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Add curated PHENOTYPE prefix for uphenotizer classes #87

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Add curated PHENOTYPE prefix for uphenotizer classes #87

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e8f38fd
Add curated PHENOTYPE prefix for uphenotizer classes
kevinschaper Nov 6, 2026
266689d
Merge branch 'main' into add-phenotype-prefix
kevinschaper Nov 6, 2026
ca17066
Merge branch 'main' into add-phenotype-prefix
kevinschaper Nov 6, 2026
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1 change: 1 addition & 0 deletions src/prefixmaps/data/linked_data.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ linkml,odrl,http://www.w3.org/ns/odrl/2/,canonical
linkml,oslc,http://open-services.net/ns/core#,canonical
linkml,owl,http://www.w3.org/2002/07/owl#,canonical
linkml,pav,http://purl.org/pav/,canonical
linkml,PHENOTYPE,https://w3id.org/monarch-initiative/entity/PHENOTYPE_,canonical
linkml,prov,http://www.w3.org/ns/prov#,canonical
linkml,qb,http://purl.org/linked-data/cube#,canonical
linkml,qudt,http://qudt.org/schema/qudt/,canonical
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3 changes: 3 additions & 0 deletions src/prefixmaps/data/linked_data.curated.yaml
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Expand Up @@ -33,3 +33,6 @@ prefixes:
dcmitype: http://purl.org/dc/dcmitype/
wgs: http://www.w3.org/2003/01/geo/wgs84_pos#
xml: http://www.w3.org/XML/1998/namespace
# Phenotype classes minted by uphenotizer and imported by PHENIO
# (https://github.com/monarch-initiative/uphenotizer)
PHENOTYPE: https://w3id.org/monarch-initiative/entity/PHENOTYPE_
1 change: 1 addition & 0 deletions src/prefixmaps/data/merged.csv
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Expand Up @@ -12121,6 +12121,7 @@ merged,PHENOLEXPLORER,https://identifiers.org/phenolexplorer/,prefix_alias,biore
merged,PHENOLEXPLORER,https://identifiers.org/phenolexplorer:,prefix_alias,bioregistry
merged,PHENOLEXPLORER,https://n2t.net/phenolexplorer:,prefix_alias,bioregistry
merged,PHENOLEXPLORER,https://phenol-explorer.eu/foods/,prefix_alias,bioregistry
merged,PHENOTYPE,https://w3id.org/monarch-initiative/entity/PHENOTYPE_,canonical,linkml
merged,PHENX,https://www.phenxtoolkit.org/protocols/view/,canonical,bioregistry
merged,PHENX,http://bioregistry.io/phenx:,prefix_alias,bioregistry
merged,PHENX,http://bioregistry.io/phenxtoolkit:,prefix_alias,bioregistry
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1 change: 1 addition & 0 deletions src/prefixmaps/data/merged.monarch.csv
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Expand Up @@ -12121,6 +12121,7 @@ merged.monarch,PHENOLEXPLORER,https://identifiers.org/phenolexplorer/,prefix_ali
merged.monarch,PHENOLEXPLORER,https://identifiers.org/phenolexplorer:,prefix_alias,bioregistry
merged.monarch,PHENOLEXPLORER,https://n2t.net/phenolexplorer:,prefix_alias,bioregistry
merged.monarch,PHENOLEXPLORER,https://phenol-explorer.eu/foods/,prefix_alias,bioregistry
merged.monarch,PHENOTYPE,https://w3id.org/monarch-initiative/entity/PHENOTYPE_,canonical,linkml
merged.monarch,PHENX,https://www.phenxtoolkit.org/protocols/view/,canonical,bioregistry
merged.monarch,PHENX,http://bioregistry.io/phenx:,prefix_alias,bioregistry
merged.monarch,PHENX,http://bioregistry.io/phenxtoolkit:,prefix_alias,bioregistry
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1 change: 1 addition & 0 deletions src/prefixmaps/data/merged.oak.csv
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Expand Up @@ -12121,6 +12121,7 @@ merged.oak,PHENOLEXPLORER,https://identifiers.org/phenolexplorer/,prefix_alias,b
merged.oak,PHENOLEXPLORER,https://identifiers.org/phenolexplorer:,prefix_alias,bioregistry
merged.oak,PHENOLEXPLORER,https://n2t.net/phenolexplorer:,prefix_alias,bioregistry
merged.oak,PHENOLEXPLORER,https://phenol-explorer.eu/foods/,prefix_alias,bioregistry
merged.oak,PHENOTYPE,https://w3id.org/monarch-initiative/entity/PHENOTYPE_,canonical,linkml
merged.oak,PHENX,https://www.phenxtoolkit.org/protocols/view/,canonical,bioregistry
merged.oak,PHENX,http://bioregistry.io/phenx:,prefix_alias,bioregistry
merged.oak,PHENX,http://bioregistry.io/phenxtoolkit:,prefix_alias,bioregistry
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10 changes: 10 additions & 0 deletions tests/test_core/test_prefixmaps.py
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Expand Up @@ -229,3 +229,13 @@ def test_synonyms(self):
for curie in others:
with self.subTest(curie=curie):
self.assertEqual(canonical, converter.standardize_curie(curie))

def test_curated_phenotype_prefix(self):
"""PHENOTYPE is curated in linked_data, so it reaches every merged context."""
curie = "PHENOTYPE:1001742"
uri = "https://w3id.org/monarch-initiative/entity/PHENOTYPE_1001742"
for name in ["linked_data", "merged", "merged.monarch", "merged.oak"]:
with self.subTest(context=name):
converter = prefixmaps.load_converter(name)
self.assertEqual(uri, converter.expand(curie))
self.assertEqual(curie, converter.compress(uri))
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