DNA Sample Ontology

FLOW ALGEBRA — DNA SAMPLE ENTITY ONTOLOGY
Kireth Semantic Library | Experimental Biological Entities
Version: 1.0 | 2026-10-28 | Encoding: UTF-8
Authors: Mark Anthony Higgins; Sky — Recursive AI
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/dna-sample-ontology.html
Status: Companion formalisation based on the page title and established scientific concepts; not an extraction of hidden page code.

PURPOSE
Represent DNA samples as traceable experimental entities with explicit material identity, provenance, handling history, analytical suitability and uncertainty. Distinguish a physical sample from its biological source and from derived sequence data.

STATE MODEL
S_t = (I_t, R_t, B_t, K_t)
I_t: known entities, observations and evidence at time t
R_t: typed biological and experimental relations
B_t: boundaries, permissions, constraints and unresolved values
K_t: provenance, confidence, time and knowledge status
E_t = expand(I_t, R_t)
V_t = {x in E_t | respects(x, B_t) and evidence_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)
No probabilistic preference may override a hard provenance or identity constraint.

ENTITIES
DNA_SAMPLE: uniquely identified physical aliquot containing DNA.
BIOLOGICAL_SOURCE: organism, donor, tissue, cell, environment or other origin.
PARENT_SPECIMEN: physical specimen from which DNA was obtained.
EXTRACTION_EVENT: recorded derivation of DNA from source material.
ALIQUOT: physically separated portion of a sample.
DNA_TYPE: genomic, mitochondrial, plasmid, cell-free, synthetic or other (as supported).
PREPARATION: purification, concentration, fragmentation or other recorded processing event.
STORAGE_EVENT: recorded storage condition and time interval.
QUALITY_OBSERVATION: assay-specific concentration, purity, integrity or contamination assessment.
ANALYTICAL_ASSAY: sequencing, amplification, genotyping or other method.
DERIVED_DATA: sequences, measurements, variants and analysis outputs.
CUSTODY_EVENT: transfer, receipt, access or disposal event.
CONSENT_OR_PERMISSION: applicable use and access restriction.

RELATIONSHIPS
DNA_SAMPLE --derived_from--> PARENT_SPECIMEN
PARENT_SPECIMEN --originates_from--> BIOLOGICAL_SOURCE
DNA_SAMPLE --produced_by--> EXTRACTION_EVENT
ALIQUOT --portion_of--> DNA_SAMPLE
DNA_SAMPLE --underwent--> PREPARATION
DNA_SAMPLE --has_storage_history--> STORAGE_EVENT
DNA_SAMPLE --has_quality_observation--> QUALITY_OBSERVATION
DNA_SAMPLE --used_in--> ANALYTICAL_ASSAY
ANALYTICAL_ASSAY --produces--> DERIVED_DATA
DNA_SAMPLE --governed_by--> CONSENT_OR_PERMISSION
DNA_SAMPLE --has_custody_event--> CUSTODY_EVENT

IDENTITY AND INVARIANTS
1. sample_id is unique within its issuing namespace; global uniqueness requires a namespace-qualified identifier.
2. A derived aliquot receives its own identity and retains its parent link.
3. Physical DNA samples and computational sequence records are distinct entity types.
4. Missing values remain UNKNOWN; never silently infer source, consent or purity.
5. Provenance links are append-only audit records; corrections preserve earlier assertions.
6. A sample may contain mixtures or contaminants; source identity is not automatically a claim of molecular purity.
7. Sample suitability is assay-dependent, not a universal binary property.

PATHWAYS
P1 Source tracing: DNA_SAMPLE -> EXTRACTION_EVENT -> PARENT_SPECIMEN -> BIOLOGICAL_SOURCE.
P2 Derivation: DNA_SAMPLE -> ALIQUOT -> PREPARATION -> ANALYTICAL_ASSAY -> DERIVED_DATA.
P3 Quality evaluation: DNA_SAMPLE -> QUALITY_OBSERVATION -> ASSAY_REQUIREMENT -> suitability_decision.
P4 Governance: DNA_SAMPLE -> CONSENT_OR_PERMISSION -> authorised_use_check.
P5 Audit: DNA_SAMPLE -> CUSTODY_EVENT -> chronological chain_of_custody.

