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"Alternative symbol" synonyms & "Formerly" - props rename #168

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"Alternative symbol" synonyms & "Formerly" - props rename #168

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"Alternative symbol" synonyms & "Formerly"
joeflack4 Nov 20, 2024
bb392ae
"Alternative symbol" synonyms & "Formerly"
joeflack4 Nov 21, 2024
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25 changes: 12 additions & 13 deletions omim2obo/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,7 @@ 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)) # like an rdfs:label subClass
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 @@ -245,14 +245,14 @@ def omim2obo(use_cache: bool = False):
for title in former_alt_titles:
clean_title = label_cleaner.clean(title, pref_abbrev)
add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasExactSynonym, clean_title)
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omim_formerly), clean_title)
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omimFormerly), clean_title)
# - related, deprecated 'former' synonyms: abbreviations
for symbol in former_alt_symbols:
add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasExactSynonym, symbol,
[(oboInOwl.hasSynonymType, OMO['0003000'])])
# Though these are abbreviations, MONDONS.omim_formerly is not (yet) a synonym
# Though these are abbreviations, MONDONS.omimFormerly is not (yet) a synonym
# type, so can't add axiom: (oboInOwl.hasSynonymType, OMO['0003000'])
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omim_formerly), symbol)
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omimFormerly), symbol)

# Add 'included' entries
# - comment
Expand All @@ -261,24 +261,23 @@ def omim2obo(use_cache: bool = False):
graph.add((omim_uri, RDFS['comment'], Literal(included_comment)))
# - titles
for title in included_titles:
graph.add((omim_uri, URIRef(MONDONS.omim_included), Literal(label_cleaner.clean(title, pref_abbrev))))
graph.add((omim_uri, URIRef(MONDONS.includedEntryInOMIM), Literal(label_cleaner.clean(title, pref_abbrev))))
# - symbols
for symbol in included_symbols:
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omim_included), symbol, [
# Though these are abbreviations, MONDONS.omim_included is not a synonym type, so can't add axiom:
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.includedEntryInOMIM), symbol, [
# Though these are abbreviations, MONDONS.includedEntryInOMIM is not a synonym type, so can't add axiom:
# (oboInOwl.hasSynonymType, OMO['0003000'])
])
# - deprecated, 'former'
for title in former_included_titles:
clean_title = label_cleaner.clean(title, pref_abbrev)
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omim_included), clean_title)
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omim_formerly), clean_title)
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.includedEntryInOMIM), clean_title)
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omimFormerly), clean_title)
for symbol in former_included_symbols:
# Though these are abbreviations, MONDONS.omim_included and MONDONS.omim_formerly is not (yet) a synonym
# Though these are abbreviations, MONDONS.includedEntryInOMIM & MONDONS.omimFormerly is not (yet) a synonym
# type, so can't add axiom: (oboInOwl.hasSynonymType, OMO['0003000'])
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omim_included), symbol)
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omim_formerly), symbol)

add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.includedEntryInOMIM), symbol)
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omimFormerly), symbol)

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