.py b/src/soulcap_cl_mapping/pro_species_support.py index a161355..6648fea 100644 --- a/src/soulcap_cl_mapping/pro_species_support.py +++ b/src/soulcap_cl_mapping/pro_species_support.py @@ -5,8 +5,8 @@ just reads e.g. "neural cell adhesion molecule 1", not "... (mouse)". This module identifies exactly which (CL cell type, PR marker) pairs need a literature check, restricted to the CL terms this project actually maps -SOULCAP cell types to (``CURATED_MAPPINGS`` in ``sssom_export.py``) rather -than all of CL — see issue #11. +SOULCAP cell types to (the ``cl_id`` values in ``mappings/curated_mappings.tsv``) +rather than all of CL — see issue #11. Downstream literature work (citation-traversal runs, the standardised output TSV) is driven by this scoping, but lives outside this module; see the plan From 2877a2fa4ee514c165236d9c0af339b7e9f8c646 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Tue, 29 Sep 2026 12:24:17 -0400 Subject: [PATCH 2/3] docs: human-specific CL term rule, two CL candidates, Friday summary for Dr. Diehl - pro_marker_species_support.tsv: CL:0000938 (a human-specific CL term) rows note "CL term is human-specific; mouse not applicable"; CD56-high and lacks-CD16 become species_scope = human (human side verified); lacks-DRA and CD84 stay unresolved. Rule stated in the skill. - Skill and reports README: the new columns take precedence over the legacy species_support value (legacy value on plasmablast CD138 left as is). - cl_term_issues.md: unfiled candidates for plasmablast "lacks CD138" and CD56-bright NK "lacks HLA-DRA", citing the verified quotes. - docs/planning/2026-10-02_diehl_summary.md: one-page pilot summary with questions for Dr. Diehl. Remaining scope is 67 pairs on 30 CL terms. Co-Authored-By: Claude Opus 5.5 --- .../pro-marker-species-support/SKILL.md | 8 +- docs/README.md | 2 +- docs/planning/2026-10-02_diehl_summary.md | 78 +++++++++++++++++++ reports/README.md | 2 +- reports/cl_term_issues.md | 38 +++++++++ reports/pro_marker_species_support.tsv | 8 +- 6 files changed, 129 insertions(+), 7 deletions(-) create mode 100644 docs/planning/2026-10-02_diehl_summary.md diff --git a/.claude/skills/pro-marker-species-support/SKILL.md b/.claude/skills/pro-marker-species-support/SKILL.md index a723250..1a7697a 100644 --- a/.claude/skills/pro-marker-species-support/SKILL.md +++ b/.claude/skills/pro-marker-species-support/SKILL.md @@ -126,7 +126,9 @@ both?** **Never edit the first 10 (legacy) columns** of an existing row. They record the original human-only check from issue #11. All new work goes in the 7 -columns after them. +columns after them. **Where the new columns disagree with the legacy +`species_support` value, the new columns take precedence** (e.g. plasmablast +"lacks CD138", where the legacy value still says `human`). | Column | Meaning | |---|---| @@ -152,6 +154,10 @@ Rules for `species_scope`: mouse" as human-only.** - Pairs whose PRO label is species-qualified, e.g. "(human)", get `species_scope = human` and the note "species from PRO label". +- **Human-specific CL terms** (label ending ", human", e.g. CL:0000938): the + mouse question doesn't apply. Set `species_scope = human` when the human + side is supported by a verified quote, otherwise `unresolved`, and start + `note` with "CL term is human-specific; mouse not applicable". - An existing mouse ortholog (Alliance of Genome Resources / MGI) is **not** evidence that a marker works in mouse. It may go in `note` with its record ID; mouse support needs literature. diff --git a/docs/README.md b/docs/README.md index 0627fb4..94bf95e 100644 --- a/docs/README.md +++ b/docs/README.md @@ -9,7 +9,7 @@ pages hold the full detail. | [pipeline.md](pipeline.md) | Each pipeline stage and its command: sheet sync, CL→PRO axioms, candidate matching, OAK lexical search, SSSOM export, ROBOT QC | | [marker_resolution.md](marker_resolution.md) | Token → PRO resolution rules, policies, lexical cache | | [matching_and_evaluation.md](matching_and_evaluation.md) | Audit dashboard, matcher evaluation, regression triage and follow-up | -| [planning/](planning/) | Sprint backlog and semester plan (hand-maintained); agenda for the [12 Oct 2026 meeting](planning/2026-10-12_meeting_summary.md) | +| [planning/](planning/) | Sprint backlog and semester plan (hand-maintained); agenda for the [12 Oct 2026 meeting](planning/2026-10-12_meeting_summary.md); [human/mouse marker pilot summary](planning/2026-10-02_diehl_summary.md) for Dr. Diehl | Related specs that live at the top level: [MARKER_SYNTAX.md](../MARKER_SYNTAX.md) (marker expression grammar) and [ROADMAP.md](../ROADMAP.md) (milestones). diff --git a/docs/planning/2026-10-02_diehl_summary.md b/docs/planning/2026-10-02_diehl_summary.md new file mode 100644 index 0000000..28aa2c2 --- /dev/null +++ b/docs/planning/2026-10-02_diehl_summary.md @@ -0,0 +1,78 @@ +# Human vs mouse validity of CL markers: pilot summary for 2 October 2026 + +For Dr. Diehl. Your request from 28 September, a pilot on 3 CL terms, and +four questions before the rest is done. + +## The task and how it's done + +For every CL term a SOULCAP cell type maps to, each PRO marker CL asserts +directly (87 pairs) is checked: **is the assertion, as CL states it, valid in +human, mouse, or both?