Standardised names and in_taxon axioms. Minor update to doc. #3386
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Pull Request Overview
This PR aims to standardize species names and ensure complete in_taxon relationships throughout the ontology, with an additional minor documentation update about synonym preservation guidelines.
- Standardized all mentions of species in names to ensure consistency
- Added complete in_taxon relationship axioms where missing
- Enhanced editing guidelines with important synonym preservation instructions
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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 annotationsAxl+ dendritic cell, human
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsAxl+ dendritic cell, human
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dosumis
requested review from
RiveraAndrea83,
aleixpuigb,
emquardokus and
gouttegd
Co-authored-by: Copilot <[email protected]>
Update to doc to cover species specific naming (We might want to consider whether order in doc is good)
…ontology into species_names
| @@ -12345,7 +12345,8 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000938 "CD16-negative, CD56 | |||
| AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000938 "CD56-bright cytokine secreting NK cell") | |||
| AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000938 "CD56-bright cytokine secreting natural killer cell") | |||
| AnnotationAssertion(rdfs:comment obo:CL_0000938 "This cell type is compatible with the HIPC Lyoplate markers for 'CD16-CD56bright NK cell'. Markers are associated with human cell types.") | |||
| AnnotationAssertion(rdfs:label obo:CL_0000938 "CD16-negative, CD56-bright natural killer cell, human") | |||
| AnnotationAssertion(rdfs:label obo:CL_0000938 "CD16-negative, CD56-bright natural killer cell (Hsap)") | |||
| AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0000938 "CD16-negative, CD56-bright natural killer cell, human") | |||
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Another illustration of the fact that AI agents don’t know how to edit a OFN file correctly, and cause spurious diffs. Those axioms have been inserted in an out-of-order fashion.
I am going to once again strongly suggest that any AI-based workflow should systematically include a ROBOT-based re-serialisation step so as to avoid polluting the history with countless of spurious diffs.
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Agree we should do this.
| @@ -13501,6 +13512,7 @@ SubClassOf(obo:CL_0001054 obo:CL_0000576) | |||
| # Class: obo:CL_0001055 (CD14-positive, CD16-low monocyte) | |||
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| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:add") Annotation(oboInOwl:hasDbXref "PMID:20628149") obo:IAO_0000115 obo:CL_0001055 "An intermediate monocyte that is CD14-positive and with low amounts of CD16.") | |||
| AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0001055 "intermediate monocyte (Hsap)") | |||
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It’s unclear whether that term is human-specific.
It does not have a in_taxon some 'Homo sapiens' relationship (and, unless I am mistaken, does not inherit one). It has a present_in_taxon some 'Homo sapiens' annotation, which merely indicates that the cell type is known to exist in humans but does not imply it only exists in humans.
There’s a comment saying that “the definition is valid for human intermediate monocytes”, but again, that doesn’t necessarily imply that the definition is not valid for other taxa.
Either the cell type is actually human-specific, in which case it should have the proper in_taxon restriction and “(Hsap)” should be added to the label (not just on a synonym); or we don’t know if it is human-specific, in which case exact synonyms should not include a species qualifier (regardless of whether it is “human” or “Hsap”).
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Based on PMID:19965649, I am convinced that this is a human specific term.
| @@ -18187,6 +18228,7 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0002395 obo:CL_0000860 | |||
| AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "PMID:20870168") obo:IAO_0000115 obo:CL_0002396 "A patrolling monocyte that is CD14-low and CD16-positive.") | |||
| AnnotationAssertion(terms:contributor obo:CL_0002396 <https://orcid.org/0000-0003-1980-3228>) | |||
| AnnotationAssertion(oboInOwl:creation_date obo:CL_0002396 "2010-10-04T12:25:42Z"^^xsd:dateTime) | |||
| AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_0002396 "non-classical monocyte (Hsap)") | |||
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Similar case to “CD14-positive, CD16-low monocyte” (CL:0001055) above. It is unclear whether that term is really human-specific.
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Based on PMID:20870168 (the original reference) and PMID:19965649, I am convinced these are human specific cells.
| @@ -24008,33 +24063,36 @@ TA: Transit Amplifying Cells") foaf:depiction obo:CL_0009080 <http://purl.obolib | |||
| EquivalentClasses(obo:CL_0009080 ObjectIntersectionOf(obo:CL_0019032 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002108))) | |||
| SubClassOf(obo:CL_0009080 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001902)) | |||
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| # Class: obo:CL_0009081 (specified double negative thymocyte (Homo sapiens)) | |||
| # Class: obo:CL_0009081 (specified double negative thymocyte (Hsap)) | |||
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Sigh… You gotta love the consistency of AI tools. For all the terms above whose label has been changed, the agent didn’t bother to update the comment to reflect the new label, and here all of a sudden it decides that it won’t do, and that the comment must be updated.
I guess deterministic tools are just boring.
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Human editors can be pretty inconsistent too...
| @@ -29928,6 +29992,7 @@ AnnotationAssertion(oboInOwl:hasExactSynonym obo:CL_4023019 "L5/6 CCK Vip (Mus m | |||
| AnnotationAssertion(oboInOwl:inSubset obo:CL_4023019 cl:BDS_subset) | |||
| AnnotationAssertion(rdfs:label obo:CL_4023019 "L5/6 cck, VIP GABAergic interneuron (Mmus)") | |||
| EquivalentClasses(obo:CL_4023019 ObjectIntersectionOf(obo:CL_4023071 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_P32648))) | |||
| SubClassOf(obo:CL_4023019 ObjectSomeValuesFrom(obo:RO_0002162 obo:NCBITaxon_10090)) | |||
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This is not wrong per se, but not necessary as CL:4023019 “inherits” the taxon restriction from CL:4023071.
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This session used only extremely basal tools. Aim in future will be to have direct OWL query tools (and editing tools?) and to work on refining doc for agents (and humans). With a decent DL query tool it would be very straightforward to detect redundancies like this.
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I shall also note that if we go ahead with the policy outlined here, we must remember to also apply it to outsourced components that are imported “as is” into CL. In particular, the |
- Reverted 9 obsolete terms (CL_4023098-4023106) back to original full species names - Obsolete terms should not be edited except for mappings and comments - Added clear policy in CLAUDE.md: "DO NOT EDIT OBSOLETE TERMS" - Fixed species naming standardization to exclude obsolete terms 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Agreed. As external component is built with ODK, we could potentially enforce with common QC checks. |
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#gogoeditdiff |
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Your branch is 2 commit/s behind, please update your branch. |
This is something that I could probably add to the “Uberon” ROBOT plugin (which despite its name is used in CL too, and it could then be used on WMBO as well). |
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This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so. |
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fixes #1829 |
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This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so. |
Edited using Claude.
Aim is to standardise all mention of species in names + ensure complete in_taxon relationships
Reports generated by Claude:
cl_intaxon_analysis_report.txt
cl_intaxon_final_report.txt