Microbiology Domain Ontology

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

flow "MicrobiologyDomainOntology" v1.0 {
  ontology:
    id: "microbiology-domain-ontology"
    parent: "biological-domains"
    purpose: "Represent microorganisms, microbial communities, biological processes, experimental evidence and context-sensitive microbiological relationships."

  types:
    Microorganism: {id: string, taxon_id: string?, kind: enum[bacterium, archaeon, microscopic_fungus, protozoan, microalga, other], strain: string?}
    Virus: {id: string, taxon_id: string?, genome_type: string?, host_range: string[]?}
    MicrobialCommunity: {id: string, habitat_id: string, sampling_time: datetime?}
    Habitat: {id: string, environment: string, location: string?}
    Host: {id: string, taxon_id: string?, organism_id: string?}
    Gene: {id: string, sequence_reference: string?, function: string?}
    Process: {id: string, kind: enum[metabolism, growth, reproduction, infection, fermentation, biofilm_formation, gene_transfer, other]}
    Sample: {id: string, collection_time: datetime?, site: string?, protocol: string, provenance: string}
    Observation: {id: string, sample_id: string, method: string, result: string, uncertainty: number?, provenance: string}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    classified_as(entity: string, taxon: string)
    inhabits(entity: string, habitat: Habitat)
    member_of(microbe: Microorganism, community: MicrobialCommunity)
    infects(agent: string, host: Host)
    interacts_with(a: string, b: string)
    participates_in(entity: string, process: Process)
    carries_gene(entity: string, gene: Gene)
    detected_in(entity: string, sample: Sample)
    supported_by(relationship: Relationship, observation: Observation)

  constraints:
    - "All relationship endpoints must resolve to typed entities."
    - "Confidence values must lie within [0,1]."
    - "Distinguish cellular microorganisms from acellular viruses."
    - "Detection of microbial material does not alone establish viability, infection or causation."
    - "Distinguish taxonomic identity, strain identity and functional similarity."
    - "Preserve sampling method, environment, temporal context and measurement uncertainty."
    - "Do not infer pathogenicity or host range from taxonomic membership alone."
    - "Do not infer causation from co-occurrence or correlation alone."

  inference:
    rule community_membership:
      if member_of(m,c) and valid(m) and valid(c)
      then associated_with_habitat(m,c.habitat_id)
      confidence: "contextual; does not prove permanent residence"
    rule supported_detection:
      if detected_in(m,s) and observation_confirms(o,m,s)
      then evidence_for_presence(m,s,o)
      confidence: "method- and contamination-control dependent"
    rule interaction_evidence:
      if interacts_with(a,b) and supported_by(relation(a,b),o)
      then evidence_backed_interaction(a,b,o)
      confidence: "retain direction, experimental conditions and source"

  SEMANTIC_EQUIVALENCE:
    - "Resolve taxon names and synonyms against versioned nomenclature authorities."
    - "Keep organism, strain, isolate, sequence and taxon identifiers distinct."
    - "Do not equate microbial association with infection or causal mechanism."

  CONFIDENCE:
    range: [0,1]
    factors: [sample_quality, assay_specificity, contamination_controls, replication, source_reliability, contextual_fit]
    policy: "Propagate uncertainty; do not manufacture certainty by chaining inferences."

  VALIDATION:
    - "Validate taxonomy, identifier resolution, types and evidence provenance."
    - "Check sample context, detection limits, controls and measurement units."
    - "Flag conflicting classifications, contamination risks and unsupported causal claims."
    - "Retain competing explanations when evidence is inconclusive."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, typed assertions, rules and provenance"
    note: "Compute 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 microbiological knowledge graph with evidence-backed relationships"
    outputs: [entity_links, relation_triples, taxonomy_mappings, evidence_records, uncertainty_annotations, inferred_edges]
    safeguards: [avoid_unsupported_pathogenicity_claims, preserve_sampling_context, distinguish_detection_from_infection, preserve_provenance]
}

END FLOW ALGEBRA