included / formerly refactor
#167
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- Rename to be in line with what is in Mondo: includedEntryInOMIM
omim2obo/main.py
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| @@ -164,7 +164,7 @@ def omim2obo(use_cache: bool = False): | |||
| # - Non-OMIM triples | |||
| graph.add((URIRef('http://purl.obolibrary.org/obo/mondo/omim.owl'), RDF.type, OWL.Ontology)) | |||
| graph.add((URIRef(oboInOwl.hasSynonymType), RDF.type, OWL.AnnotationProperty)) | |||
| graph.add((URIRef(MONDONS.omim_included), RDF.type, OWL.AnnotationProperty)) | |||
| graph.add((URIRef(MONDONS.includedEntryInOMIM), RDF.type, OWL.AnnotationProperty)) | |||
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Rename
Discussed w/ Nico today. These are not the same.We need to keep both.
- @joeflack4 Rename
omim_includedtoomimIncludedorOMIM_INCLUDED(see: comment)- Do same for 'formerly'
- @joeflack4 Don't remove
includedEntryInOMIM
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Look how clingen_label is formatted I think it's all upper case with underscore, so OMIM_INCLUDED should be as well (always check other examples of the same thing you are adding to determine correct casing) |
omim2obo/main.py
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| @@ -164,7 +164,7 @@ def omim2obo(use_cache: bool = False): | |||
| # - Non-OMIM triples | |||
| graph.add((URIRef('http://purl.obolibrary.org/obo/mondo/omim.owl'), RDF.type, OWL.Ontology)) | |||
| graph.add((URIRef(oboInOwl.hasSynonymType), RDF.type, OWL.AnnotationProperty)) | |||
| graph.add((URIRef(MONDONS.omim_included), RDF.type, OWL.AnnotationProperty)) | |||
| graph.add((URIRef(MONDONS.includedEntryInOMIM), RDF.type, OWL.AnnotationProperty)) | |||
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Snake or camel case
Look how clingen_label is formatted I think it's all upper case with underscore, so OMIM_INCLUDED should be as well (always check other examples of the same thing you are adding to determine correct casing)
Originally we were doing snake case, but then we 3 met a few weeks ago and coming out of that meeting, determined this and omimFormerly should be camel case, but I don't remember why.
Edit:
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/mondo#CLINGEN_LABEL">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>@twhetzel Can make the judgement on this one?
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Based on this, I think UPPER_SNAKE_CASE is best.
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| @@ -141,6 +142,19 @@ def add_subclassof_restriction_with_evidence_and_source( | |||
| add_axiom_annotations(graph, on, RDFS['subClassOf'], b, annotation_pred_vals) | |||
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| def add_included_synonym(graph: Graph, omim_uri: URIRef, synonym: str, is_symbol=False, is_formerly=False): | |||
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Several important changes
Trying to to open threads often. But I felt these were really important changes I should mention here.
Nico though it made sense for OMIM_INCLUDED and OMIM_FORMERLY to be synonym types, and Trish and I have started to discuss at meetings but haven't had time to fully dive in. If these changes are too much, I can undo.
- These are synonym types now
- The spelling/caps are now different
- If they are synonym types, that means I need to be adding synonyms for OMIM_INCLUDED, which we weren't doing before. This is kind of a major change. I chose
hasRelatedSynonym. owl:deprecatedwas being added forOMIM_FORMERLYnow I think does not make sense to add tohasRelatedSynonym, so I removed it. We could also useMONDO:DEPRECATED, but I think that maybeOIMIM_FORMERLYstands on its own for explanation and might not need any additional annotations.
- Update: Made OMIM_INCLUDED & OMIM_FORMERLY synonymType - Update: Renamed these to UPPER_SNAKE_CASE - Update: OMIM_INCUDED is now a type on relatedSynonym rather than its own declaration. This result in addition of new synonyms. - Update: Retained includedEntryInOMIM as annotation property on synonyms - Add: Missing property declarations - Deleted: rdfs:comment related to 'included' - Refactor: Added abstraction: add_included_synonym()
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- Delete: includedEntryInOMIM stuff just added. I had thought we had previously had this in the codebase, but we had not. This is an xref source value, but the way I was adding it in the last commit anyway was a bit confused; I had been adding it as a synonym source value.
Warning
These should be merged at the same time:
included/formerlyrefactor #167Changes
OMIM included & formerly refactor
Related: