{
  "id": "genepio",
  "acronym": "GENEPIO",
  "name": "Genomic Epidemiology Ontology",
  "category": "health",
  "domains": [
    "life",
    "agri"
  ],
  "kind": "ontology",
  "description": "The Genomic Epidemiology Ontology (GenEpiO) covers vocabulary necessary to identify, document and research foodborne pathogens and associated outbreaks.",
  "formats": [
    "OWL"
  ],
  "license": "CC BY 3.0",
  "homepage": "http://genepio.org/",
  "repository": "https://github.com/GenEpiO/genepio",
  "download": "http://purl.obolibrary.org/obo/genepio.owl",
  "ols": "genepio",
  "obo": "genepio",
  "bioportal": "GENEPIO",
  "bioregistry": "genepio",
  "publications": [],
  "usedBy": [],
  "tags": [
    "epidemiology",
    "food",
    "genome",
    "genomics",
    "obo",
    "ontology",
    "pathogen"
  ],
  "url": "https://schemascope.org/o/genepio/",
  "evaluation": {
    "links": {
      "homepage": {
        "url": "http://genepio.org/",
        "code": 200,
        "state": "ok",
        "resolvedUrl": "https://genepio.org/",
        "checkedAt": "2026-10-26T02:57:01.472Z"
      },
      "repository": {
        "url": "https://github.com/GenEpiO/genepio",
        "code": 200,
        "state": "ok",
        "checkedAt": "2026-10-26T02:57:00.960Z"
      },
      "download": {
        "url": "http://purl.obolibrary.org/obo/genepio.owl",
        "code": 200,
        "state": "ok",
        "resolvedUrl": "https://raw.githubusercontent.com/GenEpiO/genepio/master/genepio.owl",
        "checkedAt": "2026-10-26T02:57:01.002Z"
      }
    },
    "github": {
      "slug": "GenEpiO/genepio",
      "stars": 25,
      "forks": 10,
      "openIssues": 76,
      "pushedAt": "2026-07-11T05:33:45Z",
      "archived": false,
      "license": null,
      "latestRelease": {
        "tag": "v0.9",
        "date": "2026-04-13T23:17:15Z",
        "url": "https://github.com/GenEpiO/genepio/releases/tag/v0.9"
      },
      "source": "https://api.github.com/repos/GenEpiO/genepio",
      "fetchedAt": "2026-10-26T02:57:01.022Z"
    },
    "ols": {
      "portal": "OLS (EMBL-EBI)",
      "id": "genepio",
      "api": "v2",
      "title": "Genomic Epidemiology Ontology",
      "iri": "http://purl.obolibrary.org/obo/genepio.owl",
      "versionIri": "http://purl.obolibrary.org/obo/genepio/releases/2026-04-13/genepio.owl",
      "version": "2026-04-13",
      "releaseDate": "2026-04-13",
      "terms": 9159,
      "properties": 128,
      "individuals": 961,
      "importsFrom": [
        "afpo",
        "apollo_sv",
        "bao",
        "bfo",
        "bto",
        "chebi",
        "chmo",
        "cido",
        "cl",
        "clo",
        "cob",
        "cvdo",
        "dc",
        "dcterms",
        "doid",
        "ecto",
        "edam",
        "efo",
        "envo",
        "exo",
        "foodon",
        "gaz",
        "geo",
        "go",
        "gsso",
        "hancestro",
        "hp",
        "hso",
        "iao",
        "ico",
        "ido",
        "mi",
        "mmo",
        "mondo",
        "mp",
        "mpath",
        "nbo",
        "ncbitaxon",
        "ncit",
        "ncro",
        "oae",
        "oba",
        "obi",
        "obib",
        "ogms",
        "oio",
        "omit",
        "omp",
        "omrse",
        "owl",
        "pato",
        "pco",
        "peco",
        "po",
        "pr",
        "rbo",
        "rdfs",
        "ro",
        "sio",
        "so",
        "stato",
        "symp",
        "t4fs",
        "trans",
        "uberon",
        "uo",
        "vo",
        "vt",
        "xco"
      ],
      "exportsTo": [
        "ado",
        "eupath",
        "foodon",
        "hso",
        "ngbo",
        "ornaseq",
        "pride"
      ],
      "languages": [
        "af",
        "bn",
        "da",
        "de",
        "en",
        "es",
