phenopackets / phenopacket-tools

An app and library for building, conversion, and validation of GA4GH Phenopackets.
http://phenopackets.org/phenopacket-tools/stable/
GNU General Public License v3.0
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some example OntologyClasses lack a namespacePrefix entry in the metadata section #147

Closed cmungall closed 1 year ago

cmungall commented 1 year ago

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"
    }]
  }