Tissue Sample Ontology

FLOW ALGEBRA — TISSUE SAMPLE ENTITY ONTOLOGY
Version: 1.0 | Encoding: UTF-8 | Language: en-GB
Authors: Mark Anthony Higgins; Sky — Recursive AI
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/tissue-sample-ontology.html
Scope: Companion formalisation; not a verbatim extraction of embedded page code.

1. PURPOSE
Represent tissue samples as identifiable, provenance-linked biological specimens with explicitly recorded origin, collection, preservation, processing, quality, and experimental use. Separate observations from inferences; do not infer consent, identity, viability, or fitness for use without evidence.

2. STATE MODEL
S_t = (I_t, R_t, B_t, K_t)
I_t: known tissue sample instances and descriptive attributes.
R_t: typed relations connecting samples, donors, anatomical origins, events, aliquots and studies.
B_t: constraints, permissions, uncertainty and permitted inference boundaries.
K_t: provenance, evidence, timestamps, controlled vocabularies and confidence.
E_t = expand(I_t, R_t)
V_t = {x in E_t | constraints_B(x) and evidence_K(x)}
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, new_evidence_t)
Interpretation: ranking supports evidence-based retrieval, not proof of biological validity.

3. ENTITY TYPES
TissueSample: physical material collected from tissue.
SourceOrganism: organism from which material originates.
DonorRecord: governed source record, potentially pseudonymised.
AnatomicalSite: tissue location using an anatomical ontology.
TissueType: epithelial, connective, muscle, nervous or other specified tissue.
CollectionEvent: acquisition event with method, date and responsible role.
SampleContainer: labelled physical vessel or storage unit.
PreservationEvent: fixation, freezing or other preservation state.
ProcessingEvent: sectioning, embedding, extraction or other transformation.
Aliquot: derived portion with its own identifier and parent relationship.
Assay: analysis performed on material or derived aliquot.
QualityObservation: recorded integrity, composition or suitability measure.
ConsentOrAuthority: applicable governance record; never assumed.

4. RELATIONSHIPS
TissueSample --derivedFrom--> SourceOrganism
TissueSample --hasAnatomicalOrigin--> AnatomicalSite
TissueSample --classifiedAs--> TissueType
TissueSample --collectedDuring--> CollectionEvent
TissueSample --storedIn--> SampleContainer
TissueSample --underwent--> PreservationEvent
TissueSample --underwent--> ProcessingEvent
Aliquot --derivedFrom--> TissueSample
Assay --usesMaterial--> TissueSample | Aliquot
QualityObservation --describes--> TissueSample | Aliquot
TissueSample --governedBy--> ConsentOrAuthority
Every asserted edge has source, timestamp and evidence status.

5. INVARIANTS AND BOUNDARIES
INV-01: Each sample instance has a stable, unique identifier within its registry.
INV-02: Every derived aliquot has a traceable parent, or is marked provenance_unknown.
INV-03: Processing creates a new material state; it does not erase prior history.
INV-04: Collection site, tissue type and species are distinct fields.
INV-05: Missing consent or authority must never be interpreted as permission.
INV-06: An assay result does not automatically describe the entire donor or organism.
INV-07: Unknown, not measured and negative results are separate states.
INV-08: Biological viability is not inferred solely from storage conditions.

6. TRANSITIONS
registered -> collected -> accessioned -> preserved_or_fresh -> processed -> analysed_or_archived
Additional states: transferred, exhausted, disposed, quarantined, provenance_incomplete.
Transition(event, state) requires a recorded event, actor/role, time and evidence.
A branch can yield multiple aliquots, each independently tracked.

7. INFERENCE RULES
RULE-01: IF aliquot derivedFrom sample AND sample hasAnatomicalOrigin site THEN aliquot may inherit site as provenance-qualified metadata.
RULE-02: IF sample underwent processing THEN report its current processed state alongside original collection state.
RULE-03: IF a required provenance field is absent THEN flag provenance_incomplete; do not fabricate values.
RULE-04: IF a quality observation fails a study-defined acceptance criterion THEN flag review_required, not universally_invalid.
RULE-05: IF evidence conflicts across records THEN preserve both claims and mark unresolved_conflict.
RULE-06: IF a specimen is linked to a donor THEN enforce applicable privacy and access boundaries in retrieval.

8. RECURSIVE PATHWAYS
Sample -> CollectionEvent -> SourceOrganism -> AnatomicalSite -> TissueType
Sample -> ProcessingEvent -> DerivedAliquot -> Assay -> Result -> Evidence
Sample -> StorageEvent -> ConditionRecord -> QualityObservation -> Review
Recurse only through typed, authorised edges. Stop on cycles, depth limits, missing evidence or restricted records.

9. TRI-MAPPING
ENTITY: TissueSample and related material, event and evidence entities.
RELATIONSHIP: typed, directional and provenance-bearing edges.
PROCESS: collection, preservation, processing, quality assessment and use.
Mapping guarantee: each process transition preserves references to its input entities and creates traceable output states.

10. EXECUTION GUARANTEE
Inputs: sample identifier, entity graph, evidence store, access policy.
Preconditions: authenticated query context and known schema version.
Execution: validate -> expand -> filter -> rank -> explain -> return.
Outputs: matching entities, provenance paths, uncertainty labels and applicable restrictions.
Guarantee: deterministic constraint checks given fixed input data and rule versions; no guarantee that incomplete records establish biological truth.

11. CONFIDENCE AND EVIDENCE
Confidence is evidence-specific, not an intrinsic property of a tissue sample.
verified: supported by authenticated record or validated observation.
reported: supplied by an identified source, not independently verified.
inferred: derived through an explicit rule with traceable premises.
unknown: no sufficient evidence.
conflicted: incompatible claims remain unresolved.
Never replace an unknown value with a high-probability guess in a factual export.

12. AI SEARCH FLOW
flow "TissueSampleOntology" v1.0
AUTHORS: ["Mark Anthony Higgins", "Sky — Recursive AI"]
SOURCE: "https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/tissue-sample-ontology.html"
PURPOSE: "Provenance-aware semantic retrieval of tissue sample entities"
STATE_MODEL: "S=(I,R,B,K)"
ENTITIES: [TissueSample, SourceOrganism, AnatomicalSite, TissueType, CollectionEvent, PreservationEvent, ProcessingEvent, Aliquot, Assay, QualityObservation]
PATHWAYS: [origin_trace, derivation_trace, handling_history, assay_evidence]
MINI_RECURSION_ENGINE:
  expand: "Follow authorised typed relationships with cycle detection"
  filter: "Enforce provenance, governance and query constraints"
  rank: "Prefer direct, current and well-documented evidence"
  explain: "Return evidence path, rule IDs and unresolved gaps"
INFERENCE_RULES: [RULE-01, RULE-02, RULE-03, RULE-04, RULE-05, RULE-06]
CONFIDENCE: [verified, reported, inferred, unknown, conflicted]
SEMANTIC_EQUIVALENCE:
  exact: "Same registry identifier and material instance"
  related: "Shared donor, anatomical origin or parent specimen"
  prohibited: "Do not equate distinct aliquots or donors"
UPDATE_MODEL: "Append provenance-bearing events; version corrections"
CITATION_BACKLINK: "https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/tissue-sample-ontology.html"

END OF FLOW