Molecular Biology Domain Ontology

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

flow "MolecularBiologyDomainOntology" v1.0 {
  ontology:
    id: "molecular-biology-domain-ontology"
    parent: "biological-domains"
    purpose: "Represent evidence-backed molecular entities, processes, interactions and observations across molecular biology."

  types:
    Biomolecule: {id: string, kind: enum[DNA,RNA,protein,lipid,carbohydrate,metabolite,other], designation: string, sequence: string?}
    Gene: {id: string, organism: string, locus: string?, reference_version: string?}
    Transcript: {id: string, gene_id: string?, isoform: string?, sequence: string?}
    Protein: {id: string, accession: string?, isoform: string?, organism: string?}
    MolecularProcess: {id: string, kind: enum[replication,transcription,translation,splicing,regulation,repair,signalling,degradation,other]}
    Interaction: {id: string, participants: string[], kind: string, context: string?, confidence: number, evidence: string[]}
    Experiment: {id: string, method: string, sample: string?, conditions: string?, provenance: string}
    Observation: {id: string, experiment_id: string, measured_entity: string, value: number?, unit: string?, uncertainty: number?, provenance: string}
    Assertion: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    encodes(gene: Gene, product: Biomolecule)
    transcribed_to(gene: Gene, transcript: Transcript)
    translated_to(transcript: Transcript, protein: Protein)
    participates_in(entity: Biomolecule, process: MolecularProcess)
    interacts_with(a: Biomolecule, b: Biomolecule)
    regulates(regulator: Biomolecule, target: string)
    measured_by(entity: string, observation: Observation)
    supported_by(assertion: Assertion, experiment: Experiment)

  constraints:
    - "Every identifier must resolve to a typed, versioned entity."
    - "Confidence values must lie within [0, 1]."
    - "Sequence comparisons require explicit organism, reference and version where applicable."
    - "Distinguish genes, transcripts, proteins, isoforms and molecular complexes."
    - "Do not infer functional causation from co-expression, binding or correlation alone."
    - "Preserve experimental conditions, tissue, cell type and temporal context."
    - "Measurements require units and uncertainty where applicable."
    - "No automatic transitivity for molecular interaction, regulation or participation."

  inference:
    rule transcript_origin:
      if transcribed_to(g,t) and valid(g) and valid(t)
      then derived_from(t,g)
      confidence: "evidence dependent"
    rule protein_origin:
      if translated_to(t,p) and valid(t) and valid(p)
      then derived_from(p,t)
      confidence: "evidence dependent"
    rule observation_support:
      if measured_by(e,o) and valid(o)
      then evidence_for(e,o)
      confidence: "method and quality dependent"
    rule evidence_chain:
      if supported_by(a,x) and valid(x)
      then traceable_evidence(a,x)
      confidence: "retain provenance; no automatic certainty increase"

  SEMANTIC_EQUIVALENCE:
    - "Normalise identifiers against versioned biological reference databases."
    - "Distinguish orthology, homology, similarity, alias and identity."
    - "Do not merge entities across organisms or isoforms without justified mappings."

  CONFIDENCE:
    range: [0,1]
    factors: [experimental_quality, replication, measurement_uncertainty, annotation_reliability, biological_context, provenance]
    policy: "Calibrate confidence against evidence; do not increase it merely by chaining inferences."

  VALIDATION:
    - "Check entity types, accession versions and biological context."
    - "Verify provenance and compatible measurement units."
    - "Flag contradictory annotations, unsupported interactions and ambiguous mappings."
    - "Retain alternative interpretations where evidence is inconclusive."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, assertions, rules, references and provenance"
    note: "Compute hash during execution; no precomputed value is asserted."

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

  AI_CONSUMPTION:
    representation: "typed molecular biology knowledge graph with evidence-backed relationships"
    outputs: [entity_links, molecular_relations, inferred_edges, uncertainty_annotations, provenance_records]
    safeguards: [no_unsupported_causal_claims, no_unqualified_entity_merges, preserve_biological_context, preserve_reference_versions]
}

END FLOW ALGEBRA