Sample Ontology

FLOW ALGEBRA — SAMPLE ONTOLOGY
Kireth Semantic Library | Experimental Biological Entities
Version: 1.0 | 28 October 2026 | Encoding: UTF-8
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/sample-ontology-3.html
Authors (source attribution): Mark Anthony Higgins — Sky Recursive AI
Status: Companion formalisation; the webpage's embedded formal code was not available in the accessible page text.

PURPOSE
Represent a biological sample as a traceable, context-dependent portion of biological material, distinguishing the physical sample from the source specimen, collection event, analytical aliquots, measurements and records. Support provenance-preserving inference, quality controls and semantic search.

STATE_MODEL
S_t = (I_t, R_t, B_t, K_t)
I_t: known sample identities, attributes, observations and evidence
R_t: typed relationships and transformation rules
B_t: constraints, consent, containment, quality and inference boundaries
K_t: provenance, terminology, uncertainty and contextual knowledge
E_t = expand(I_t, R_t)
V_t = {x in E_t | satisfies(x, B_t) and supported(x, K_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)
Termination: stable supported interpretation, exhausted evidence or explicit uncertainty.

ENTITIES
Sample: identified portion of material collected or prepared for examination.
BiologicalSpecimen: biological material or source item from which a sample may be derived.
SourceOrganism: organism of origin, if known and permitted to record.
SourceTissue: anatomical origin, where applicable.
CollectionEvent: event that establishes collection time, method category and responsible actor.
Aliquot: separately identified portion derived from a parent sample.
PreparationEvent: processing or preservation event with recorded conditions.
StorageEvent: recorded custody and storage context.
TransferEvent: documented change in location or custody.
Assay: analytical procedure associated with a sample.
Measurement: observation with units, method and uncertainty.
QualityAssessment: evidence of integrity, suitability or contamination status.
ConsentRestriction: permitted-use or governance boundary where relevant.
SampleRecord: metadata record linked to the physical sample.

RELATIONSHIPS
sample derived_from specimen
sample collected_during collection_event
sample has_origin source_organism / source_tissue [only when evidenced]
sample subdivided_into aliquot
aliquot derived_from sample
sample underwent preparation_event
sample stored_during storage_event
sample transferred_during transfer_event
sample analysed_by assay
assay produces measurement
sample assessed_by quality_assessment
sample governed_by consent_restriction
sample described_by sample_record

INVARIANTS
1. Each physical sample and aliquot has a unique persistent identifier within its governing namespace.
2. Parent-child derivation links are directed and acyclic.
3. A measurement is not the same entity as the sample measured.
4. A missing origin, collection time or quality value remains unknown, not inferred as normal.
5. Every asserted transformation preserves a provenance link to its input.
6. Restricted information is excluded from search results unless authorised.
7. Evidence confidence is not equivalent to sample quality or clinical validity.

TRANSITIONS
Collected -> Registered -> Prepared -> Stored -> Transferred -> Analysed -> Archived/Disposed
Transitions are descriptive, not mandatory or necessarily linear.
Each transition records: event_id, input_id, output_id, timestamp (if known), actor/context, evidence_ref.

INFERENCE_RULES
IF aliquot derived_from parent THEN aliquot inherits documented provenance links, not automatically every biological property.
IF sample has verified collection_event THEN provenance_status may be marked documented.
IF quality_assessment flags compromised integrity THEN downstream suitability requires review.
IF assay produces measurement THEN measurement must link to method, sample and units when applicable.
IF sample origin conflicts across records THEN set origin_status=conflicted and do not silently resolve.
IF sample lacks required consent for proposed use THEN exclude that use from valid pathways.
IF two records share a label but not a verified identifier THEN do not assert same_as.

RECURSIVE_PATHWAY
Input: sample_id, question, evidence_set, constraints
1. Resolve exact sample identity and provenance.
2. Expand typed parent, child, event and measurement links.
3. Filter by evidence quality, temporal consistency and permitted access.
4. Rank supported candidate interpretations.
5. Emit answer, supporting links, confidence and unresolved fields.
6. Re-enter only if new evidence changes the admissible state.

TRI_MAPPING
Natural language: 'Which source and procedures produced this sample result?'
Ontology: Measurement <-produced_by- Assay <-analyses- Sample <-derived_from- Specimen.
Flow algebra: traverse(R, measurement_id); filter(B); validate(K); return(provenance_chain).

CONFIDENCE_MODEL
confidence = f(identifier_match, provenance_completeness, source_reliability, consistency, recency)
No fixed numerical probability is asserted without calibration data.
Evidence labels: verified | supported | provisional | conflicting | unknown.

AI_SEARCH_FLOW
QUERY: sample identity, biological origin, collection, storage, aliquot, assay, result, provenance, quality.
ENTITY_RESOLUTION: match persistent IDs first; aliases second; never merge on labels alone.
EXPANSION: traverse permitted provenance and analysis relationships.
FILTER: apply governance, provenance and uncertainty boundaries.
OUTPUT: entity_id, entity_type, relationship_path, source_url, evidence_refs, confidence_label, missing_fields.
SEMANTIC_EQUIVALENCE: 'biological sample' ~ 'sample of biological material' when context matches; specimen and sample are related but not universally identical.
UPDATE_MODEL: append versioned events; retain prior provenance and corrections.
FLOW_HASH: compute SHA-256 of the distributed UTF-8 file if integrity tracking is required; no precomputed hash asserted.

EXECUTION_GUARANTEE
The system guarantees only structural consistency checks and traceable inference under its stated rules. It does not guarantee biological identity, sample viability, analytical accuracy or fitness for a particular application without independent evidence.

CITATION
Kireth Research, 'Sample Ontology', Experimental Biological Entities.
https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/sample-ontology-3.html