linkml / linkml

Linked Open Data Modeling Language
https://linkml.io/linkml
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Use bioregistry.io for prefixregistry #604

Closed cmungall closed 1 year ago

cmungall commented 2 years ago

Discussing with @hsolbrig

Currently default_curi_maps use https://pypi.org/project/curieutil/ which fetches from prefixcommons

we should get prefixes from bioregistry

eg.

>>> from bioregistry import get_iri, get_prefix_map
>>> prefix_map = get_prefix_map(priority=["obofoundry"])
>>> prefix_map['pato']
'http://purl.obolibrary.org/obo/PATO_'
>>> get_iri('skos','')
'http://www.w3.org/2004/02/skos/core#'

We need bioregistry to have the correct casing first

hrshdhgd commented 2 years ago

Related issues: https://github.com/mapping-commons/sssom-py/issues/247

cmungall commented 2 years ago

See also #502

sierra-moxon commented 1 year ago

done: https://github.com/linkml/linkml-runtime/pull/231