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Enable overriding auto-generated URLs from registries #641

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Enable overriding auto-generated URLs from registries #641

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57cb98a
First step to enabling override of default OLS and BioPortal URI cons…
cthoyt Sep 17, 2022
2f7f6a3
Update tests
cthoyt Oct 25, 2022
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14 changes: 14 additions & 0 deletions src/bioregistry/data/bioregistry.json
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Expand Up @@ -6360,6 +6360,20 @@
"homepage": "https://www.biomodels.net",
"name": "Legacy Biomodels URL",
"uri_format": "https://www.biomodels.net/kisao/KISAO#KISAO_$1"
},
{
"code": "ols",
"description": "An override for the default construction of OLS URI patterns, since this ontology does not use OBO PURLs",
"homepage": "https://www.ebi.ac.uk/ols",
"name": "OLS",
"uri_format": "https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http://www.biomodels.net/kisao/KISAO#KISAO_$1"
},
{
"code": "bioportal",
"description": "An override for the default construction of BioPortal URI patterns, since this ontology does not use OBO PURLs",
"homepage": "https://www.ebi.ac.uk/ols",
"name": "BioPortal",
"uri_format": "https://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=kisao:KISAO_$1"
}
],
"publications": [
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6 changes: 6 additions & 0 deletions src/bioregistry/resolve_identifier.py
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Expand Up @@ -468,6 +468,12 @@ def get_iri(
A custom provider is given, which makes the Bioregistry very extensible
>>> get_iri("chebi:24867", provider="chebi-img")
'https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=24867'

An override for a metaregistry is built-in to the record
>>> get_iri("kisao:0000057", provider="ols")
'https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http://www.biomodels.net/kisao/KISAO#KISAO_0000057'
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should be able to get base IRI from ols, however, bioportal is a completely different situation

>>> get_iri("kisao:0000057", provider="bioportal")
'https://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=kisao:KISAO_0000057'
"""
return manager.get_iri(
prefix=prefix,
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