Merge pull request #146 from monarch-initiative/anno-prop-dec-refactor

Annotation prop declaration refactor & `oio` refactor
monarch-initiative · Sep 23, 2024 · e812939 · e812939
2 parents 5b5eae1 + 093253e
commit e812939
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diff --git a/omim2obo/main.py b/omim2obo/main.py
@@ -135,8 +135,9 @@ 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('http://www.geneontology.org/formats/oboInOwl#hasSynonymType'), RDF.type, OWL.AnnotationProperty))
+    graph.add((URIRef(oboInOwl.hasSynonymType), 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((TAX_URI, RDF.type, OWL.Class))
     graph.add((TAX_URI, RDFS.label, Literal(TAX_LABEL)))

diff --git a/omim2obo/namespaces.py b/omim2obo/namespaces.py
@@ -53,6 +53,7 @@
 OBAN = Namespace('http://purl.org/oban/')                                     # Open Biomedical Annotation Model
 OBI = Namespace('http://purl.obolibrary.org/obo/OBI_')                        # Ontology of Biomedical Investigations
 OBO = Namespace('http://purl.obolibrary.org/obo/')                            # Biological Ontology namespace (this is not itself an ontology)
+oboInOwl = Namespace('http://www.geneontology.org/formats/oboInOwl#')         # obo-specific annotation properties, like synonym types
 # 'OMIA' was http://omia.angis.org.au/ IS https://omia.org/         # (see about helping to update original data)
 OMIA = Namespace('https://omia.org/OMIA')                                     # Online Mendelian Inheritance in Animals (disease/species)
 OMO = Namespace('http://purl.obolibrary.org/obo/OMO_')                        # OBO Metadata Ontology
@@ -249,7 +250,6 @@
 PMID = Namespace('http://www.ncbi.nlm.nih.gov/pubmed/')
 ORPHANET = Namespace('http://www.orpha.net/ORDO/Orphanet_')
 UMLS = Namespace('http://linkedlifedata.com/resource/umls/id/')
-oboInOwl = Namespace('http://www.geneontology.org/formats/oboInOwl#')
 
 # # Monarch-specific
 # '': 'https://monarchinitiative.org/'                                # local BASE IRI
@@ -323,7 +323,6 @@
 # 'OBAN': 'http://purl.org/oban/'                                     # Open Biomedical Annotation Model
 # 'OBI': 'http://purl.obolibrary.org/obo/OBI_'                        # Ontology of Biomedical Investigations
 # 'OBO': 'http://purl.obolibrary.org/obo/'                            # Biological Ontology namespace (this is not itself an ontology)
-# 'oboInOwl': 'http://www.geneontology.org/formats/oboInOwl#'         # obo-specific annotation properties, like synonym types
 # # 'OMIA' was http://omia.angis.org.au/ IS https://omia.org/         # (see about helping to update original data)
 # 'OMIA': 'https://omia.org/OMIA'                                     # Online Mendelian Inheritance in Animals (disease/species)
 # # LIDIA seems retired. so these are not resovable                   # Also: http://www.vetsci.usyd.edu.au/lida/