Update crustacea (NCBITaxon:6657) references to pancrustacea (NCBITaxon:197562)

[ai4c-agent]

Closes #3771

Summary

NCBITaxon has obsoleted Crustacea (NCBITaxon:6657) in favour of Pancrustacea (NCBITaxon:197562). This PR updates all references to the obsolete taxon in src/ontology/uberon-edit.obo to point to the replacement taxon.

Terms updated (11)

Term	Field
UBERON:0000972 (antenna)	gci_filler in has_quality PATO:0000402 axiom
UBERON:0006583 (statocyst)	present_in_taxon
UBERON:0009963 (antennal gland)	in_taxon
UBERON:0009964 (crustacean maxillary gland)	in_taxon
UBERON:0010264 (hepatopancreas)	present_in_taxon
UBERON:0010266 (arthropod hepatopancreas)	in_taxon
UBERON:0014857 (zoea stage)	in_taxon
UBERON:0014861 (glaucothoe stage)	in_taxon
UBERON:0015170 (nauplius eye)	in_taxon
UBERON:0018378 (crustacean larval stage)	in_taxon
UBERON:8480039 (Oka organ)	in_taxon

Verified with obo-grep.pl that NCBITaxon:6657 no longer appears in the edit file. The edit file was reserialised via robot convert before committing.

Test plan

• CI passes (QC / reasoner)
• Reviewer confirms Pancrustacea is the intended replacement for the taxon-restriction semantics on all affected terms (in particular the note that several of these terms flag as arthropod/crustacean-specific; Pancrustacea also includes Hexapoda, so a curator may want to consider narrower replacements per-term).

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[ai4c-reviewer]

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Review: PR #3772 — Crustacea → Pancrustacea taxon update

Checklist

• Hierarchy and parents are consistent — no is_a/parent changes in this PR, only taxon-restriction relationships.
• Definitions and supporting references look adequate — no def/xref changes.
• Obsolete or replacement handling — not fully safe, see below.
• OBO and ODK conventions appear preserved — diff is minimal and consistent with robot's canonical serialization; no stray formatting issues.
• No obvious CI, auth, or workflow regression — only src/ontology/uberon-edit.obo touched.

What's good

• Confirmed via obo-grep.pl that NCBITaxon:6657 no longer appears anywhere in the edit file — the stated goal (removing the obsolete Crustacea taxon ID) is achieved.
• The diff is clean/minimal (11 lines changed), consistent with proper robot convert reserialization.

Issues found

🔴 CRITICAL — UBERON:0000972 antenna, line 9340: the has_quality PATO:0000402 relationship uses a GCI (gci_relation="part_of", gci_filler=...), which universally asserts "every antenna part_of an organism in the filler taxon is branched." Widening the filler from Crustacea to Pancrustacea pulls in Hexapoda (insects, NCBITaxon:6960), whose antennae are overwhelmingly uniramous/unbranched. This is an anatomically incorrect universal claim, not just a loosened restriction — see inline comment for detail.

🟡 IMPORTANT — the other 10 changes swap in_taxon/present_in_taxon NCBITaxon:6657 for the strictly broader NCBITaxon:197562 (Pancrustacea = Crustacea + Hexapoda) on terms that are explicitly crustacean-specific by name/definition (crustacean maxillary gland, antennal/green gland, arthropod hepatopancreas, zoea stage, glaucothoe stage, nauplius eye, crustacean larval stage, Oka organ). in_taxon acts as an upper-bound restriction (not "all members have this"), so these aren't logically false, but they silently lose the original Crustacea-only precision for structures that don't occur in insects. Two of the eleven (statocyst, hepatopancreas) use present_in_taxon, which is existential/multi-taxon by design and is fine as-is. Recommend pairing the new Pancrustacea assertions with never_in_taxon NCBITaxon:6960 ! Hexapoda for the genuinely crustacean-only terms — the same narrowing idiom the PR already uses for the antenna term (in_taxon Arthropoda + never_in_taxon Chelicerata). This is exactly the open question the PR's own (unchecked) test-plan item raises — it should be resolved before merge, not left to a follow-up.

🔵 SUGGESTION: a couple of pre-existing imprecisions (predating this PR) worth a follow-up issue — Oka organ's synonym "penaeid lymphoid organ" and glaucothoe stage's "hermit crab" def suggest these were already narrower than plain Crustacea; a future pass could tighten to family/infraorder-level taxa if suitable non-obsolete NCBITaxon terms exist.

Left two inline comments with specifics (line 9340 for the critical GCI issue, line 134367 summarizing the broader in_taxon precision-loss issue across all affected terms).

Recommendation: Request changes — the antenna GCI widening should not go in as-is, and the crustacean-specific in_taxon terms should get compensating never_in_taxon Hexapoda exclusions (or a documented rationale for why that's unnecessary) before merge.

