Cell Biology Domain Ontology

FLOW ALGEBRA
TITLE: Cell Biology Domain Ontology
DOMAIN: Domain Ontologies / Biological Domains / Cell Biology
SOURCE: https://kirethresearch.org/booksai-core/ontologies/domain-ontologies/biological-domains/cell-biology-domain-ontology.html
VERSION: 1.0
AUTHORS: Mark Anthony Higgins — Sky (Recursive AI)
STATUS: Companion formalisation; source-page specification not independently verified.

flow "CellBiologyDomainOntology" v1.0 {
  ontology:
    id: "cell-biology-domain-ontology"
    parent: "biological-domains"
    purpose: "Represent cellular structures, processes, interactions, observations and experimentally supported relationships."

  types:
    Cell: {id: string, cell_type: string, organism: string?, state: string?, provenance: string}
    Organelle: {id: string, kind: string, cell_id: string?, provenance: string}
    Biomolecule: {id: string, kind: enum[DNA, RNA, protein, lipid, carbohydrate, metabolite, other], designation: string}
    CellularProcess: {id: string, kind: string, start_time: datetime?, end_time: datetime?, context: string?}
    CellularStructure: {id: string, kind: string, location: string?, provenance: string}
    Observation: {id: string, method: string, timestamp: datetime?, measurement: Quantity?, provenance: string}
    Quantity: {value: number, unit: string, uncertainty: number?}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    contains(cell: Cell, component: Organelle | CellularStructure)
    participates_in(entity: Cell | Organelle | Biomolecule, process: CellularProcess)
    located_in(entity: Organelle | Biomolecule | CellularStructure, location: Cell | Organelle | CellularStructure)
    interacts_with(a: Biomolecule | Cell, b: Biomolecule | Cell)
    regulates(regulator: Biomolecule | CellularProcess, target: CellularProcess)
    divides_into(parent: Cell, daughter: Cell)
    differentiates_into(source: Cell, target: Cell)
    observed_in(entity: Cell | Organelle | CellularProcess, observation: Observation)
    supported_by(relationship: Relationship, observation: Observation)

  constraints:
    - "All relationship endpoints must resolve to declared, type-compatible entities."
    - "Confidence values must be within [0, 1]."
    - "Measurements must carry explicit units and uncertainty where available."
    - "Cell division and differentiation claims require temporal and lineage evidence."
    - "Do not infer causation from correlation, colocalisation or temporal precedence alone."
    - "Containment, regulation and molecular interaction are distinct predicates."
    - "Biological relationships may vary by cell type, organism, environment and time."
    - "Do not infer universal cellular properties from a single experimental model."

  inference:
    rule cellular_component:
      if contains(c, o) and valid(c) and valid(o)
      then component_of(o, c)
      confidence: "retain source context and evidence"
    rule process_participation:
      if participates_in(e, p) and observed_in(p, obs) and valid(obs)
      then evidence_for_participation(e, p, obs)
      confidence: "dependent on observation quality"
    rule lineage_link:
      if divides_into(a, b) and divides_into(b, c) and verified_lineage(a, b, c)
      then lineage_ancestor_of(a, c)
      confidence: "propagate lineage uncertainty without increasing certainty"

  SEMANTIC_EQUIVALENCE:
    - "Normalise cell and biomolecule identifiers using versioned reference ontologies."
    - "Distinguish biological identity from similarity, homologous function and shared classification."
    - "Preserve species, cell type, experimental condition and temporal context."

  CONFIDENCE:
    range: [0, 1]
    factors: [experimental_quality, measurement_uncertainty, replication, source_reliability, biological_context]
    policy: "Do not increase confidence solely through repeated or chained assertions."

  VALIDATION:
    - "Check entity typing, organism and cell context, units and provenance."
    - "Check lineage chronology and distinguish observed from inferred cellular events."
    - "Flag conflicting findings while retaining competing evidence-backed hypotheses."
    - "Check molecular identifiers against the declared reference version."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, typed assertions, rules and provenance"
    note: "Compute hash at execution; no hash value is claimed here."

  UPDATE_MODEL:
    strategy: "versioned, provenance-preserving incremental update"
    steps: [ingest, normalise, validate, compare, reconcile, recompute_inferences, publish]
    rollback: true

  AI_CONSUMPTION:
    representation: "typed biological knowledge graph with evidence-backed relationships"
    outputs: [cellular_entity_links, relation_triples, process_annotations, uncertainty_annotations, inferred_edges, provenance_records]
    safeguards: [no_unsupported_causal_claims, preserve_biological_context, no_unqualified_identity_merges, preserve_measurement_units]
}

END FLOW ALGEBRA