{
  "id": "pharmgkb-disease",
  "acronym": "pharmgkb.disease",
  "name": "PharmGKB Disease",
  "category": "life",
  "domains": [
    "health"
  ],
  "kind": "ontology",
  "description": "The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains.",
  "formats": [
    "OWL",
    "OBO",
    "JSON"
  ],
  "license": "CC BY-SA 4.0",
  "homepage": "http://www.pharmgkb.org/",
  "download": "https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.owl",
  "bioregistry": "pharmgkb.disease",
  "publications": [
    {
      "title": "From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource",
      "doi": "10.2217/bmm.11.94",
      "year": 2011
    },
    {
      "title": "Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base",
      "doi": "10.1038/sj.tpj.6500035",
      "year": 2001
    }
  ],
  "usedBy": [],
  "tags": [
    "ontology",
    "pharmacogenomics"
  ],
  "url": "https://schemascope.org/o/pharmgkb-disease/",
  "evaluation": {
    "links": {
      "homepage": {
        "url": "http://www.pharmgkb.org/",
        "code": 200,
        "state": "ok",
        "resolvedUrl": "https://www.clinpgx.org/",
        "checkedAt": "2026-10-26T03:14:19.522Z"
      },
      "repository": null,
      "download": {
        "url": "https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.owl",
        "code": 200,
        "state": "ok",
        "resolvedUrl": "https://raw.githubusercontent.com/biopragmatics/obo-db-ingest/main/export/pharmgkb.disease/pharmgkb.disease.owl",
        "checkedAt": "2026-10-26T03:14:19.747Z"
      }
    },
    "github": null,
    "ols": null,
    "obo": null,
    "bioportal": null,
    "citations": [
      {
        "doi": "10.2217/bmm.11.94",
        "count": 132,
        "source": "https://api.crossref.org/works/10.2217%2Fbmm.11.94",
        "fetchedAt": "2026-10-26T03:14:18.954Z"
      },
      {
        "doi": "10.1038/sj.tpj.6500035",
        "count": 265,
        "source": "https://api.crossref.org/works/10.1038%2Fsj.tpj.6500035",
        "fetchedAt": "2026-10-26T03:14:18.953Z"
      }
    ],
    "git": null,
    "tib": null,
    "dashboard": null,
    "quality": null,
    "oops": null,
    "releases": {
      "dates": [],
      "lastYear": 0,
      "from": null
    },
    "bioregistry": {
      "prefix": "pharmgkb.disease",
      "name": "PharmGKB Disease",
      "mappings": {
        "biocontext": "PHARMGKB.DISEASE",
        "biolink.resource": "PHARMGKB.DISEASE",
        "edam.data": "2651",
        "miriam": "pharmgkb.disease",
        "n2t": "pharmgkb.disease",
        "prefixcommons": "pharmgkb.disease"
      },
      "dependsOn": [],
      "appearsIn": [],
      "license": "CC-BY-SA-4.0",
      "version": null,
      "deprecated": false,
      "page": "https://bioregistry.io/pharmgkb.disease",
      "source": "https://bioregistry.io/api/registry/pharmgkb.disease",
      "fetchedAt": "2026-10-26T03:14:18.728Z"
    },
    "artifact": {
      "source": "https://raw.githubusercontent.com/biopragmatics/obo-db-ingest/main/export/pharmgkb.disease/pharmgkb.disease.owl",
      "isRdf": true,
      "etag": "\"1cf5cb9b3a1fd4cd7516d1b63cf0ef298ec8eb92b2f6e1ad99369331958f8e47\"",
      "contentType": "text/plain",
      "fetchedAt": "2026-10-26T03:14:19.894Z"
    },
    "score": 30,
    "gross": 35,
    "earned": 35,
    "possible": 100,
    "qualityApplies": true,
    "penalty": {
      "score": -5,
      "reason": "no commits, releases or dated files found",
      "steps": [
        {
          "label": "No activity evidence",
          "pts": -5,
          "detail": "no commits, releases or dated files found"
        },
        {
          "label": "Inactive status",
          "pts": 0,
          "detail": "not archived, legacy or inactive"
        },
        {
          "label": "Consistency",
          "pts": 0,
          "detail": "not yet checked by a reasoner"
        }
      ]
    },
    "consistent": null,
    "grade": "E",
    "fair": 33,
    "breakdown": {
      "findable": {
        "score": 8,
        "max": 12,
        "steps": [
          {
            "label": "Persistent identifier (F1)",
            "pts": 4,
            "max": 4,
            "detail": "w3id.org"
          },
          {
            "label": "Indexed in services (F4)",
            "pts": 1,
            "max": 5,
            "detail": "1: Bioregistry"
          },
          {
            "label": "Citable reference (F2)",