[dosumis]

#gogoeditdiff

[ai4c-reviewer]

🔴 CRITICAL: This is a GCI axiom, not a plain taxon restriction — has_quality PATO:0000402 {gci_relation="part_of", gci_filler="NCBITaxon:197562"} universally asserts that every antenna that is part_of an organism in the gci_filler taxon has the quality "branched" (biramous).

Widening the filler from Crustacea (NCBITaxon:6657) to Pancrustacea (NCBITaxon:197562) pulls Hexapoda (NCBITaxon:6960 — insects) into that universal claim. Insect antennae are overwhelmingly uniramous/unbranched (filiform, moniliform, clavate, etc.), so this now asserts something anatomically false for a huge fraction of Pancrustacea.

Unlike plain in_taxon/present_in_taxon (which act as upper-bound restrictions and remain true under widening), a GCI filler widening changes the quantified domain of a defining axiom, so this one needs a real anatomical review rather than a mechanical ID swap — e.g. restrict to a non-obsolete crustacean-only clade if one exists, or add a compensating never_in_taxon NCBITaxon:6960 ! Hexapoda-style exclusion, or drop the GCI if biramy isn't universal even within Crustacea sensu stricto.

[dosumis]

@ai4c-reviewer is there a subclass of pancrustacea/sibling of hexapoda we could use here? Maybe we could attach to multiple siblings. Under Allotriocaridia we have:

Branchiopoda (2,851)
Cephalocarida (15)
Copepoda (6,678)
Hexapoda (880,070)
Remipedia (56)
unclassified Allotriocarida

[ai4c-reviewer]

🟡 IMPORTANT: This term is literally named "crustacean maxillary gland" and its def is crustacean-specific, but in_taxon now points to the strictly broader Pancrustacea (which also includes Hexapoda/insects, NCBITaxon:6960 — insects don't have maxillary glands, they use Malpighian tubules).

in_taxon acts as an upper bound (SubClassOf: in_taxon some Y), so this isn't logically false, but it silently discards the original Crustacea-only precision. The same applies to the other 8 plain in_taxon/present_in_taxon swaps in this PR for equally crustacean-specific terms: UBERON:0009963 (antennal/green gland — absent in Hexapoda), UBERON:0010266 (arthropod hepatopancreas — absent in Hexapoda), UBERON:0014857 (zoea stage), UBERON:0014861 (glaucothoe stage — specific to hermit crabs), UBERON:0015170 (nauplius eye), UBERON:0018378 (crustacean larval stage), UBERON:8480039 (Oka organ). (UBERON:0006583 statocyst and UBERON:0010264 hepatopancreas use present_in_taxon, which is existential/multi-taxon by design — those two are fine as-is.)

Suggest pairing the new in_taxon NCBITaxon:197562 ! Pancrustacea with never_in_taxon NCBITaxon:6960 ! Hexapoda on each of these, mirroring the existing pattern already used elsewhere in this same PR (UBERON:0000972 antenna pairs in_taxon Arthropoda with never_in_taxon Chelicerata). This is also the exact open question the PR author flagged in the (unchecked) test-plan item.

[ai4c-reviewer]

Review summary: this PR correctly removes all references to the obsolete NCBITaxon:6657 (Crustacea), but the chosen replacement (Pancrustacea, NCBITaxon:197562, which also includes Hexapoda/insects) needs closer per-term review before merge.

🔴 CRITICAL: UBERON:0000972 (antenna) line ~9340 widens the gci_filler in a has_quality PATO:0000402 GCI axiom from Crustacea to Pancrustacea. This is a universally-quantified defining axiom ("every antenna part_of an organism in this taxon is branched"), not a simple upper-bound restriction, so this now incorrectly asserts insect antennae are branched (most are uniramous/unbranched).

🟡 IMPORTANT: The other 10 in_taxon/present_in_taxon swaps replace Crustacea with the strictly broader Pancrustacea for terms that are explicitly crustacean-specific by name/definition (crustacean maxillary gland, antennal/green gland, arthropod hepatopancreas, zoea stage, glaucothoe stage, nauplius eye, crustacean larval stage, Oka organ). in_taxon acts as an upper-bound restriction so these aren't strictly false, but they lose the original Crustacea-only precision for structures absent in Hexapoda. Recommend pairing with never_in_taxon NCBITaxon:6960 ! Hexapoda, mirroring the pattern already used on the antenna term itself (in_taxon Arthropoda + never_in_taxon Chelicerata). This is also the exact open question flagged (unchecked) in the PR's own test plan.

Full details in inline comments and the PR conversation comment.

[dosumis]

@ai4c-agent please add never_in_taxon NCBITaxon:6960 ! Hexapoda to classes as recommended by the review agent above.

Please also delete this axiom on antenna
has_quality PATO:0000402 {gci_relation="part_of", gci_filler="NCBITaxon:197562"}

It is not even true for all crustaceans

[ai4c-agent]

🤖 Working on it...

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[ai4c-agent]

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[ai4c-agent]

Done — pushed 4ee0bd0 to this branch.

