Add NTR: entorhinal cortex layer II stellate cell (CL_9900001)#3631
Add NTR: entorhinal cortex layer II stellate cell (CL_9900001)#3631Copilot wants to merge 16 commits into
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…sue #3630) - Added Declaration(Class(obo:CL_9900001)) in the declarations section - Added class definition for 'entorhinal cortex layer II stellate cell' with: - Definition referencing PMID:26223342, PMID:26711115, PMID:20512133, PMID:32039761, PMID:31680885 - Exact synonyms: MEC layer II stellate cell, entorhinal stellate cell, EC LII stellate cell, layer II stellate cell of medial entorhinal cortex - Related synonym: reelin-positive entorhinal cortex layer II neuron - Logical definition: glutamatergic neuron EquivalentTo CL:0000679 AND has_soma_location some UBERON:0022337 - SubClassOf: stellate neuron (CL:0000122) per issue recommendation - Term tracker link to GitHub issue #3630 - Date and creator metadata Signed-off-by: GitHub Copilot Agent-Logs-Url: https://github.com/obophenotype/cell-ontology/sessions/2a87c645-9327-461c-bf3d-56282ef39a70 Co-authored-by: RiveraAndrea83 <205639972+RiveraAndrea83@users.noreply.github.com>
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -base file):Ontology comparisonLeft
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Ontology importsOntology annotationsGPi Core neuron (Primate)
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsentorhinal cortex layer 2
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NCBI taxon 6657 crustacea has been merged with pancrustacea which i believe is causing the issue |
All that is required is for CL to replace all its references to |
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But this won’t fix the other issue (which is currently “hidden” by the NCBITaxon:6657 issue) which is that the “HRA subset” is asserting (not for the first time, I believe…) that a cell type explicitly defined as being mouse-specific (CL:0002042) is being “present in Homo sapiens”… |
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@copilot: can you fix the issue? |
…197562 (Pancrustacea) NCBITaxon:6657 (Crustacea) has been merged into NCBITaxon:197562 (Pancrustacea) in the upstream NCBI taxonomy ontology. The deprecated term was still referenced in merged_import.owl which caused a SPARQL violation: FAIL Rule obsolete-replaced_by-violation.sparql: 1 violation(s) blank node, owl:someValuesFrom, NCBITaxon_6657, NCBITaxon_197562 Changes: - Remove NCBITaxon_6657 from non_native_classes.txt (NCBITaxon_197562 already present) - Remove Declaration, class section, and DisjointClasses axiom for NCBITaxon_6657 from merged_import.owl (NCBITaxon_197562 already has its own DisjointClasses axiom) Signed-off-by: GitHub Copilot Agent-Logs-Url: https://github.com/obophenotype/cell-ontology/sessions/34a5f0e5-42b7-4a21-a8a0-54d5acd120b6 Co-authored-by: RiveraAndrea83 <205639972+RiveraAndrea83@users.noreply.github.com>
Fixed in commit 880ffd2. The CI was failing because |
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All that was needed, after syncing with the master branch (in which my PR #3633 had been merged) was to refresh the imports – as I had written above. Once the edit file no longer contained any reference to NCBITaxon:6657, the import generation module would have automatically produced a Manual edits (and by “manual” I include operations performed by a large crap generator) to |
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Hi Damien, thank you very much i will revert the changes copilot made in this case. thanks! |
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@copilot please revert the changes you just made. |
These are ODK-generated files that should not be manually edited. The correct approach is to refresh imports after the edit file no longer references the deprecated NCBITaxon:6657 term. Signed-off-by: GitHub Copilot Agent-Logs-Url: https://github.com/obophenotype/cell-ontology/sessions/661eedd0-896b-4f57-83a6-2b87afbf5704 Co-authored-by: RiveraAndrea83 <205639972+RiveraAndrea83@users.noreply.github.com>
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/clara |
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Looks good. Just be careful of species-specificity of markers & e-phys.
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Claude finished @dosumis's task in 13m 22s —— View job CLARA Review — CL:9900001 (entorhinal cortex layer II stellate cell)Overall term-level result: ✅ PASS 16/17 assertions pass. One exact synonym has a minor terminological uncertainty (does not affect the core definition or structural axioms). NTR: Definition and structural axiomsAll 12 assertions verified against PMID:32039761, PMID:26223342, PMID:20512133, PMID:31680885, PMID:26711115.
Two assertions required full-text retrieval (PMID:32039761, PMID:26711115):
Synonyms
s4 — "EC LII stellate cell" (UNCERTAIN): The sole cited reference (Fuchs et al., PMID:26711115) consistently uses "MEC LII" (medial entorhinal cortex layer II), not "EC LII". The abbreviation "EC LII" is not attested verbatim in the cited reference. The underlying concept is well-supported; only the specific abbreviation is unverified.
Summary
All core definitional and structural assertions are supported by the cited literature. The term is ready for review subject to the minor synonym question above. |
CLARA review for PR #3631
Stage 2/3 verification ran for Routed verification results
Artifacts uploaded:
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#gogoeditdiff |
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#gogoeditdiff |
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/clara |
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Claude finished @RiveraAndrea83's task in 11m 34s —— View job CLARA Review — CL:9900001 entorhinal cortex layer II stellate cellResult: ✅ PASS — 17/18 assertions supported; 1 uncertain (synonym attestation); 0 fail. TermCL:9900001 — entorhinal cortex layer II stellate cell (new term) References: PMID:32039761 · PMID:26223342 · PMID:20512133 · PMID:31680885 · PMID:26711115 NTR: Definition assertions
NTR: Relationship assertions
Synonyms
Summary
The term definition, hierarchy placement, and synonyms are well supported by the cited literature. The one uncertain item ( Output files
CLARA automated review · [claude-sonnet-4-6] |
CLARA review for PR #3631
Stage 2/3 verification ran for Routed verification results
Artifacts uploaded:
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New term request for a glutamatergic principal neuron of entorhinal cortex layer II, characterized by stellate morphology, reelin expression, and perforant pathway projections to the dentate gyrus.
New term:
CL_9900001entorhinal cortex layer II stellate cellCL_0000679(glutamatergic neuron) ∩RO_0002100someUBERON_0022337(entorhinal cortex layer 2)CL_0000122(stellate neuron) — morphology represented in asserted hierarchy per issue guidance