            "pts": 3,
            "max": 3,
            "detail": "doi:10.2217/bmm.11.94"
          }
        ],
        "notes": [
          "Indexed in services (F4): 1: Bioregistry"
        ]
      },
      "accessible": {
        "score": 12,
        "max": 12,
        "steps": [
          {
            "label": "Homepage reachable",
            "pts": 3,
            "max": 3,
            "detail": "HTTP 200"
          },
          {
            "label": "Artefact retrievable over HTTP(S) (A1)",
            "pts": 6,
            "max": 6,
            "detail": "download HTTP 200"
          },
          {
            "label": "Metadata persists in a registry (A2)",
            "pts": 3,
            "max": 3,
            "detail": "Bioregistry"
          }
        ],
        "notes": []
      },
      "interoperable": {
        "score": 8,
        "max": 12,
        "steps": [
          {
            "label": "Formal machine-readable format (I1)",
            "pts": 5,
            "max": 5,
            "detail": "OWL, OBO"
          },
          {
            "label": "Semantic-web IRIs (I2)",
            "pts": 3,
            "max": 3,
            "detail": "OWL, OBO"
          },
          {
            "label": "References other vocabularies (I3)",
            "pts": 0,
            "max": 4,
            "detail": "no imported vocabularies found"
          }
        ],
        "notes": [
          "References other vocabularies (I3): no imported vocabularies found"
        ]
      },
      "reusable": {
        "score": 5,
        "max": 12,
        "steps": [
          {
            "label": "Clear license (R1.1)",
            "pts": 5,
            "max": 5,
            "detail": "CC BY-SA 4.0"
          },
          {
            "label": "Release provenance (R1.2)",
            "pts": 0,
            "max": 4,
            "detail": "no version in artefact, registry or release tags"
          },
          {
            "label": "Community standards (R1.3)",
            "pts": 0,
            "max": 3,
            "detail": "no independent compliance report (not on the OBO Dashboard)"
          }
        ],
        "notes": [
          "Release provenance (R1.2): no version in artefact, registry or release tags",
          "Community standards (R1.3): no independent compliance report (not on the OBO Dashboard)"
        ]
      },
      "quality": {
        "score": 0,
        "max": 20,
        "steps": [
          {
            "label": "Logical consistency",
            "pts": 0,
            "max": 10,
            "detail": "never checked by a reasoner"
          },
          {
            "label": "OWL 2 DL profile",
            "pts": 0,
            "max": 2,
            "detail": "profile not checked"
          },
          {
            "label": "Upper-ontology alignment",
            "pts": 0,
            "max": 3,
            "detail": "no BFO/COB/DOLCE import found"
          },
          {
            "label": "Standard relations (RO)",
            "pts": 0,
            "max": 1,
            "detail": "does not import the Relation Ontology"
          },
          {
            "label": "ROBOT report: no errors",
            "pts": 0,
            "max": 2,
            "detail": "no ROBOT report available"
          },
          {
            "label": "ROBOT report: warning density",
            "pts": 0,
            "max": 1,
            "detail": "no ROBOT report available"
          },
          {
            "label": "Pitfall scan: no critical pitfalls",
            "pts": 0,
            "max": 1,
            "detail": "no pitfall scan or ROBOT report yet"
          }
        ],
        "notes": [
          "Logical consistency: never checked by a reasoner",
          "OWL 2 DL profile: profile not checked",
          "Upper-ontology alignment: no BFO/COB/DOLCE import found",
          "Standard relations (RO): does not import the Relation Ontology",
          "ROBOT report: no errors: no ROBOT report available",
          "ROBOT report: warning density: no ROBOT report available",
          "Pitfall scan: no critical pitfalls: no pitfall scan or ROBOT report yet"
        ]
      },
      "maintenance": {
        "score": 0,
        "max": 16,
        "steps": [
          {
            "label": "Recency",
            "pts": 0,
            "max": 10,
            "detail": "no activity evidence"