        "fr",
        "hi",
        "hy",
        "it",
        "nb",
        "pt-br",
        "sq",
        "tr",
        "zh"
      ],
      "loaded": "2026-10-25T00:09:08.389173542",
      "sourceFileTimestamp": "Sun Oct 25 00:09:05 UTC 2026",
      "obsolete": false,
      "status": "LOADED",
      "page": "https://www.ebi.ac.uk/ols4/ontologies/genepio",
      "source": "https://www.ebi.ac.uk/ols4/api/v2/ontologies/genepio",
      "fetchedAt": "2026-10-26T02:57:00.741Z"
    },
    "obo": {
      "id": "genepio",
      "status": "active",
      "domain": "health",
      "license": "CC BY 3.0",
      "usages": [],
      "source": "https://obofoundry.org/registry/ontologies.jsonld",
      "fetchedAt": "2026-10-26T02:37:39.556Z"
    },
    "bioportal": null,
    "citations": [],
    "git": {
      "commit": "dcd17ec6ccb63c87677155718b0d2f74b2adb550",
      "ref": "master",
      "headTag": null,
      "latestTag": {
        "name": "v2021-05-24",
        "commit": "63b84330b4ba56a108c2cc7ad620086e5372e48a",
        "url": "https://github.com/GenEpiO/genepio/releases/tag/v2021-05-24"
      },
      "tagCount": 9,
      "tagDates": [
        "2021-05-24"
      ],
      "url": "https://github.com/GenEpiO/genepio/tree/dcd17ec6ccb63c87677155718b0d2f74b2adb550",
      "source": "https://github.com/GenEpiO/genepio.git/info/refs?service=git-upload-pack",
      "fetchedAt": "2026-10-26T02:57:00.726Z"
    },
    "tib": null,
    "dashboard": {
      "ns": "genepio",
      "checks": {
        "FP01 Open": "PASS",
        "FP02 Common Format": "PASS",
        "FP03 URIs": "PASS",
        "FP04 Versioning": "ERROR",
        "FP05 Scope": "PASS",
        "FP06 Textual Definitions": "ERROR",
        "FP07 Relations": "INFO",
        "FP08 Documented": "PASS",
        "FP09 Plurality of Users": "ERROR",
        "FP11 Locus of Authority": "PASS",
        "FP12 Naming Conventions": "ERROR",
        "FP16 Maintenance": "PASS",
        "FP20 Responsiveness": "PASS",
        "ROBOT Report": "ERROR"
      },
      "robot": {
        "ERROR": 88,
        "INFO": 18,
        "WARN": 639
      },
      "consistent": true,
      "unsatisfiable": 0,
      "classes": 2221,
      "axioms": 19485,
      "owl2dl": false,
      "reusedPct": 11.25,
      "usedBy": [
        "hso",
        "ngbo",
        "ornaseq"
      ],
      "oboScore": 0.304,
      "summary": "ERROR",
      "checkedVersion": "http://purl.obolibrary.org/obo/genepio/releases/2026-04-13/genepio.owl",
      "checkedAt": "2026-05-08T17:48:49.253Z",
      "page": "https://dashboard.obofoundry.org/dashboard/genepio/dashboard.html",
      "source": "https://dashboard.obofoundry.org/dashboard/dashboard-results.json",
      "fetchedAt": "2026-10-26T02:37:39.856Z"
    },
    "quality": null,
    "oops": null,
    "releases": {
      "dates": [
        "2021-05-25",
        "2023-06-21",
        "2023-07-11",
        "2026-04-13"
      ],
      "lastYear": 1,
      "from": "GitHub releases"
    },
    "bioregistry": {
      "prefix": "genepio",
      "name": "Genomic Epidemiology Ontology",
      "mappings": {
        "aberowl": "GENEPIO",
        "biocontext": "GENEPIO",
        "bioportal": "GENEPIO",
        "fairsharing": "FAIRsharing.y1mmbv",
        "obofoundry": "genepio",
        "ols": "genepio",
        "ontobee": "GENEPIO",
        "wikidata.entity": "Q55118402"
      },
      "dependsOn": [
        "chebi",
        "ncbitaxon",
        "po",
        "ro",
        "uberon"
      ],
      "appearsIn": [],
      "license": "CC-BY-3.0",
      "version": "2026-04-13",
      "deprecated": false,
      "page": "https://bioregistry.io/genepio",
      "source": "https://bioregistry.io/api/registry/genepio",
      "fetchedAt": "2026-10-26T02:57:00.627Z"
    },
    "artifact": {
      "source": "https://raw.githubusercontent.com/GenEpiO/genepio/master/genepio.owl",
      "isRdf": true,
      "versionIri": "http://purl.obolibrary.org/obo/genepio/releases/2026-04-13/genepio.owl",
      "versionInfo": "2026-04-13",
      "etag": "\"2c1f3cf11aedf5a15861d30e5abbce00650a022e28c31f933a403ff68d6a3df3\"",
      "contentType": "text/plain",
      "fetchedAt": "2026-10-26T02:57:00.833Z"
    },
    "score": 66,
    "gross": 72,
    "earned": 72,
    "possible": 100,
    "qualityApplies": true,
    "penalty": {
      "score": -6,
      "reason": "88 errors",
      "steps": [
        {
          "label": "Time since last activity",
          "pts": 0,
          "detail": "0.3 years → 4 × max(0, 0.3 − 1)"
        },
        {
          "label": "Inactive status",
          "pts": 0,
          "detail": "not archived, legacy or inactive"
        },
        {
          "label": "Consistency",
          "pts": 0,
          "detail": "consistent, no unsatisfiable classes"
        },
        {
          "label": "ROBOT report errors",
          "pts": -6,
          "detail": "88 errors"
        }
      ]
    },
    "consistent": true,
    "grade": "C",
    "fair": 44,
    "breakdown": {
      "findable": {
        "score": 9,
        "max": 12,
        "steps": [
          {
            "label": "Persistent identifier (F1)",
            "pts": 4,
            "max": 4,
            "detail": "purl.obolibrary.org"
          },
          {
            "label": "Indexed in services (F4)",
            "pts": 5,
            "max": 5,
            "detail": "5: OLS, BioPortal, OBO Foundry, Bioregistry, FAIRsharing"
          },
          {
            "label": "Citable reference (F2)",
            "pts": 0,
            "max": 3,
            "detail": "no reference publication listed"
          }
        ],
        "notes": [
          "Citable reference (F2): no reference publication listed"
        ]
      },
      "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": "OBO Foundry, Bioregistry"
          }
        ],
        "notes": []
      },
      "interoperable": {
        "score": 12,
        "max": 12,
        "steps": [
          {
            "label": "Formal machine-readable format (I1)",
            "pts": 5,
            "max": 5,
            "detail": "OWL"
          },
          {
            "label": "Semantic-web IRIs (I2)",
            "pts": 3,
            "max": 3,
            "detail": "OWL"
          },
          {
            "label": "References other vocabularies (I3)",
            "pts": 4,
            "max": 4,
            "detail": "imports 64: afpo, apollo_sv, bao, bfo, bto, chebi, chmo, cido…"
          }
        ],
        "notes": []
      },
      "reusable": {
        "score": 11,
        "max": 12,
        "steps": [
          {
            "label": "Clear license (R1.1)",
            "pts": 5,
            "max": 5,
            "detail": "CC BY 3.0"
          },
          {
            "label": "Release provenance (R1.2)",
            "pts": 4,
            "max": 4,
            "detail": "2026-04-13 (version IRI in the artefact)"
          },
          {
            "label": "Community standards (R1.3)",
            "pts": 2,
            "max": 3,
            "detail": "OBO principles: 8/13 checks pass"
          }
        ],
        "notes": [
          "Community standards (R1.3): OBO principles: 8/13 checks pass"
        ]
      },
      "quality": {
        "score": 14,
        "max": 20,
        "steps": [
          {
            "label": "Logical consistency",
            "pts": 10,
            "max": 10,
            "detail": "consistent, 0 unsatisfiable classes (OBO Dashboard)"
          },
          {
            "label": "OWL 2 DL profile",
            "pts": 0,
            "max": 2,
            "detail": "outside OWL 2 DL"
          },
          {
            "label": "Upper-ontology alignment",
