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CL new term request: colonocyte progenitor #3775
Description
Drafted from data/hca_ontology_findings.csv row 066_gut_colonocyte-progenitors — atlas: Gut, project_id: 1030 (Integrated Human Gut Cell Atlas, labelset hgca_celltype_v1, datasets 3397 "Epithelial Lineage" and 3400 "All Cells").
Preferred term label
colonocyte progenitor
Synonyms (add reference(s), please)
- absorptive progenitor (related) — CAP curator synonym, project 1030
- colonocyte early progenitor (related) — CAP curator synonym, project 1030
Definition (free text, with reference(s), please. PubMed ID format is PMID:XXXXXX)
An early colonocyte of the human colon that retains residual proliferative activity and has not yet acquired the surface maturation markers (e.g. AQP8) characteristic of fully differentiated colonocytes. These cells are committed to the absorptive colonocyte lineage rather than being multipotent transit-amplifying cells, and are marked by expression of NOTCH1 and EDN1. Identified as a distinct transcriptomic cluster in the Human Gut Cell Atlas (CAP project 1030).
Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols4/ontologies/cl)
early colonocyte (CL:4047018) — https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_4047018
Anatomical structure where the cell type is found (check Uberon for anatomical structures: https://www.ebi.ac.uk/ols4/ontologies/uberon)
colon (UBERON:0001155) — https://www.ebi.ac.uk/ols4/ontologies/uberon/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0001155
Your ORCID
Not provided
Additional notes or concerns
class: new-term-requested-by-curators; section_ref: 5a.
CAP's own curator rationale (from the project 1030 OLS report, data/2026_01_09_ols_report.csv): "Absorptive colonic progenitors, NOTCH1 and EDN1 with some residual cycling, committed towards the colonocyte lineage but not yet showing surface maturation like AQP8. There isn't a colonocyte progenitor term so these map to early colonocyte." CAP's current interim mapping for this label is CL:4047018 (early colonocyte) — this NTR requests a more specific child term for the distinct progenitor/cycling state, it does not propose changing that interim mapping.
We considered CL:0009011 "transit amplifying cell of colon" as an alternative parent, but rejected it: that term describes a multipotent proliferative precursor (colonocyte/goblet/enteroendocrine/tuft), whereas this label's own rationale describes a population already committed specifically to the colonocyte lineage with only residual cycling — closer to CL:4047018's lineage-committed, differentiating character than to the multipotent transit-amplifying compartment.
Drafted by cap_tracking from data/hca_ontology_findings.csv#066_gut_colonocyte-progenitors. Review before posting — in particular, add your ORCID.
Activity
ct31-sanger commentedon Oct 2, 2026
@ai4c-agent please fix
ai4c-agent commentedon Oct 2, 2026
🤖 Working on it...
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— @ai4c-agent
Link CL:9900000 to issue #3775 and add CAP synonyms
ai4c-agent commentedon Oct 2, 2026
Hi @ct31-sanger — this NTR describes essentially the same cell type as the one already staged in open PR #3755 (NTR from issue #3753), so I've consolidated the two requests on that PR rather than creating a duplicate term.
What I did on PR #3755 (branch
ai4c-agent-issue-3753-run906, commit bf72c0eb)related_synonym:absorptive progenitorcolonocyte early progenitorterm_tracker_item→ issue CL new term request: colonocyte progenitor #3775 (alongside the existing link to [NTR] colonocyte progenitor cell #3753), so both NTRs resolve against this term.Current staged term
CL:9900000(temporary NTR ID; replaced at release)colonocyte progenitor cellearly colonocyte(CL:4047018) — matches your requested parent.crypt of Lieberkuhn of colon(UBERON:0013485) — more specific than thecolon(UBERON:0001155) in your NTR, but strictly a subclass (crypt of Lieberkuhn of colon ispart_ofcolon) and consistent with the colonocyte-progenitor literature placing these cells in the crypt. Let me (or the PR reviewers) know if you'd prefer the looserpart_ofcolon.colonocyte progenitor(PMID:38600382),absorptive progenitor(CAP 1030),colonocyte early progenitor(CAP 1030).PMID:38600382,doi:10.1101/2023.05.03.539269.Points worth confirming before PR #3755 merges
colonocyte progenitor cell; this NTR requestedcolonocyte progenitor(now a related synonym). CL conventionally labels cell classes with thecellsuffix, so I kept… cellas the primary label — flag it if you'd prefer the shorter label be primary.Please leave further review comments on PR #3755 so the discussion stays in one place.
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