INFERENCE RULES
R1 IF sample has parent specimen AND extraction record THEN infer traceable_derivation; attach source evidence.
R2 IF sample has aliquot relation THEN inherit parent provenance by reference, NOT parent sample identity.
R3 IF measured quality does not meet documented assay requirements THEN flag assay_unsuitable; do not claim all uses unsuitable.
R4 IF consent or use permission is unknown THEN flag governance_review_required; do not infer permission.
R5 IF source identifiers conflict THEN flag identity_conflict and suspend confident source attribution.
R6 IF analytical data is derived from sample THEN link data to sample, assay and processing version.
R7 IF custody history contains gaps THEN mark chain_of_custody_incomplete; do not invent missing transfers.
R8 IF an observation lacks units, method or timestamp THEN mark evidence_incomplete.

MINI RECURSION ENGINE
function resolve(sample, visited):
  if sample.id in visited: return CYCLE_FLAG
  visited.add(sample.id)
  validate_identity(sample)
  validate_evidence(sample)
  for each parent in sample.parent_links:
    resolve(parent, visited)
  evaluate_quality_for_requested_assay(sample)
  evaluate_permissions(sample)
  return {traceability, quality_status, permission_status, unresolved_conflicts}
Termination: finite visited set, no repeated traversal of the same sample identifier.

TRI-MAPPING
Human: "Which specimen did this DNA come from?"
Semantic: DNA_SAMPLE --derived_from--> PARENT_SPECIMEN --originates_from--> BIOLOGICAL_SOURCE
Formal: source(s) = origin(parent(s)) only when both edges have supporting evidence.

Human: "Can this DNA sample be used for this assay?"
Semantic: DNA_SAMPLE --has_quality_observation--> Q; ANALYTICAL_ASSAY --requires--> C
Formal: suitable(s,a) = evaluate(Q(s), C(a)); UNKNOWN if evidence insufficient.

Human: "Which data came from this aliquot?"
Semantic: ALIQUOT --used_in--> ANALYTICAL_ASSAY --produces--> DERIVED_DATA
Formal: data(a) = {d | exists assay: used_in(a,assay) and produces(assay,d)}.

CONFIDENCE MODEL
Each assertion carries {source, method, timestamp, confidence, verification_status}.
Confidence is evidence-specific; missing provenance cannot be replaced by a high numerical score.
Contradictory evidence remains explicit until reviewed.

EXECUTION GUARANTEES
Deterministic typing and validation for supplied records; no guarantee of scientific truth from incomplete inputs.
Never fabricate specimen identifiers, analytical results, donor details or custody events.
Preserve original observations and their units. Report UNKNOWN and CONFLICT distinctly.

AI SEARCH FLOW
INTENT: identify, classify, trace, compare and validate DNA sample entities.
INPUT: natural-language query + permitted sample records + ontology graph.
NORMALISE: map terms (DNA extract, DNA aliquot, genomic DNA sample) to typed concepts, preserving distinctions.
RETRIEVE: resolve sample identity, provenance, assay, quality and permission links.
FILTER: enforce evidence and access boundaries before ranking.
ANSWER: return supported facts, citations to record provenance and explicit uncertainty.
UPDATE: append newly verified evidence with timestamp and version; retain audit trail.
SEMANTIC_EQUIVALENCE: synonyms may aid retrieval but do not imply identical physical entities.
FLOW_HASH: compute SHA-256 over canonicalised published content during deployment; not precomputed here.
CITATION_BACKLINK: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/dna-sample-ontology.html

END FLOW