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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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41 changes: 22 additions & 19 deletions omim2obo/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,6 +142,18 @@ def add_subclassof_restriction_with_evidence_and_source(
add_axiom_annotations(graph, on, RDFS['subClassOf'], b, annotation_pred_vals)


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.

  1. These are synonym types now
  2. The spelling/caps are now different
  3. 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.
  4. owl:deprecated was being added for OMIM_FORMERLY now I think does not make sense to add to hasRelatedSynonym, so I removed it. We could also use MONDO:DEPRECATED, but I think that maybe OIMIM_FORMERLY stands on its own for explanation and might not need any additional annotations.

"""Add title or symbol as synonym"""
annotations = [
(oboInOwl.hasSynonymType, URIRef(MONDONS['OMIM_INCLUDED'])),
]
if is_symbol:
annotations.append((oboInOwl.hasSynonymType, OMO['0003000']))
if is_formerly:
annotations.append((oboInOwl.hasSynonymType, URIRef(MONDONS['OMIM_FORMERLY'])))
add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasRelatedSynonym, synonym, annotations)


# Classes
class DeterministicBNode(BNode):
"""Overrides BNode to create a deterministic ID"""
Expand Down Expand Up @@ -201,11 +213,15 @@ def omim2obo(use_cache: bool = False):
# Populate graph
# - 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(oboInOwl.source), RDF.type, OWL.AnnotationProperty))
graph.add((URIRef(MONDONS.omim_included), RDF.type, OWL.AnnotationProperty))
graph.add((URIRef(OMO['0003000']), RDF.type, OWL.AnnotationProperty))
graph.add((BIOLINK['has_evidence'], RDF.type, OWL.AnnotationProperty))
graph.add((URIRef(oboInOwl.SynonymTypeProperty), RDF.type, OWL.AnnotationProperty))
graph.add((URIRef(oboInOwl.hasSynonymType), RDF.type, OWL.AnnotationProperty))
graph.add((URIRef(MONDONS.OMIM_INCLUDED), RDFS.subPropertyOf, oboInOwl.SynonymTypeProperty))
graph.add((URIRef(MONDONS.OMIM_FORMERLY), RDFS.subPropertyOf, oboInOwl.SynonymTypeProperty))

graph.add((TAX_URI, RDF.type, OWL.Class))
graph.add((TAX_URI, RDFS.label, Literal(TAX_LABEL)))

Expand Down Expand Up @@ -236,7 +252,6 @@ 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

# Recapitalize acronyms in titles
all_abbrevs: Set[str] = \
Expand Down Expand Up @@ -291,29 +306,17 @@ def omim2obo(use_cache: bool = False):
[(OWL.deprecated, Literal(True)), (oboInOwl.hasSynonymType, OMO['0003000'])])

# Add 'included' entries
# - comment
if included_is_included:
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(title)))
add_included_synonym(graph, omim_uri, title)
# - 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:
# (oboInOwl.hasSynonymType, OMO['0003000'])
])
add_included_synonym(graph, omim_uri, symbol, is_symbol=True)
# - deprecated, 'former'
for title in former_included_titles:
add_triple_and_optional_annotations(graph, omim_uri, URIRef(MONDONS.omim_included), title,
[(OWL.deprecated, Literal(True))])
add_included_synonym(graph, omim_uri, title, is_formerly=True)
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'])
])
add_included_synonym(graph, omim_uri, symbol, is_symbol=True, is_formerly=True)

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