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[WIP] add FMA ontology #1371

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[WIP] add FMA ontology #1371

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e42934f
Fix prefix removal bug in OWL client
bgyori Mar 8, 2022
cf56efe
Add FMA resource
bgyori Mar 8, 2022
2b6b972
Add FMA to ontology
bgyori Mar 8, 2022
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2 changes: 1 addition & 1 deletion indra/databases/owl_client.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ def entry_from_term(
term_ns = term_ns.lower()
return {
"namespace": term_ns,
"id": term_id,
"id": term_id if remove_prefix else term.id,
"name": term.name,
"synonyms": [s.description for s in term.synonyms],
"xrefs": xrefs,
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5 changes: 3 additions & 2 deletions indra/ontology/bio/ontology.py
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Expand Up @@ -19,10 +19,10 @@ class BioOntology(IndraOntology):
# should be incremented to "force" rebuilding the ontology to be consistent
# with the underlying resource files.
name = 'bio'
version = '1.22'
version = '1.23'
ontology_namespaces = [
'go', 'efo', 'hp', 'doid', 'chebi', 'ido',
'mondo',
'mondo', 'fma'
]

def __init__(self):
Expand Down Expand Up @@ -222,6 +222,7 @@ def add_obo_nodes(self):
'chebi': lambda x: 'small_molecule',
'ido': lambda x: 'infectious_disease_concept',
'mondo': lambda x: 'disease',
'fma': lambda x: 'anatomical_concept'
}
for ns in self.ontology_namespaces:
oc = obo_client.OntologyClient(prefix=ns)
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