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included / formerly refactor #167

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included / formerly refactor #167

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5ec1680
Rename annotation prop: omim_included
joeflack4 Nov 20, 2024
6a68607
Merge branch 'develop' into omim-included-rename
joeflack4 Jan 3, 2025
e806fe2
OMIM included & formerly refactor
joeflack4 Jan 3, 2025
5edfeb0
OMIM included & formerly refactor
joeflack4 Jan 4, 2025
95f78c2
Merge branch 'develop' into omim-included-rename
joeflack4 Jan 4, 2025
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4 changes: 2 additions & 2 deletions omim2obo/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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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@joeflack4 joeflack4 Dec 16, 2024 •
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Rename

Discussed w/ Nico today. These are not the same.We need to keep both.

  • @joeflack4 Rename omim_included to omimIncluded or OMIM_INCLUDED (see: comment)
    • Do same for 'formerly'
  • @joeflack4 Don't remove includedEntryInOMIM

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@joeflack4 joeflack4 Dec 17, 2024 •
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Snake or camel case

Nico wrote:

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.

graph.add((URIRef(OMO['0003000']), RDF.type, OWL.AnnotationProperty))
graph.add((BIOLINK['has_evidence'], RDF.type, OWL.AnnotationProperty))
graph.add((TAX_URI, RDF.type, OWL.Class))
Expand Down Expand Up @@ -252,7 +252,7 @@ def omim2obo(use_cache: bool = False):
if label_endswith_included_alt or label_endswith_included_inc:
graph.add((omim_uri, RDFS['comment'], Literal(included_detected_comment)))
for included_label in cleaned_inc_labels:
graph.add((omim_uri, URIRef(MONDONS.omim_included), Literal(label_cleaner.clean(included_label, abbrev))))
graph.add((omim_uri, URIRef(MONDONS.includedEntryInOMIM), Literal(label_cleaner.clean(included_label, abbrev))))

# Gene ID
# Why is 'skos:exactMatch' appropriate for disease::gene relationships? - joeflack4 2022/06/06
Expand Down