** For a negative assertion such as "lacks CD14", +absence in a species counts as support. + +- Each species needs its own **exact quote**, checked word for word against + the paper's full text in Europe PMC. Nothing is inferred from a marker's name + or from memory. +- `both` requires a supporting quote for each species. "Not tested in mouse" + gives `unresolved`, never "human only". An existing mouse ortholog is not + counted as evidence. +- Results are in `reports/pro_marker_species_support.tsv` (new columns + `species_scope`, `human_*`, `mouse_*`, `note`). The original human-only + check is kept unchanged alongside. + +## Pilot: 3 CL terms, 10 pairs + +| CL term: assertion | Human | Mouse | Scope | +|---|---|---|---| +| NK cell (CL:0000623): lacks CD20 | Supported | No evidence found | unresolved | +| NK cell: lacks CD14 | Supported | No evidence found | unresolved | +| Plasmablast (CL:0000980): CD38 high | Supported | No evidence found | unresolved | +| Plasmablast: CD27 high | Supported | No evidence found | unresolved | +| Plasmablast: lacks CD20 | Supported | No evidence found | unresolved | +| Plasmablast: lacks CD138 | Conflicting | **Contradicted** | unresolved | +| CD56-bright NK, human (CL:0000938): CD56 high | Supported | Contradicted | **human** | +| CD56-bright NK: lacks CD16 | Supported | Not applicable | **human** | +| CD56-bright NK: lacks HLA-DRA | **Not supported** | Not applicable | unresolved | +| CD56-bright NK: CD84 positive | No evidence found | Not applicable | unresolved | + +Also, 10 pairs whose PRO term is itself human-specific, e.g. "(human)" in the +label, are marked `human` from the label. + +## Three notable findings + +1. **CD56 is the clearest human-only marker.** "Because mice lack CD56, murine + NK cell subsets are classified using alternative markers, particularly CD27 + and Mac-1." (PMID 41898531). The mouse gene *Ncam1* exists (MGI:97281), but + it isn't used for NK cells. +2. **Plasmablast "lacks CD138" doesn't hold in mouse and is disputed in + human.** Mouse: "plasmablasts as B220+CD138+" (PMID 42774878). Human: + "short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)" + (PMID 41771939). +3. **CD56-bright NK "lacks HLA-DRA" isn't well supported even in human:** "the + proportion of HLA-DR+CD56bright cells ex vivo" (PMID 42450353). PRO notes + the mouse counterpart is H2-Ea. + +Findings 2 and 3 are logged as unfiled candidates in +`reports/cl_term_issues.md`. + +## Questions for you + +a. **Can you share your references?** They'll be used first, before any new + searching (they go in `literature/reviews/`). + +b. **Negative lineage markers.** For assertions like "lacks CD14 / CD19 / CD20" + on non-myeloid or non-B cells, will you accept `both` on biological + grounds, or require a quote for each species? The mouse literature rarely + states these absences, so requiring quotes leaves most of them + `unresolved`. + +c. **Human-specific CL terms.** For terms like CL:0000938 ("…, human"), is + "mouse not applicable", scoped `human` when the human side is supported, + the right rule? + +d. **Order of work.** Any CL terms or markers to prioritise? + +## Remaining scope + +**67 pairs on 30 CL terms**, waiting for your answers. Four of those pairs +already have a corrected human quote; their mouse side is still to do. diff --git a/reports/README.md b/reports/README.md index 9467844..c7757c7 100644 --- a/reports/README.md +++ b/reports/README.md @@ -60,7 +60,7 @@ These are generated, but they are inputs to other code and need network access |---|---|---|---| | [gaps.tsv](gaps.tsv) | Cases with no good CL match, CL/marker conflicts, CL axiom gaps, or sheet data problems. Filed as GitHub issues by the `gap-issue-filing` skill | Hand-maintained | Curated | | [cl_term_issues.md](cl_term_issues.md) | Proposed Cell Ontology corrections found during mapping | Hand-maintained | Curated | -| [pro_marker_species_support.tsv](pro_marker_species_support.tsv) | 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) | `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) | For every directly asserted PRO marker on a mapped CL term (87 pairs): is the assertion valid in human, mouse, or both? The first 10 columns are the original human-only check (issue #11, read-only); `species_scope`, `human_*`/`mouse_*` citation and quote, `note` and `checked_on` hold the human/mouse assessment (Dr. Diehl's request, 2026-09-28; pilot on 3 CL terms so far). Where they disagree with the legacy `species_support`, the new columns take precedence | `pro-marker-species-support` skill; every quote checked against the paper's full text | Curated | ## Not tracked diff --git a/reports/cl_term_issues.md b/reports/cl_term_issues.md index 43b7dfd..3b927e4 100644 --- a/reports/cl_term_issues.md +++ b/reports/cl_term_issues.md @@ -185,6 +185,44 @@ confirmed)? The same question applies to CD57 (HNK-1 epitope, made by B3GAT1, PR:000001440): CL has one such axiom, CL:4033092 "CD57-positive enterocyte" `expresses` PR:000001440. +### Plasmablast "lacks CD138" — CL:0000980, PR:000001935 (syndecan-1) + +**Status:** candidate — not filed + +CL asserts CL:0000980 "plasmablast" `lacks_plasma_membrane_part` +PR:000001935 "syndecan-1" (CD138). Found during the human/mouse marker +review (2026-09-28; row in +[pro_marker_species_support.tsv](pro_marker_species_support.tsv)). Both +quotes were checked word for word against the Europe PMC full text: + +- **Contradicted in mouse:** "plasmablasts as B220+CD138+" (PMID 42774878; + PMC13594723, 2026). +- **Conflicting in human:** one human scheme defines plasmablasts as CD138++: + "short-lived plasmablasts (CD19+CD138++ or CD19+CD27+CD38++)" (PMID + 41771939; PMC13066544, 2026). The earlier human quote supporting the + assertion (Woodruff 2020 gating labels) could not be verified. + +**Question for review:** should this axiom be removed, weakened (e.g. "low"), +or restricted to human? + +### CD56-bright NK "lacks HLA-DRA" — CL:0000938, PR:000002015 + +**Status:** candidate — not filed + +CL asserts CL:0000938 "CD16-negative, CD56-bright natural killer cell, human" +`lacks_plasma_membrane_part` PR:000002015 "MHC class II histocompatibility +antigen alpha chain DRA". Human evidence reports HLA-DR+ CD56-bright cells: +"the proportion of HLA-DR+CD56bright cells ex vivo" (PMID 42450353; +PMC13362507, 2026; checked word for word against the full text). The +supporting quote from the earlier check (Rebuffet 2024) concerns a different +NK cluster (NK3B) and does not address CD56-bright cells. + +**Question for review:** is "lacks HLA-DRA" right for resting CD56-bright NK +cells, with HLA-DR appearing only on an activated subset, or should the axiom +be dropped? This is also Dr. Diehl's example of HLA-DRA as a human-only proxy +for MHC class II: PRO notes "The mouse ortholog is called H2-Ea" +(PR:000002015, OLS4). + --- ## Resolved issues diff --git a/reports/pro_marker_species_support.tsv b/reports/pro_marker_species_support.tsv index 987fafa..80309a8 100644 --- a/reports/pro_marker_species_support.tsv +++ b/reports/pro_marker_species_support.tsv @@ -47,10 +47,10 @@ CL:0000907 central memory CD8-positive, alpha-beta T cell PR:000001015 receptor- 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.""" 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. 2026-09-28 -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 unresolved 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""" 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). 2026-09-28 -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""" 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). 2026-09-28 -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 human or mouse evidence found for CD84 on CD56-bright NK cells (legacy verdict was insufficient_evidence). 2026-09-28 +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 From c4a968393e121264b952fe7a976cc5db6b4c4635 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Tue, 29 Sep 2026 12:24:34 -0400 Subject: [PATCH 3/3] docs: keep the Friday summary to the three requested questions Co-Authored-By: Claude Opus 5.5 --- docs/planning/2026-10-02_diehl_summary.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/planning/2026-10-02_diehl_summary.md b/docs/planning/2026-10-02_diehl_summary.md index 28aa2c2..6176c7b 100644 --- a/docs/planning/2026-10-02_diehl_summary.md +++ b/docs/planning/2026-10-02_diehl_summary.md @@ -1,7 +1,7 @@ # Human vs mouse validity of CL markers: pilot summary for 2 October 2026 For Dr. Diehl. Your request from 28 September, a pilot on 3 CL terms, and -four questions before the rest is done. +three questions before the rest is done. ## The task and how it's done @@ -70,8 +70,6 @@ c. **Human-specific CL terms.** For terms like CL:0000938 ("…, human"), is "mouse not applicable", scoped `human` when the human side is supported, the right rule? -d. **Order of work.** Any CL terms or markers to prioritise? - ## Remaining scope **67 pairs on 30 CL terms**, waiting for your answers. Four of those pairs