Skip to content

Add crustin hemocyte and TGase hemocyte (fixes #3690) - #3735

Merged
dosumis merged 1 commit into
masterfrom
ai4c-agent-issue-3690-run714
Sep 18, 2026
Merged

Add crustin hemocyte and TGase hemocyte (fixes #3690)#3735
dosumis merged 1 commit into
masterfrom
ai4c-agent-issue-3690-run714

Conversation

@ai4c-agent

@ai4c-agent ai4c-agent Bot commented Sep 8, 2026

Copy link
Copy Markdown
Contributor

Resolves #3690.

Summary

Adds two new hemocyte subtype terms described in penaeid shrimp:

ID Label Parent Taxon
CL:9900000 crustin hemocyte hemocyte (CL:0000387) Decapoda (NCBITaxon:6683)
CL:9900001 TGase hemocyte hemocyte (CL:0000387) Decapoda (NCBITaxon:6683)

crustin hemocyte (CL:9900000)

  • Definition: A hemocyte, found in penaeid shrimp, that is characterized by high expression of crustin-family antimicrobial peptide transcripts. Crustin hemocytes function in antimicrobial peptide production and in arthropod-specific immune processes such as melanization and coagulation.
  • Synonym: crustin-positive hemocyte
  • References: PMID:40750028, doi:10.1016/j.aquaculture.2026.744306

TGase hemocyte (CL:9900001)

  • Definition: A hemocyte, found in penaeid shrimp, that is characterized by high expression of hemocyte transglutaminase genes (TGase1, TGase). TGase hemocytes play a role in hemolymph coagulation, and likely represent an earlier, progenitor-like stage of hemocyte differentiation.
  • Synonyms: TGase-positive hemocyte, transglutaminase-positive hemocyte
  • References: PMID:40750028, PMID:8093242, doi:10.1016/j.aquaculture.2026.744306

Notes

  • Both terms are placed as subclasses of hemocyte (CL:0000387) (i.e. hemocyte (sensu Arthropoda)).
  • Taxon constraint: in taxon Decapoda (NCBITaxon:6683). The requester noted either Penaeidae (NCBITaxon:6685) or the broader Decapoda would be acceptable; Decapoda was chosen for consistency with the existing shrimp cell term CL:0020076 (blister-like cell) and because NCBITaxon:6685 is not currently declared in the edit file.
  • No part_of hemolymph (UBERON:0001011) axiom was added — the requester noted the cell is "found in but not exclusive to" hemolymph and to follow the parent term's pattern; CL:0000387 does not carry a part_of UBERON axiom either.
  • Contributor ORCID: 0009-0002-8634-7138 recorded via dc:contributor.

Test plan

  • robot convert succeeds on src/ontology/cl-edit.owl (syntax validated)
  • Reviewer to confirm textual definitions and taxon-constraint choice

🤖 Generated by @ai4c-agent

@github-actions
Add crustin hemocyte (CL:9900000) and TGase hemocyte (CL:9900001) - i…
3db0ed9 
…ssue #3690

Adds two new hemocyte subtype terms described in penaeid shrimp:

- CL:9900000 'crustin hemocyte': hemocyte characterized by high expression of
  crustin-family antimicrobial peptide transcripts, functioning in AMP
  production and arthropod-specific immune processes such as melanization and
  coagulation. Synonym: crustin-positive hemocyte.

- CL:9900001 'TGase hemocyte': hemocyte characterized by high expression of
  hemocyte transglutaminase genes (TGase1, TGase); plays a role in hemolymph
  coagulation and likely represents an earlier, progenitor-like stage of
  hemocyte differentiation. Synonyms: TGase-positive hemocyte,
  transglutaminase-positive hemocyte.

Both terms:
- SubClassOf hemocyte (CL:0000387)
- in taxon Decapoda (NCBITaxon:6683) — using the more general clade as
  suggested by the requester and consistent with the taxon constraint used
  for the related shrimp cell term CL:0020076 (blister-like cell).
- References: PMID:40750028, doi:10.1016/j.aquaculture.2026.744306
  (PMID:8093242 additionally cited for TGase hemocyte).

Contributor ORCID: 0009-0002-8634-7138

Signed-off-by: Claude
@ai4c-agent ai4c-agent Bot mentioned this pull request Sep 8, 2026
Closed
@ct31-sanger

ct31-sanger commented Sep 8, 2026

Copy link
Copy Markdown
Collaborator

/clara #gogoeditdiff

@github-actions

github-actions Bot commented Sep 8, 2026 •
edited
Loading

Copy link
Copy Markdown
Contributor

Claude finished @ct31-sanger's task in 4m 32s —— View job

CLARA routed review — complete

  • Read clara_workflow_ref/clara_workflow/agent_instructions.md
  • Load routing.json (2 terms, 5 targets: CL:9900000, CL:9900001)
  • Process term group CL:9900000 (crustin hemocyte)
  • Process term group CL:9900001 (TGase hemocyte)
  • Write runs/CL_9900000/{verdicts.json,tool_calls.jsonl,report.md} and runs/CL_9900001/{verdicts.json,tool_calls.jsonl,report.md}
  • Post summary

mcp__Asta_semanticscholar__snippet_search was not available in this environment, so verification went straight to full-text retrieval (Europe PMC) for every core assertion instead of snippet search.

