{
  "id": "bican-models",
  "acronym": "BICAN models",
  "name": "BICAN Knowledge Graph Models",
  "category": "neuro",
  "kind": "schema",
  "description": "LinkML data models for the BRAIN Initiative Cell Atlas Network (BICAN) knowledgebase: taxonomies, assertions and evidence, library generation, anatomical structures, genome annotation, donors and a BICAN subset of Biolink. JSON Schema and Pydantic models are generated from the LinkML sources.",
  "formats": [
    "LinkML",
    "JSON Schema",
    "Pydantic"
  ],
  "maintainer": "BICAN",
  "homepage": "https://brain-bican.github.io/models/",
  "repository": "https://github.com/brain-bican/models",
  "publications": [],
  "usedBy": [
    {
      "name": "BICAN Knowledgebase",
      "url": "https://www.portal.brain-bican.org/teams/bican-knowledgebase",
      "note": "Knowledge graph built on these models"
    },
    {
      "name": "BICAN",
      "url": "https://www.portal.brain-bican.org/",
      "note": "Knowledge graph data models"
    }
  ],
  "modules": [
    {
      "name": "BKE Taxonomy",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/bke_taxonomy.yaml",
      "note": "Types and relationships of the BKE taxonomy"
    },
    {
      "name": "Cell Taxonomy",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/cell_taxonomy.yaml",
      "note": "Cell type taxonomy structure"
    },
    {
      "name": "Assertion & Evidence",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/assertion_evidence.yaml",
      "note": "Assertions and the evidence supporting them"
    },
    {
      "name": "Library Generation",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/library_generation.yaml",
      "note": "Samples and digital assets produced while generating sequencing libraries"
    },
    {
      "name": "Anatomical Structure",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/anatomical_structure.yaml",
      "note": "Anatomical brain structures, parcellations and coordinate spaces"
    },
    {
      "name": "Genome Annotation",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/genome_annotation.yaml",
      "note": "An organism's annotated genome"
    },
    {
      "name": "Donor",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/donor.yaml",
      "note": "Donor and subject information"
    },
    {
      "name": "BICAN Core",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/bican_core.yaml",
      "note": "Shared core classes and slots"
    },
    {
      "name": "BICAN Biolink",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/bican_biolink.yaml",
      "note": "BICAN subset of classes from the Biolink model"
    },
    {
      "name": "BICAN PROV",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/bican_prov.yaml",
      "note": "Provenance classes (W3C PROV)"
    },
    {
      "name": "BICAN SKOS",
      "url": "https://github.com/brain-bican/models/blob/main/linkml-schema/bican_skos.yaml",
      "note": "SKOS concepts used by the models"
    }
  ],
  "tools": [
    {
      "name": "bkbit",
      "url": "https://github.com/brain-bican/bkbit",
      "note": "Brain Knowledge Base Interaction Toolkit: Pydantic models, validation and JSON-LD conversion (pip install bkbit)"
    }
  ],
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    "LinkML",
    "knowledge graph",
    "cell atlas",
    "BICAN"
  ],
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        "2025-01-07"
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    "artifact": null,
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    "gross": 31,
    "earned": 25,
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    "qualityApplies": false,
    "penalty": {
      "score": 0,
      "reason": "no penalties (active)",
      "steps": [
        {
          "label": "Time since last activity",
          "pts": 0,
          "detail": "0.0 years → 4 × max(0, 0.0 − 1)"
        },
        {
          "label": "Inactive status",
          "pts": 0,
          "detail": "not archived, legacy or inactive"
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    "grade": "E",
    "fair": 13,
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        "max": 12,
        "steps": [
          {
            "label": "Persistent identifier (F1)",
            "pts": 0,
            "max": 4,
            "detail": "no PURL / w3id / DOI for the artefact"
          },
          {
            "label": "Indexed in services (F4)",
            "pts": 0,
            "max": 5,
            "detail": "not indexed anywhere"
          },
          {
            "label": "Citable reference (F2)",
            "pts": 0,
            "max": 3,
            "detail": "no reference publication listed"
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        "notes": [
          "Persistent identifier (F1): no PURL / w3id / DOI for the artefact",
          "Indexed in services (F4): not indexed anywhere",
          "Citable reference (F2): no reference publication listed"
        ]
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        "steps": [
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            "label": "Homepage reachable",
            "pts": 3,
            "max": 3,
            "detail": "HTTP 200"
          },
          {
            "label": "Artefact retrievable over HTTP(S) (A1)",
            "pts": 3,
            "max": 6,
            "detail": "only the source repository is reachable (no direct download)"
          },
          {
            "label": "Metadata persists in a registry (A2)",
            "pts": 0,
            "max": 3,
            "detail": "not in Bioregistry or OBO Foundry"
          }
        ],
        "notes": [
          "Artefact retrievable over HTTP(S) (A1): only the source repository is reachable (no direct download)",
          "Metadata persists in a registry (A2): not in Bioregistry or OBO Foundry"
        ]
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            "label": "Formal machine-readable format (I1)",
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            "detail": "LinkML, JSON Schema"
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          {
            "label": "Semantic-web IRIs (I2)",
            "pts": 0,
            "max": 3,
            "detail": "no RDF/OWL/JSON-LD representation"
          },
          {
            "label": "References other vocabularies (I3)",
            "pts": 0,
            "max": 4,
            "detail": "no imported vocabularies found"
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        ],
        "notes": [
          "Semantic-web IRIs (I2): no RDF/OWL/JSON-LD representation",
          "References other vocabularies (I3): no imported vocabularies found"
        ]
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            "label": "Clear license (R1.1)",
            "pts": 0,
            "max": 5,
            "detail": "none found"
          },
          {
            "label": "Release provenance (R1.2)",
            "pts": 2,
            "max": 4,
            "detail": "0.2.0 (latest GitHub release); not declared inside the artefact"
          },
          {
            "label": "Community standards (R1.3)",
            "pts": 0,
            "max": 3,
            "detail": "no independent compliance report (not on the OBO Dashboard)"
          }
        ],
        "notes": [
          "Clear license (R1.1): none found",
          "Release provenance (R1.2): 0.2.0 (latest GitHub release); not declared inside the artefact",
          "Community standards (R1.3): no independent compliance report (not on the OBO Dashboard)"
        ]
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        "max": 20,
        "steps": [
          {
            "label": "Not applicable",
            "pts": 0,
            "max": 0,
            "detail": "schema without an OWL/OBO/RDF artefact; total scaled from 80 to 100"
          }
        ],
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        "applicable": false
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        "max": 16,
        "steps": [
          {
            "label": "Recency",
            "pts": 10,
            "max": 10,
            "detail": "2026-10-22 → 0.1 months (≤ 3 months)"
          },
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            "label": "Release cadence (12 months)",
            "pts": 0,
            "max": 6,
            "detail": "0 releases (GitHub releases)"
          }
        ],
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          "Release cadence (12 months): 0 releases (GitHub releases)"
        ]
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        "max": 16,
        "steps": [
          {
            "label": "Documented adopting projects",
            "pts": 2,
            "max": 7,
            "detail": "2 projects"
          },
          {
            "label": "Reused by other ontologies",
            "pts": 0,
            "max": 4,
            "detail": "0"
          },
          {
            "label": "Community signal",
            "pts": 0,
            "max": 5,
            "detail": "max(stars 4 → 0, citations 0 → 0)"
          }
        ],
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        ]
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