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"Alternative symbol" synonyms & "formerly" updates #132

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"Alternative symbol" synonyms & "formerly" updates #132

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e4a244c
"Alternative symbol" synonyms & "Formerly"
joeflack4 Sep 23, 2024
112a19f
"Alternative symbol" synonyms & "Formerly"
joeflack4 Oct 12, 2024
042296b
"Alternative symbol" synonyms & "Formerly"
joeflack4 Nov 20, 2024
bb392ae
"Alternative symbol" synonyms & "Formerly"
joeflack4 Nov 21, 2024
d6265fd
Merge pull request #168 from monarch-initiative/abbrevs-alt-n-include…
joeflack4 Nov 28, 2024
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51 changes: 26 additions & 25 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 @@ -202,7 +202,6 @@ def omim2obo(use_cache: bool = False):
get_alt_and_included_titles_and_symbols(alt_titles_str)
included_titles, included_symbols, former_included_titles, former_included_symbols = \
get_alt_and_included_titles_and_symbols(inc_titles_str)
included_is_included = included_titles or included_symbols # redundant. can't be included symbol w/out title

# Special cases depending on OMIM term type
is_gene = omim_type == OmimType.GENE or omim_type == OmimType.HAS_AFFECTED_FEATURE
Expand Down Expand Up @@ -233,50 +232,52 @@ def omim2obo(use_cache: bool = False):
pref_abbrev: Union[str, None] = None if not pref_symbols else pref_symbols[0]
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# Add synonyms
# - exact titles
# - exact synonyms: titles
graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(label_cleaner.clean(pref_title, pref_abbrev))))
for title in alt_titles:
graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(label_cleaner.clean(title, pref_abbrev))))
# - exact abbreviations
for abbrevs in [pref_symbols, alt_symbols]:
for abbreviation in abbrevs:
add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasExactSynonym, abbreviation,
# - exact synonyms: abbreviations
for symbols in [pref_symbols, alt_symbols]:
for symbol in symbols:
add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasExactSynonym, symbol,
[(oboInOwl.hasSynonymType, OMO['0003000'])])
# - related, deprecated 'former' titles
# - related, deprecated 'former' synonyms: titles
for title in former_alt_titles:
clean_title = label_cleaner.clean(title, pref_abbrev)
add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasRelatedSynonym, clean_title,
[(OWL.deprecated, Literal(True))])
# - related, deprecated 'former' abbreviations
for abbreviation in former_alt_symbols:
add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasRelatedSynonym, abbreviation,
[(OWL.deprecated, Literal(True)), (oboInOwl.hasSynonymType, OMO['0003000'])])
add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasExactSynonym, 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.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.omimFormerly), symbol)

# Add 'included' entries
# - comment
if included_is_included:
if included_titles: # fyi: only need to check titles; there will never be included symbols w/out titles
included_comment = "This term has one or more labels that end with ', INCLUDED'."
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,
[(OWL.deprecated, Literal(True))])
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:
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omim_included), symbol, [
(OWL.deprecated, Literal(True)),
# Though these are abbreviations, MONDONS.omim_included is not a synonym type, so can't add axiom:
# (oboInOwl.hasSynonymType, OMO['0003000'])
])
# 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.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