some example OntologyClasses lack a namespacePrefix entry in the metadata section
cmungall opened this issue · 0 comments
cmungall commented
https://phenopacket-schema.readthedocs.io/en/latest/ontologyclass.html#id states that:
The ID of an OntologyClass element MUST take the form of a CURIE format. In order that the class is resolvable, it MUST reference the namespace prefix of a Resource named in the MetaData.
many of the examples don't adhere to this.
E.g. thrombocytopenia2 has:
"evidence": [{
"evidenceCode": {
"id": "ECO:0000033",
"label": "author statement supported by traceable reference"
},
the range of evidenceCode
is an OntologyClass
but the metadata record is:
"metaData": {
"created": "2021-05-14T10:35:00Z",
"createdBy": "anonymous biocurator",
"resources": [{
"id": "hp",
"name": "human phenotype ontology",
"url": "http://purl.obolibrary.org/obo/hp.owl",
"version": "2021-08-02",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}, {
"id": "geno",
"name": "Genotype Ontology",
"url": "http://purl.obolibrary.org/obo/geno.owl",
"version": "2020-03-08",
"namespacePrefix": "GENO",
"iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
}],
"phenopacketSchemaVersion": "2.0",
"externalReferences": [{
"id": "PMID:21211618",
"description": "Mutations in the 5\u0027 UTR of ANKRD26, the ankirin repeat domain 26 gene, cause an autosomal-dominant form of inherited thrombocytopenia, THC2"
}]
}