            "pts": 3,
            "max": 3,
            "detail": "imports BFO, COB"
          },
          {
            "label": "Standard relations (RO)",
            "pts": 1,
            "max": 1,
            "detail": "imports RO"
          },
          {
            "label": "ROBOT report: no errors",
            "pts": 0,
            "max": 2,
            "detail": "88 errors"
          },
          {
            "label": "ROBOT report: warning density",
            "pts": 0,
            "max": 1,
            "detail": "639 warnings / 2221 classes = 0.29"
          },
          {
            "label": "Pitfall scan: no critical pitfalls",
            "pts": 0,
            "max": 1,
            "detail": "no pitfall scan yet; ROBOT report has 88 errors"
          }
        ],
        "notes": [
          "OWL 2 DL profile: outside OWL 2 DL",
          "ROBOT report: no errors: 88 errors",
          "ROBOT report: warning density: 639 warnings / 2221 classes = 0.29",
          "Pitfall scan: no critical pitfalls: no pitfall scan yet; ROBOT report has 88 errors"
        ]
      },
      "maintenance": {
        "score": 10,
        "max": 16,
        "steps": [
          {
            "label": "Recency",
            "pts": 8,
            "max": 10,
            "detail": "2026-07-11 → 3.5 months (≤ 6 months)"
          },
          {
            "label": "Release cadence (12 months)",
            "pts": 2,
            "max": 6,
            "detail": "1 release (GitHub releases)"
          }
        ],
        "notes": [
          "Recency: 2026-07-11 → 3.5 months (≤ 6 months)",
          "Release cadence (12 months): 1 release (GitHub releases)"
        ]
      },
      "adoption": {
        "score": 4,
        "max": 16,
        "steps": [
          {
            "label": "Documented adopting projects",
            "pts": 0,
            "max": 7,
            "detail": "0 projects"
          },
          {
            "label": "Reused by other ontologies",
            "pts": 2,
            "max": 4,
            "detail": "7: hso, ngbo, ornaseq, ado, eupath, foodon…"
          },
          {
            "label": "Community signal",
            "pts": 2,
            "max": 5,
            "detail": "max(stars 25 → 2, citations 0 → 0)"
          }
        ],
        "notes": [
          "Documented adopting projects: 0 projects",
          "Reused by other ontologies: 7: hso, ngbo, ornaseq, ado, eupath, foodon…",
          "Community signal: max(stars 25 → 2, citations 0 → 0)"
        ]
      }
    },
    "lastActivity": "2026-07-11T05:33:45.000Z",
    "adopterCount": 0,
    "reuseCount": 7,
    "importCount": 64,
    "registries": [
      "OLS",
      "BioPortal",
      "OBO Foundry",
      "Bioregistry",
      "FAIRsharing"
    ],
    "evaluatedVersion": {
      "label": "2026-04-13",
      "from": "version IRI in the artefact",
      "value": "http://purl.obolibrary.org/obo/genepio/releases/2026-04-13/genepio.owl",
      "inArtefact": true,
      "all": [
        {
          "label": "2026-04-13",
          "from": "version IRI in the artefact",
          "value": "http://purl.obolibrary.org/obo/genepio/releases/2026-04-13/genepio.owl",
          "inArtefact": true
        },
        {
          "label": "2026-04-13",
          "from": "version info in the artefact",
          "value": "2026-04-13",
          "inArtefact": true
        },
        {
          "label": "2026-04-13",
          "from": "OLS",
          "value": "http://purl.obolibrary.org/obo/genepio/releases/2026-04-13/genepio.owl"
        },
        {
          "label": "v0.9",
          "from": "latest GitHub release",
          "value": "https://github.com/GenEpiO/genepio/releases/tag/v0.9"
        },
        {
          "label": "v2021-05-24 + commit dcd17ec",
