Biological Specimen Ontology

FLOW ALGEBRA — BIOLOGICAL SPECIMEN 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/biological-specimen-ontology.html
Citation: Kireth Research, Biological Specimen Ontology (revised 27 July 2026).
Status: Companion formalisation; the webpage's complete embedded formal rules were not accessible in extracted text. Do not treat this as a verbatim transcription.
Purpose: Represent biological specimens, their provenance, collection context, custody, processing and evidential suitability for semantic retrieval and reasoning.

FLOW "BiologicalSpecimenEntityOntology" v1.0

STATE_MODEL
  S_t = (I_t, R_t, B_t, K_t)
  I_t : set of asserted specimen entities and observations
  R_t : typed relationships and inference rules
  B_t : biological, ethical, temporal and evidential constraints
  K_t : provenance, taxonomic and methodological knowledge
  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)
  Stop when no admissible new assertions or iteration budget reached.

ENTITIES
  BiologicalSpecimen: a collected or retained biological material unit for observation or analysis
  SourceOrganism: organism from which specimen originates, when applicable
  SourcePopulation: population or cohort associated with source
  TissueSample: anatomical material sampled from a source
  CellSample: isolated or cultured cellular material
  FluidSample: biological fluid collected for analysis
  EnvironmentalBiologicalSample: material containing biological components from an environment
  MicrobialIsolate: microbial material obtained from a defined source
  ReferenceSpecimen: material retained for comparison or identification
  VoucherSpecimen: archived material supporting a taxonomic or research claim
  Aliquot: identifiable subdivision of a parent specimen
  DerivedMaterial: product of documented specimen processing
  CollectionEvent: occurrence during which material was obtained
  CollectionSite: spatial context at an appropriate privacy granularity
  CollectionTime: time or interval of collection
  CustodyEvent: recorded transfer, receipt or storage responsibility
  ProcessingEvent: documented transformation or preparation
  StorageCondition: recorded storage environment and duration
  Assay: method of observation or measurement
  Observation: result linked to an assay and its evidence
  ConsentOrPermit: applicable permission, approval or authorisation
  SpecimenIdentifier: stable unique identifier within a defined namespace
  QualityRecord: viability, integrity, contamination or fitness assessment

RELATIONSHIPS
  specimen --originates_from--> source organism or source environment
  specimen --collected_during--> collection event
  collection event --occurred_at--> collection site
  collection event --occurred_during--> collection time
  specimen --has_identifier--> specimen identifier
  specimen --subject_to--> custody event
  specimen --subject_to--> processing event
  specimen --stored_under--> storage condition
  specimen --analysed_by--> assay
  assay --produces--> observation
  specimen --has_quality_record--> quality record
  specimen --governed_by--> consent or permit (where applicable)
  aliquot --derived_from--> parent specimen
  derived material --derived_from--> source specimen
  voucher specimen --supports--> taxonomic or research claim

PATHWAYS
  P1 Collection: source -> collection event -> specimen -> identifier
  P2 Traceability: specimen -> custody event(s) -> storage -> analysis
  P3 Derivation: parent specimen -> processing event -> derived material / aliquot
  P4 Evidence: specimen -> assay -> observation -> supported claim
  P5 Suitability: intended analysis + specimen condition + constraints -> eligibility decision

INFERENCE_RULES
  R1 IF aliquot derived_from parent THEN preserve parent linkage and assign distinct aliquot identifier.
  R2 IF an observation is attributed to a specimen THEN require a documented specimen-to-assay association.
  R3 IF a specimen's source is unknown THEN mark source provenance as unknown; do not infer an organism.
  R4 IF collection time or custody history is missing THEN mark provenance completeness as partial.
  R5 IF processing changes material identity or composition THEN create a derived-material entity rather than silently overwriting the parent.
  R6 IF a quality result indicates contamination THEN flag assay suitability for review; do not assume all assays are invalid.
  R7 IF consent, access rights or permits prohibit a use THEN exclude that use from admissible pathways.
  R8 IF two identifiers appear equivalent THEN merge only with authoritative mapping evidence.
  R9 IF specimens share a source THEN do not infer that they are the same physical specimen.
  R10 IF taxonomic identification is provisional THEN retain the provisional status and evidence source.

CONSTRAINTS
  B1 Unique identifiers must be scoped to their issuing namespace.
  B2 Provenance must not be fabricated when absent.
  B3 Parent-child derivation relationships must be acyclic.
  B4 Sensitive donor and location information must respect access restrictions.
  B5 Measurements must preserve units, methods, uncertainty and observation times when available.
  B6 Biological viability and analytical suitability are distinct properties.
  B7 Temporal ordering: collection precedes processing; processing precedes derived observations unless explicitly documented otherwise.
  B8 No inferred research or clinical suitability without appropriate supporting evidence.

TRI_MAPPING
  Natural-language layer: "This specimen was collected, labelled, stored and analysed."
  Semantic layer: BiologicalSpecimen -> CollectionEvent -> StorageCondition -> Assay -> Observation
  Formal layer: collected_during(s,c) AND stored_under(s,k) AND analysed_by(s,a) AND produces(a,o)

MINI_RECURSION_ENGINE
  seed := supplied specimen identifiers and verified metadata
  repeat:
    candidates := expand(seed, typed_relationships)
    candidates := filter(candidates, constraints and provenance)
    accepted := rank(candidates, evidence_quality, relevance, consistency)
    seed := seed union accepted
  until fixed_point OR max_iterations
  return accepted assertions with source lineage and uncertainty

CONFIDENCE
  confidence(assertion) := calibrated assessment based on direct evidence,
                           provenance completeness, methodological reliability,
                           consistency and source independence
  Never present a numerical probability without a calibrated model.
  States: verified | supported | provisional | unknown | contradicted
  Contradictory records remain linked and flagged for review.

AI_SEARCH_FLOW
  QUERY_INPUT: specimen type, source, identifier, method, observation or lineage
  NORMALISE: resolve synonyms and identifier namespaces
  RETRIEVE: specimen entities and provenance-linked relationships
  EXPAND: permitted parent-child, collection, assay and custody links
  FILTER: evidence, access constraints, temporal validity and ambiguity
  RANK: semantic match, evidence quality and provenance completeness
  OUTPUT: entity identifiers, typed links, evidence, uncertainty and citation
  NO_MATCH: return explicit no-supported-match rather than inventing data

EXECUTION_GUARANTEE
  Deterministic rule application given the same inputs, knowledge snapshot and tie-breaking order.
  No guarantee of biological truth, complete provenance or clinical validity.
  Every inferred assertion must retain its supporting chain and rule identifier.

UPDATE_MODEL
  Append versioned changes with timestamp, source, responsible actor and reason.
  Preserve prior states for audit and reproducibility.
  Revalidate affected inferences after provenance, identity or quality updates.

END FLOW