Changes

1. Deleted the has_quality PATO:0000402 GCI axiom on UBERON:0000972 (antenna) — the gci_relation=part_of, gci_filler=NCBITaxon:197562 universal axiom removed entirely, since (as you noted) branched antennae are not true for all crustaceans, let alone all Pancrustacea.

2. Added never_in_taxon NCBITaxon:6960 ! Hexapoda to the 8 crustacean-specific terms whose in_taxon was broadened to Pancrustacea in the previous commit:

   • UBERON:0009963 antennal gland
   • UBERON:0009964 crustacean maxillary gland
   • UBERON:0010266 arthropod hepatopancreas
   • UBERON:0014857 zoea stage
   • UBERON:0014861 glaucothoe stage
   • UBERON:0015170 nauplius eye
   • UBERON:0018378 crustacean larval stage
   • UBERON:8480039 Oka organ

   statocyst (UBERON:0006583) and hepatopancreas (UBERON:0010264) were left alone — they use present_in_taxon (existential/multi-taxon), so no exclusion needed.

Edit file reserialised via robot convert before committing.

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Review checklist

• Hierarchy and parents are consistent
• Definitions and supporting references look adequate
• Obsolete or replacement handling is safe
• OBO and ODK conventions appear preserved
• No obvious CI, auth, or workflow regression

Re-review of PR #3772 (commit 4ee0bd0)

This is a re-review after the latest push, which addresses the two issues raised in the earlier review round.

Previously flagged issues — now resolved:

• 🔴 CRITICAL (antenna GCI): The has_quality PATO:0000402 {gci_relation="part_of", gci_filler=...} axiom on UBERON:0000972 (antenna) has been deleted entirely, per @dosumis's instruction that it isn't universally true even within Crustacea sensu stricto. Confirmed via obo-grep.pl — the term now has no has_quality GCI at all, and its in_taxon Arthropoda / never_in_taxon Chelicerata restrictions are untouched.
• 🟡 IMPORTANT (crustacean-specific in_taxon precision loss): never_in_taxon NCBITaxon:6960 ! Hexapoda has been added to all 8 terms where in_taxon was widened from Crustacea to Pancrustacea (antennal gland, crustacean maxillary gland, arthropod hepatopancreas, zoea stage, glaucothoe stage, nauplius eye, crustacean larval stage, Oka organ). This correctly restores Crustacea-only precision using the same in_taxon+never_in_taxon idiom already used elsewhere (e.g. antenna's in_taxon Arthropoda + never_in_taxon Chelicerata). Verified each of the 8 stanzas individually.
• The two present_in_taxon terms (statocyst UBERON:0006583, hepatopancreas UBERON:0010264) were correctly left without a never_in_taxon exclusion, consistent with present_in_taxon being existential rather than an upper-bound restriction.

Checks performed:

• obo-grep.pl on all 11 affected term stanzas — relationships are well-formed, correctly labelled (! Pancrustacea, ! Hexapoda), and alphabetically ordered consistent with robot convert reserialization.
• Confirmed NCBITaxon:6657 (obsolete Crustacea) no longer appears anywhere in the file.
• Commit message clearly documents rationale and is signed off by @ai4c-agent.
• Note: I was unable to run robot (reasoner/QC) locally in this environment — robot is not on PATH here — so CI should be relied on to confirm reasoner consistency.

Outstanding (non-blocking): @dosumis's question about whether a narrower Pancrustacea sub-clade (e.g. Allotriocarida) would be preferable to Pancrustacea+never_in_taxon Hexapoda is still open in the thread, but the current never_in_taxon compensation is logically sound and addresses the precision-loss concern either way — narrowing further can be a follow-up if a suitable non-obsolete NCBITaxon term is identified.

No new issues found. Approving.
· branch ai4c-agent-issue-3771-run1773

[ai4c-reviewer]

Re-review after commit 4ee0bd0, which addresses both previously flagged issues:

• 🔴 CRITICAL: the antenna (UBERON:0000972) has_quality PATO:0000402 GCI axiom (gci_filler widened to Pancrustacea) has been deleted entirely, as requested — confirmed no has_quality GCI remains on the term.
• 🟡 IMPORTANT: never_in_taxon NCBITaxon:6960 ! Hexapoda has been added to all 8 crustacean-specific terms whose in_taxon was widened Crustacea → Pancrustacea (antennal gland, crustacean maxillary gland, arthropod hepatopancreas, zoea stage, glaucothoe stage, nauplius eye, crustacean larval stage, Oka organ), correctly restoring Crustacea-only precision using the existing in_taxon+never_in_taxon idiom. The two present_in_taxon terms (statocyst, hepatopancreas) were left as-is, correctly, since present_in_taxon is existential.

Verified all 11 affected stanzas via obo-grep.pl; relationships are well-formed and consistent with robot's canonical serialization. NCBITaxon:6657 no longer appears anywhere in the file. Note: could not run robot/reasoner locally in this environment (not on PATH) — relying on CI for reasoner consistency confirmation.

No new issues found. Approving.