diff --git a/src/prefixmaps/data/linked_data.csv b/src/prefixmaps/data/linked_data.csv index 041d713..8694c79 100644 --- a/src/prefixmaps/data/linked_data.csv +++ b/src/prefixmaps/data/linked_data.csv @@ -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 diff --git a/src/prefixmaps/data/linked_data.curated.yaml b/src/prefixmaps/data/linked_data.curated.yaml index e04cb68..7718246 100644 --- a/src/prefixmaps/data/linked_data.curated.yaml +++ b/src/prefixmaps/data/linked_data.curated.yaml @@ -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_ diff --git a/src/prefixmaps/data/merged.csv b/src/prefixmaps/data/merged.csv index 6c3de9d..caac1cb 100644 --- a/src/prefixmaps/data/merged.csv +++ b/src/prefixmaps/data/merged.csv @@ -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 diff --git a/src/prefixmaps/data/merged.monarch.csv b/src/prefixmaps/data/merged.monarch.csv index b87346c..e74c372 100644 --- a/src/prefixmaps/data/merged.monarch.csv +++ b/src/prefixmaps/data/merged.monarch.csv @@ -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 diff --git a/src/prefixmaps/data/merged.oak.csv b/src/prefixmaps/data/merged.oak.csv index 6a45ae8..93c471b 100644 --- a/src/prefixmaps/data/merged.oak.csv +++ b/src/prefixmaps/data/merged.oak.csv @@ -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 diff --git a/tests/test_core/test_prefixmaps.py b/tests/test_core/test_prefixmaps.py index 565a2c9..dc7107b 100644 --- a/tests/test_core/test_prefixmaps.py +++ b/tests/test_core/test_prefixmaps.py @@ -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))