Term-level result for both CL:9900000 and CL:9900001: UNCERTAIN. No assertion could be confirmed or contradicted — not because the content looks wrong, but because the cited literature wasn't reachable/consistent enough to check it against:

  1. Reference mismatch (flagged for both terms): the definitions and synonyms cite PMID:40750028 together with doi:10.1016/j.aquaculture.2026.744306 as if they were one reference. They are not — PMID:40750028 resolves in Europe PMC to Söderhäll et al., "Hemocyte diversity in crustaceans," Fish & Shellfish Immunology (2025), DOI 10.1016/j.fsi.2025.110612. The doi:10.1016/j.aquaculture.2026.744306 identifier does not resolve to any Europe PMC record at all (checked via get_europepmc_paper_by_id, get_all_identifiers_from_europepmc, and keyword search). This pairing should be double-checked before merge — it looks like two different citations got collapsed into one.
  2. PMID:40750028 has no accessible full text (subscription-only), and its abstract is a generic review of hemocyte classification that doesn't itself mention "crustin" or "TGase," so it can't be used to confirm the specific claims.
  3. For TGase hemocyte, PMID:8093242 (Limulus hemocyte transglutaminase, Tokunaga et al. 1993) is a real, correctly-resolving reference, but it's about Limulus (horseshoe crab, Chelicerata), not penaeid shrimp (Decapoda) — it offers only cross-species background plausibility for a coagulation role, not direct confirmation of the shrimp-specific cell type or its TGase1/TGase marker genes.

For reviewer context only (found via an unrestricted background search, not used to affect any verdict since it's outside the routed reference set): Koiwai et al. 2021, eLife (PMID:34132195), "Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process," looks like it may be a more directly relevant primary source than the review currently cited — it describes a HemTGase-high, early-stage hemocyte cluster (matching the "TGase hemocyte"/progenitor claim) and granulocyte clusters co-expressing crustin alongside other AMPs (penaeidin, stylicin) rather than a crustin-exclusive cluster.

Full per-term detail (assertion-by-assertion) is in runs/CL_9900000/report.md and runs/CL_9900001/report.md in this branch's working tree. Per the routing instructions for this run, only the runs/<TERM_ID>/ verification bundles were produced — no ontology files, changes.json, or routing.json were modified, and nothing was committed or pushed.
· branch ai4c-agent-issue-3690-run714

@github-actions

github-actions Bot commented Sep 8, 2026

Copy link
Copy Markdown
Contributor
Here's a diff of how these changes impact the classified ontology (on -base file):

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2026-09-08/cl-base.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
  • Version IRI: http://purl.obolibrary.org/obo/cl/releases/2026-09-08/cl-base.owl
  • Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

TGase hemocyte http://purl.obolibrary.org/obo/CL_9900001

Added

crustin hemocyte http://purl.obolibrary.org/obo/CL_9900000

Added

@github-actions

github-actions Bot commented Sep 8, 2026

Copy link
Copy Markdown
Contributor
Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

  • Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
  • Version IRI: None
  • Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

TGase hemocyte http://purl.obolibrary.org/obo/CL_9900001

Added

crustin hemocyte http://purl.obolibrary.org/obo/CL_9900000

Added

@github-actions

github-actions Bot commented Sep 8, 2026

Copy link
Copy Markdown
Contributor

CLARA review for PR #3735

  • Base SHA: 82f8285d7d60175be72c3e1487b2850fd259a24a
  • Head SHA: 3db0ed9cb4728ad9f416f39b06411d030a342e2e
  • Terms touched: 2
  • Total extracted changes: 21
  • Reviewable changes: 9
  • Decomposable changes: 2
  • Routed validation targets: 5
  • Routed NTR bundles: 2
  • Routed relationship targets: 0
  • Routed synonym targets with refs: 3

Stage 2/3 verification ran for 2 routed term(s).

Routed verification results

  • CL_9900000 — crustin hemocyte: UNCERTAIN (core: 8, fail: 0, uncertain: 8, background warnings: 0)
  • CL_9900001 — TGase hemocyte: UNCERTAIN (core: 8, fail: 0, uncertain: 8, background warnings: 0)

Artifacts uploaded:

  • changes.json
  • routing.json
  • runs/

@dosumis

dosumis commented Sep 9, 2026

Copy link
Copy Markdown
Contributor

@saracarsanaro - apologies for being slow to add this term. Would you be able to take a look at the CLARA review above and respond?

@ct31-sanger

ct31-sanger commented Sep 9, 2026

Copy link
Copy Markdown
Collaborator
  1. PMID:40750028 and https://doi.org/10.1016/j.aquaculture.2026.744306 are independent references and shouldn't be merged. https://doi.org/10.1016/j.aquaculture.2026.744306 does not appear to have a PMID ID.
  2. PMID:40750028 does mention "TGase" in main body of text.
  3. Limited literature available for direct penaeid shrimp TGase/TGase1 marker expression. I think keep the current reference for cross-species background plausibility, unless a stronger ref is found.
  4. PMID:34132195 - agree, looks like a better primary source.

@dosumis
dosumis merged commit 97d20ae into master Sep 18, 2026
5 checks passed
@dosumis
dosumis deleted the ai4c-agent-issue-3690-run714 branch September 18, 2026 07:58
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@dosumis dosumis dosumis approved these changes

Assignees

@dosumis dosumis

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

[NTR] Crustin Hemocyte and TGase Hemocyte

2 participants

@ct31-sanger @dosumis