          "from": "latest release tag; master evaluated at commit",
          "value": "dcd17ec6ccb63c87677155718b0d2f74b2adb550",
          "release": "v2021-05-24"
        },
        {
          "label": "commit dcd17ec",
          "from": "master at evaluation time",
          "value": "dcd17ec6ccb63c87677155718b0d2f74b2adb550"
        }
      ]
    },
    "evaluatedAt": "2026-10-26T02:57:01.742Z",
    "runId": "2026-10-26T02-37-38Z",
    "adopters": []
  },
  "history": [
    {
      "runId": "2026-10-26T02-37-38Z",
      "at": "2026-10-26T03:31:18.947Z",
      "score": 66,
      "grade": "C",
      "fair": 44,
      "version": "2026-04-13",
      "terms": 9159,
      "stars": 25,
      "license": "CC BY 3.0",
      "lastActivity": "2026-07-11T05:33:45.000Z",
      "adopters": 0,
      "links": {
        "homepage": "ok",
        "repository": "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": "genepio",
        "url": "https://bioregistry.io/api/registry/genepio",
        "retrievedAt": "2026-10-25T21:49:00Z"
      },
      {
        "registry": "OBO Foundry",
        "key": "obo",
        "id": "genepio",
        "url": "https://obofoundry.org/ontology/genepio.html",
        "retrievedAt": "2026-10-25T21:49:00Z"
      },
      {
        "registry": "OLS (EMBL-EBI)",
        "key": "ols",
        "id": "genepio",
        "url": "https://www.ebi.ac.uk/ols4/ontologies/genepio",
        "retrievedAt": "2026-10-25T21:49:00Z"
      }
    ],
    "fields": {
      "acronym": "Bioregistry",
      "name": "Bioregistry",
      "description": "Bioregistry",
      "homepage": "Bioregistry",
      "repository": "Bioregistry",
      "download": "Bioregistry",
      "formats": "Bioregistry",
      "license": "Bioregistry",
      "ols": "Bioregistry",
      "obo": "Bioregistry",
      "bioportal": "Bioregistry",
      "tags": "Bioregistry"
    }
  },
  "evaluationProvenance": {
    "@context": {
      "prov": "http://www.w3.org/ns/prov#",
      "schemascope": "https://schemascope.org/ns#"
    },
    "@id": "https://schemascope.org/o/genepio/#evaluation",
    "@type": "prov:Entity",
    "prov:specializationOf": {
      "@id": "http://purl.obolibrary.org/obo/genepio.owl",
      "schemascope:evaluatedVersion": "http://purl.obolibrary.org/obo/genepio/releases/2026-04-13/genepio.owl"
    },
    "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://genepio.org/",
          "prov:atTime": "2026-10-26T02:57:01.472Z"
        },
        {
          "@id": "https://github.com/GenEpiO/genepio",
          "prov:atTime": "2026-10-26T02:57:00.960Z"
        },
        {
          "@id": "http://purl.obolibrary.org/obo/genepio.owl",
          "prov:atTime": "2026-10-26T02:57:01.002Z"
        },
        {
          "@id": "https://raw.githubusercontent.com/GenEpiO/genepio/master/genepio.owl",
          "prov:atTime": "2026-10-26T02:57:00.833Z"
        },
        {
          "@id": "https://github.com/GenEpiO/genepio.git/info/refs?service=git-upload-pack",
          "prov:atTime": "2026-10-26T02:57:00.726Z"
        },
        {
          "@id": "https://api.github.com/repos/GenEpiO/genepio",
          "prov:atTime": "2026-10-26T02:57:01.022Z"
        },
        {
          "@id": "https://www.ebi.ac.uk/ols4/api/v2/ontologies/genepio",
          "prov:atTime": "2026-10-26T02:57:00.741Z"
        },
        {
          "@id": "https://obofoundry.org/registry/ontologies.jsonld",
          "prov:atTime": "2026-10-26T02:37:39.556Z"
        },
        {
          "@id": "https://dashboard.obofoundry.org/dashboard/dashboard-results.json",
          "prov:atTime": "2026-10-26T02:37:39.856Z"
        },
        {
          "@id": "https://bioregistry.io/api/registry/genepio",
          "prov:atTime": "2026-10-26T02:57:00.627Z"
        }
      ]
    },
    "prov:generatedAtTime": "2026-10-26T02:57:01.742Z"
  }
}