Closed caufieldjh closed 1 year ago
Does not appear to be fixed in most recent KG-Phenio (20230302):
$ grep PATO:0001447 merged-kg_nodes.tsv
PATO:0001447 biolink:PhenotypicQuality calcified A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311). Graph
~/kg-phenio/data/merged/20230302$ grep PATO:0001447 merged-kg_edges.tsv
urn:uuid:bc483055-65da-4abd-ba42-47ab00248bef PATO:0001447 biolink:subclass_of PATO:0000025 infores:phenio Graph infores:pato
urn:uuid:9dcef768-d736-4c31-a695-fce57c28ac9c PATO:0001447 biolink:category biolink:NamedThing infores:phenio Graph infores:pato
urn:uuid:4e176049-fdc2-4577-b498-dee0a6d212b2 PATO:0001447 biolink:category biolink:OntologyClass infores:phenio Graph infores:pato
urn:uuid:9874c639-a33a-4ea9-9e5a-b1ab797730cb UPHENO:0067765 biolink:related_to PATO:0001447 infores:phenio Graph infores:upheno
This does appear to be fixed in the most recent KG-Phenio (20230808):
$ grep PATO:0001447 merged-kg_nodes.tsv
PATO:0001447 biolink:PhenotypicQuality calcified A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311). Graph calcareous|calcification
$ grep PATO:0001447 merged-kg_edges.tsv
urn:uuid:134278ea-d0ce-4b74-a7b6-ec683d1451dc PATO:0001447 biolink:subclass_of PATO:0000025 infores:phenio Graph infores:pato
urn:uuid:18d1f573-1671-41df-ac45-98162d07e94e UPHENO:0067765 biolink:related_to PATO:0001447 infores:phenio Graph infores:upheno
Processing of the most recent KG-Phenio build (20221215) assigns a correct entity type to nodes (or at least more specific than OntologyClass) but retains the old
biolink:category
edges, with incorrect objects. Example:Or:
The
biolink:category
edges shouldn't be present at all, and they definitely shouldn't refer to incorrect categories.