          },
          {
            "label": "Release cadence (12 months)",
            "pts": 0,
            "max": 6,
            "detail": "0 releases"
          }
        ],
        "notes": [
          "Recency: no activity evidence",
          "Release cadence (12 months): 0 releases"
        ]
      },
      "adoption": {
        "score": 2,
        "max": 16,
        "steps": [
          {
            "label": "Documented adopting projects",
            "pts": 0,
            "max": 7,
            "detail": "0 projects"
          },
          {
            "label": "Reused by other ontologies",
            "pts": 0,
            "max": 4,
            "detail": "0"
          },
          {
            "label": "Community signal",
            "pts": 2,
            "max": 5,
            "detail": "max(stars 0 → 0, citations 265 → 2)"
          }
        ],
        "notes": [
          "Documented adopting projects: 0 projects",
          "Reused by other ontologies: 0",
          "Community signal: max(stars 0 → 0, citations 265 → 2)"
        ]
      }
    },
    "lastActivity": null,
    "adopterCount": 0,
    "reuseCount": 0,
    "importCount": 0,
    "registries": [
      "Bioregistry"
    ],
    "evaluatedVersion": null,
    "evaluatedAt": "2026-10-26T03:14:19.895Z",
    "runId": "2026-10-26T02-37-38Z",
    "adopters": []
  },
  "history": [
    {
      "runId": "2026-10-26T02-37-38Z",
      "at": "2026-10-26T03:31:18.947Z",
      "score": 30,
      "grade": "E",
      "fair": 33,
      "version": null,
      "terms": null,
      "stars": null,
      "license": null,
      "lastActivity": null,
      "adopters": 0,
      "links": {
        "homepage": "ok",
        "download": "ok"
      },
      "archived": false,
      "rubric": "3.4",
      "snapshot": "https://schemascope.org/runs/2026-10-26T02-37-38Z.json"
    }
  ],
  "changes": [],
  "recordProvenance": {
    "source": "harvest",
    "retrievedAt": "2026-10-25T21:49:00Z",
    "registries": [
      {
        "registry": "Bioregistry",
        "key": "bioregistry",
        "id": "pharmgkb.disease",
        "url": "https://bioregistry.io/api/registry/pharmgkb.disease",
        "retrievedAt": "2026-10-25T21:49:00Z"
      }
    ],
    "fields": {
      "acronym": "Bioregistry",
      "name": "Bioregistry",
      "description": "Bioregistry",
      "homepage": "Bioregistry",
      "download": "Bioregistry",
      "formats": "Bioregistry",
      "license": "Bioregistry",
      "publications": "Bioregistry",
      "tags": "Bioregistry"
    }
  },
  "evaluationProvenance": {
    "@context": {
      "prov": "http://www.w3.org/ns/prov#",
      "schemascope": "https://schemascope.org/ns#"
    },
    "@id": "https://schemascope.org/o/pharmgkb-disease/#evaluation",
    "@type": "prov:Entity",
    "prov:specializationOf": {
      "@id": "https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.owl",
      "schemascope:evaluatedVersion": null
    },
    "prov:wasGeneratedBy": {
      "@id": "https://schemascope.org/runs/2026-10-26T02-37-38Z",
      "@type": "prov:Activity",
      "prov:startedAtTime": "2026-10-26T02:37:38.997Z",
      "prov:endedAtTime": "2026-10-26T03:31:18.947Z",
      "prov:wasAssociatedWith": {
        "@id": "https://schemascope.org/ns#evaluator",
        "@type": "prov:SoftwareAgent",
        "schemascope:version": "2.0.0"
      },
      "prov:used": [
        {
          "@id": "http://www.pharmgkb.org/",
          "prov:atTime": "2026-10-26T03:14:19.522Z"
        },
        {
          "@id": "https://w3id.org/biopragmatics/resources/pharmgkb.disease/pharmgkb.disease.owl",
          "prov:atTime": "2026-10-26T03:14:19.747Z"
        },
        {
          "@id": "https://raw.githubusercontent.com/biopragmatics/obo-db-ingest/main/export/pharmgkb.disease/pharmgkb.disease.owl",
          "prov:atTime": "2026-10-26T03:14:19.894Z"
        },
        {
          "@id": "https://bioregistry.io/api/registry/pharmgkb.disease",
          "prov:atTime": "2026-10-26T03:14:18.728Z"
        },
        {
          "@id": "https://api.crossref.org/works/10.2217%2Fbmm.11.94",
          "prov:atTime": "2026-10-26T03:14:18.954Z"
        },
        {
          "@id": "https://api.crossref.org/works/10.1038%2Fsj.tpj.6500035",
          "prov:atTime": "2026-10-26T03:14:18.953Z"
        }
      ]
    },
    "prov:generatedAtTime": "2026-10-26T03:14:19.895Z"
  }
}