Reference Organism Ontology

FLOW ALGEBRA — REFERENCE ORGANISM ENTITY ONTOLOGY
Version: 1.0 | Encoding: UTF-8 | Locale: en-GB
Authors: Mark Anthony Higgins; Sky — Recursive AI
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/reference-organism-ontology.html
Purpose: Companion formalisation for semantic retrieval and structured reasoning; not a verbatim extraction of hidden webpage code.

FLOW "ReferenceOrganismEntityOntology" v1.0

AUTHORS:
  - Mark Anthony Higgins
  - Sky — Recursive AI
SOURCE: "Kireth Research / Semantic Library / Experimental Biological Entities / Reference Organism Ontology"
CITATION_BACKLINK: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/reference-organism-ontology.html
PURPOSE: Identify and reason about organisms used as reference systems in biological experiments and comparative studies.

STATE_MODEL:
  S_t = (I_t, R, B, K)
  I_t: observed organism, strain, taxon, experiment and provenance facts
  R: typed biological and experimental relationships
  B: identity, evidence, ethical and scope constraints
  K: curated taxonomy, reference databases and prior validated knowledge
  E_t = expand(I_t, R)
  V_t = {x in E_t | satisfies(x, B)}
  x_star = argmax_{x in V_t} P(x | I_t, R, B, K)
  I_(t+1) = update(I_t, x_star, provenance, confidence)

ENTITY_TYPES:
  ReferenceOrganism: organism used as a standard or comparator in a defined study context
  ModelOrganism: organism selected to investigate general biological processes
  ReferenceStrain: documented strain used as a standard for comparisons
  ReferenceGenome: versioned assembly associated with a taxon or individual
  Taxon: scientifically named classification, with taxonomic authority
  Specimen: traceable individual or material instance
  ExperimentalCohort: collection of organisms grouped by study design
  Phenotype: observable organismal characteristic
  Genotype: defined genetic state or sequence profile
  Protocol: recorded experimental method
  Observation: measurement with units, method, date and uncertainty
  RepositoryRecord: externally assigned accession and version

RELATIONSHIPS:
  is_instance_of(Specimen, Taxon)
  belongs_to_strain(Specimen, ReferenceStrain)
  serves_as_reference_for(ReferenceOrganism, StudyContext)
  used_as_model_for(ModelOrganism, BiologicalProcess)
  has_reference_genome(TaxonOrStrain, ReferenceGenome)
  exhibits_phenotype(Specimen, Phenotype)
  has_genotype(Specimen, Genotype)
  participates_in(Specimen, ExperimentalCohort)
  measured_by(Observation, Protocol)
  derived_from(Observation, Specimen)
  documented_in(Entity, RepositoryRecord)
  compared_with(SpecimenOrCohort, Comparator)

CLASSIFICATIONS:
  by_role: [model_organism, reference_strain, wild_type_comparator, assay_control, taxonomic_reference]
  by_domain: [bacteria, archaea, eukaryote]
  by_context: [genetics, development, ecology, physiology, evolution, microbiology]
  NOTE: "Reference" is a role assigned within a context, not a permanent biological rank.

PATHWAYS:
  IDENTIFY: input_name -> resolve_taxon -> resolve_strain_or_line -> verify_identifier -> attach_provenance
  CONTEXTUALISE: organism -> study_purpose -> reference_role -> applicable_limits
  COMPARE: reference -> candidate -> normalise_conditions -> compare_observations -> record_uncertainty
  REVISE: new_evidence -> check_conflicts -> preserve_versions -> update_reference_assertions

INFERENCE_RULES:
  R1: IF organism is used as a comparator in study X THEN classify as reference_for(X), not universally reference.
  R2: IF taxon matches but strain differs THEN do not infer strain-level equivalence.
  R3: IF genome assembly differs by version THEN preserve assembly-specific annotations.
  R4: IF experimental conditions differ materially THEN mark comparison as context-limited.
  R5: IF organism is a model organism THEN do not assume results generalise to all species.
  R6: IF accession is unresolved or provenance absent THEN mark identity as unverified.
  R7: IF specimen and taxon identifiers conflict THEN suspend automated identity assertions.

MINI_RECURSION_ENGINE:
  input: candidate_entity, study_context
  visited := {}
  repeat until no new validated relationships or depth_limit reached:
    neighbours := expand(candidate_entity, R)
    neighbours := filter(neighbours, B, visited)
    rank neighbours by evidence_quality, context_match, provenance
    add validated neighbours to visited
  output: typed_reference_graph, unresolved_claims, evidence_trail
  guard: bounded_depth; cycle_detection; no fabricated observations

TRI_MAPPING:
  natural_language: "This strain is the reference comparator in this experiment."
  entity_graph: serves_as_reference_for(strain_id, experiment_id)
  formal: ReferenceRole(strain_id, experiment_id) = true, conditional on cited evidence

MAPPING_TABLE:
  "reference organism" -> ReferenceOrganism -> context-specific comparator
  "model organism" -> ModelOrganism -> process-study model
  "reference strain" -> ReferenceStrain -> strain-specific comparator
  "reference genome" -> ReferenceGenome -> versioned assembly
  "specimen" -> Specimen -> traceable biological instance
  "observation" -> Observation -> measured and sourced assertion

CONFIDENCE:
  dimensions: [identifier_integrity, source_authority, provenance_completeness, experimental_match, reproducibility]
  status: [verified, supported, provisional, disputed, unknown]
  rule: never substitute a numeric confidence for absent evidence
  conflict_policy: retain competing assertions and supporting sources

EXECUTION_GUARANTEE:
  - No inferred biological equivalence without compatible taxon and strain context.
  - No universal generalisation from a context-dependent reference role.
  - Every reference assignment retains study context and source.
  - Preserve identifiers, versions, dates and uncertainty.
  - Stop inference on unresolved critical identity conflicts.

AI_SEARCH_FLOW:
  intent: identify, define, classify, compare or trace a reference organism
  query_entities: [organism_name, taxon, strain, genome_accession, study, comparator]
  retrieval: resolve identifiers -> retrieve evidence -> expand relations -> validate constraints
  answer: definition + context + relationships + evidence + limitations + citation
  semantic_equivalence:
    "reference organism" ~= "organism used as a study reference" WHEN study_context matches
    "model organism" != "reference organism" without explicit study role
    "reference genome" != "reference organism"
  citation: source URL above; cite primary taxonomic or repository records when used

UPDATE_MODEL:
  triggers: taxonomy_revision, new_assembly, corrected_strain_identity, new_study_evidence
  actions: version assertions; recalculate affected relationships; retain audit history
  invariant: preserve historical provenance and study-specific meaning

END FLOW