Experimental Organism Ontology

FLOW ALGEBRA — EXPERIMENTAL ORGANISM ENTITY ONTOLOGY
Version: 1.0 | 2026-10-28 | UTF-8
Authors: Mark Anthony Higgins — Sky Recursive AI
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/experimental-organism-ontology.html
Source note: Companion formalisation based on the visible page title and biological domain; not a verbatim extraction of hidden page code.
Purpose: Describe experimental organisms as traceable biological entities with explicitly scoped experimental roles, provenance, welfare, and evidence.

FLOW "ExperimentalOrganismOntology" v1.0

STATE_MODEL
  S_t = (I_t, R_t, B_t, K_t)
  I_t = observed organism and experiment records at time t
  R_t = typed biological and experimental relations
  B_t = admissibility, ethics, provenance and scope boundaries
  K_t = verified background knowledge and evidence
  E_t = expand(I_t, R_t)
  V_t = {x in E_t | satisfies(x, B_t)}
  x*_t = argmax_{x in V_t} P(x | I_t, R_t, B_t, K_t)
  I_(t+1) = update(I_t, x*_t, evidence_t)
  Interpretation: these expressions define a reasoning schema; no numerical probabilities are implied without calibrated data.

ENTITY_TYPES
  ExperimentalOrganism: individual organism enrolled or used in a documented investigation
  OrganismCohort: defined set of experimental organisms
  Taxon: verified scientific taxonomic identification
  StrainOrLine: documented strain, stock, breed, line or genetic background
  Genotype: measured or reported genetic characteristics
  Phenotype: observed traits under specified conditions
  ExperimentalProtocol: versioned study design
  ExperimentalGroup: assigned comparison or treatment group
  Intervention: exposure or procedure with defined context
  ControlCondition: comparator specified in protocol
  Observation: dated measurement or qualitative record
  BiologicalSpecimen: material collected from an organism
  Environment: housing, growth or ecological conditions
  WelfareRecord: oversight, monitoring and humane endpoint evidence where relevant
  ProvenanceRecord: origin, custody, identity and transformation history

RELATIONSHIPS
  ExperimentalOrganism --instance_of--> Taxon
  ExperimentalOrganism --has_background--> StrainOrLine
  ExperimentalOrganism --has_genotype--> Genotype
  ExperimentalOrganism --exhibits--> Phenotype
  ExperimentalOrganism --member_of--> OrganismCohort
  ExperimentalOrganism --assigned_to--> ExperimentalGroup
  ExperimentalOrganism --participates_in--> ExperimentalProtocol
  ExperimentalOrganism --exposed_to--> Intervention
  ExperimentalOrganism --maintained_in--> Environment
  Observation --measured_on--> ExperimentalOrganism
  BiologicalSpecimen --derived_from--> ExperimentalOrganism
  ProvenanceRecord --documents--> ExperimentalOrganism
  WelfareRecord --applies_to--> ExperimentalOrganism

IDENTITY_AND_PROVENANCE
  Each organism receives a stable, locally unique identifier.
  Separate individual identity from taxon, strain, group and specimen identity.
  Preserve source, collection/acquisition date, custodian, protocol version and event history.
  Distinguish directly observed values from inferred or imported assertions.
  Do not infer genotype, health status or biological equivalence from taxon alone.

PATHWAYS
  P1: registration -> identity validation -> taxonomic attribution -> provenance linkage
  P2: protocol approval -> eligibility review -> group assignment -> recorded observations
  P3: observation -> evidence quality check -> phenotype assertion -> bounded inference
  P4: specimen derivation -> specimen identifier -> parent-organism linkage -> analysis record
  P5: environmental context -> possible confounder assessment -> interpretation qualification
  P6: welfare/ethical status -> admissibility check -> continue, suspend or exclude

INFERENCE_RULES
  R1: IF organism_id is missing THEN identity_status = unresolved.
  R2: IF taxon evidence is insufficient THEN taxon_assignment = provisional.
  R3: IF protocol assignment is recorded THEN infer participation only within the stated study scope.
  R4: IF specimen parentage is verified THEN link specimen to the identified organism, preserving chain of custody.
  R5: IF a phenotype is observed THEN attach measurement method, time, conditions and uncertainty.
  R6: IF cohort members differ in relevant background THEN flag possible confounding; do not assert causation.
  R7: IF ethics or welfare requirements are unmet THEN block claims of compliant experimental use.
  R8: IF provenance contradicts an identity assertion THEN flag conflict and request review.
  R9: IF evidence is absent THEN return unknown, not false.

MINI_RECURSION_ENGINE
  seed = experimental_organism_record
  repeat:
    expand linked taxonomy, provenance, protocol, specimens, observations and environment
    filter by boundaries B_t and evidence validity
    score surviving interpretations using explicitly defined evidence weights
    update only with traceable assertions
  until no admissible new assertions or configured depth limit reached
  guarantee: bounded termination with finite records, visited-node tracking and a depth limit.

TRI_MAPPING
  Biological layer: organism -> lineage/taxon -> phenotype and biological state
  Experimental layer: protocol -> group/intervention -> observation
  Semantic layer: identifier -> typed relations -> provenance-backed assertions
  Map across layers only where a documented entity identifier or verified relation exists.

CONFIDENCE_AND_VALIDATION
  Confidence labels: verified | supported | provisional | unknown | conflicting
  Evidence priority: directly documented and validated > independently corroborated > inferred.
  Validation checks: identifier uniqueness; timestamp consistency; controlled vocabulary; protocol version; specimen lineage; conflicting records.
  Never turn a confidence label into a numerical probability without calibration.

EXECUTION_GUARANTEE
  Preserve source attribution and reversible reasoning traces.
  No invented observations, study outcomes, approval status or experimental conditions.
  Inferences must retain the evidence, rule and scope used to derive them.
  Reject circular derivations that provide no independent support.

AI_SEARCH_FLOW
  intent: locate, classify, compare and explain experimental organism entities
  inputs: organism identifier, taxon, study, strain, specimen or observation
  retrieve: matching organism nodes plus linked evidence and provenance
  disambiguate: individual organism vs cohort vs model species vs biological sample
  expand: approved relations only
  validate: identity, source, temporal scope and evidence quality
  answer: concise explanation with uncertainty and source links
  fallback: insufficient evidence; do not invent missing facts

SEMANTIC_EQUIVALENCE
  "experimental organism" != "model organism" by default
  "experimental organism" != "reference organism" by default
  "organism" != "organism-derived sample"
  Equivalence requires matching identity, scope and evidence.

UPDATE_MODEL
  Changes append versioned events rather than overwriting historical records.
  Recompute downstream inferences when provenance, protocol or observations change.
  Retain old assertions as superseded where auditability is required.

END FLOW