Genetics Domain Ontology

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

flow "GeneticsDomainOntology" v1.0 {
  ontology:
    id: "genetics-domain-ontology"
    parent: "biological-domains"
    purpose: "Represent genetic entities, inheritance, variation, expression and evidence-backed genotype–phenotype relationships."

  types:
    Organism: {id: string, taxon: string, provenance: string}
    Genome: {id: string, organism_id: string, assembly_version: string?, provenance: string}
    Chromosome: {id: string, genome_id: string, designation: string}
    Gene: {id: string, identifier: string, genome_id: string, locus: string?, provenance: string}
    Allele: {id: string, gene_id: string, variant_id: string?}
    Variant: {id: string, reference_sequence: string, position: string, reference_allele: string, alternate_allele: string, assembly_version: string}
    Genotype: {id: string, organism_id: string, alleles: string[], ploidy: integer?, phase: string?}
    Phenotype: {id: string, trait: string, measurement: number?, unit: string?, context: string?}
    InheritanceEvent: {id: string, parent_ids: string[], offspring_id: string, provenance: string}
    ExpressionObservation: {id: string, gene_id: string, tissue: string?, value: number, unit: string, method: string, provenance: string}
    Evidence: {id: string, source: string, method: string?, quality: number?, timestamp: datetime?}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    part_of(chromosome: Chromosome, genome: Genome)
    located_on(gene: Gene, chromosome: Chromosome)
    allele_of(allele: Allele, gene: Gene)
    has_genotype(organism: Organism, genotype: Genotype)
    exhibits(organism: Organism, phenotype: Phenotype)
    inherited_from(offspring: Organism, parent: Organism)
    associated_with(variant: Variant, phenotype: Phenotype)
    regulates(gene_a: Gene, gene_b: Gene)
    expressed_in(gene: Gene, tissue: string)

  constraints:
    - "Every relationship endpoint must resolve to a typed entity."
    - "Confidence values must lie within [0, 1]."
    - "Variant coordinates must specify a reference assembly and unambiguous sequence notation."
    - "Distinguish association, linkage, regulation, inheritance and demonstrated causation."
    - "Genotype interpretation must respect ploidy, phase and organism context."
    - "Do not infer phenotype deterministically from genotype without a validated model."
    - "Missing evidence is not evidence of absence."
    - "Protect identifiable genetic and familial information; do not expose sensitive records."

  inference:
    rule allele_gene_membership:
      if allele_of(a,g) and valid(a) and valid(g)
      then associated_gene(a,g)
      confidence: "retain evidence and provenance"
    rule inherited_variant_candidate:
      if inherited_from(child,parent) and observed_variant(child,v) and observed_variant(parent,v)
      then candidate_transmission(parent,child,v)
      confidence: "requires phasing, sample quality and pedigree validation"
    rule gene_phenotype_hypothesis:
      if associated_with(v,p) and variant_in_gene(v,g)
      then candidate_gene_phenotype_association(g,p)
      confidence: "hypothesis only; not a causal or clinical conclusion"

  SEMANTIC_EQUIVALENCE:
    - "Normalise gene and variant identifiers against versioned reference catalogues."
    - "Distinguish aliases from molecular identity and orthology from equivalence."
    - "Preserve species, reference assembly, transcript and context."

  CONFIDENCE:
    range: [0,1]
    factors: [study_quality, sample_size, replication, assay_accuracy, population_context, annotation_version]
    policy: "Evidence-dependent; never increase certainty solely by chaining inferred edges."

  VALIDATION:
    - "Check entity types, identifiers, reference assemblies, genomic coordinates and allele notation."
    - "Validate inheritance assertions against ploidy, phase and pedigree evidence."
    - "Flag contradictory observations and incompatible annotations without deleting alternatives."
    - "Require traceable provenance for reported genotype–phenotype associations."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, typed assertions, rules and provenance"
    note: "Compute at execution; no precomputed hash 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 genetics knowledge graph with evidence-backed relationships"
    outputs: [entity_links, relation_triples, inheritance_candidates, uncertainty_annotations, provenance_records]
    safeguards: [no_unsupported_causal_claims, no_unqualified_clinical_interpretation, preserve_reference_versions, protect_sensitive_genetic_data]
}

END FLOW ALGEBRA