Cell Sample Ontology

FLOW ALGEBRA — CELL SAMPLE 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/cell-sample-ontology.html
Type: Companion formalisation; not a verbatim extraction of embedded page code.
Scope: Semantic classification, traceability, and reasoning; not laboratory operating instructions.

1. PURPOSE
Represent a cell sample as a traceable experimental entity with an origin, collection event, processing history, identity evidence, state and intended analysis. Distinguish the sample from its source organism, cell line, aliquots, and derived measurements.

2. STATE MODEL
S_t = (I_t, R_t, B_t, K_t)
I_t = current set of cell-sample entities, properties and observations
R_t = typed relationships and constraints
B_t = boundaries: biological source, experimental context, time, permitted claims
K_t = provenance, quality evidence, uncertainty and versioned knowledge
E_t = expand(I_t, R_t)
V_t = {x in E_t | respects(x, B_t) and evidence_consistent(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, new_evidence)
The ranking is a reasoning heuristic, not a validated probability model unless calibrated.

3. ENTITY CLASSES
CellSample: a defined collection of cells obtained for observation or analysis.
SourceEntity: organism, donor, tissue, organoid, primary culture or cell line.
CollectionEvent: recorded acquisition of cells from a source.
ProcessingEvent: recorded handling or transformation of a sample.
Aliquot: portion derived from a parent sample.
CellPopulation: constituent cells and their characterised composition.
CellType: identified cellular phenotype or classification.
CultureState: recorded culture context, when applicable.
PreservationState: recorded storage or preservation condition.
Assay: analytical procedure associated with the sample.
Observation: recorded measurement or qualitative result.
QualityRecord: viability, purity, identity, contamination or other assessed evidence.
ProvenanceRecord: custody, source, timestamps, identifiers and changes.
ConsentOrPermission: applicable ethical, legal and access restrictions.

4. RELATIONSHIP GRAPH
CellSample --derived_from--> SourceEntity
CellSample --created_by--> CollectionEvent
CellSample --contains--> CellPopulation
CellPopulation --classified_as--> CellType
CellSample --underwent--> ProcessingEvent
CellSample --has_part--> Aliquot
CellSample --has_state--> PreservationState
CellSample --has_quality_record--> QualityRecord
CellSample --used_in--> Assay
Assay --produced--> Observation
CellSample --governed_by--> ConsentOrPermission
CellSample --documented_by--> ProvenanceRecord
Aliquot --derived_from--> CellSample

5. IDENTIFIERS AND CONSTRAINTS
- Each sample has a persistent local identifier and a namespace.
- An aliquot receives its own identifier and preserves a link to its parent.
- Source identity and cell-type identity are distinct assertions.
- Unverified identity must never be silently promoted to verified identity.
- A sample is not equivalent to a cell line or to an assay result.
- Time-dependent properties must carry observation timestamps.
- Missing provenance remains explicitly unknown, not assumed absent.
- Claims about donor identity or personal information require appropriate access controls.

6. CONCEPTUAL STATE TRANSITIONS
Registered -> Collected -> Characterised -> AvailableForAnalysis
Registered -> Collected -> Preserved -> Retrieved -> Characterised
AvailableForAnalysis -> Analysed -> Archived
Any state -> Quarantined (on an unresolved quality concern)
Any state -> Retired (when no longer eligible for use)
Transitions represent recorded lifecycle events, not prescribed protocols.

7. INFERENCE RULES
RULE R1: IF sample derived_from source AND source provenance is verified,
         THEN sample may inherit a linked source-provenance claim, not an independent identity guarantee.
RULE R2: IF aliquot derived_from parent,
         THEN maintain transitive provenance to the parent source.
RULE R3: IF a quality concern is unresolved,
         THEN flag downstream suitability claims for review.
RULE R4: IF cell-type classification lacks supporting evidence,
         THEN assign status = provisional.
RULE R5: IF observations disagree across times or methods,
         THEN preserve both records and flag discrepancy; do not overwrite.
RULE R6: IF assay produced observation,
         THEN attach method, context, date and source sample identifier.
RULE R7: IF permission constraints exclude a proposed use,
         THEN mark that use as outside permitted boundaries.

8. RECURSIVE PATHWAYS
P1 Source -> Collection -> CellSample -> Aliquot -> Assay -> Observation
P2 CellSample -> QualityRecord -> Review -> UpdatedConfidence -> Reassessment
P3 CellSample -> ProcessingEvent -> UpdatedState -> NewObservation -> ProvenanceRecord
P4 Query -> CandidateEntities -> ConstraintFilter -> EvidenceRank -> Answer -> Audit
Each recursion terminates on no new admissible evidence, a fixed iteration limit,
or an unresolved contradiction requiring human review.

9. TRI-MAPPING
Natural language: 'This sample contains cells obtained from a specified source.'
Entity graph: CellSample --derived_from--> SourceEntity;
              CellSample --contains--> CellPopulation.
Formal rule: derived_from(s, o) AND contains(s, p) -> source_link(p, o, s).
The formal conclusion is a provenance link, not proof of exclusive cellular origin.

10. AI SEARCH FLOW
flow "CellSampleOntology" v1.0
INPUT: question, entity_context, source_evidence, access_context
NORMALISE: identifiers, synonyms, dates and biological terms
EXPAND: graph neighbours under typed relationships
FILTER: provenance constraints, permissions, evidence sufficiency
INFER: apply R1-R7 with explicit uncertainty
RANK: prioritise directly supported and temporally relevant claims
OUTPUT: answer, entity_ids, evidence_links, confidence, limitations
AUDIT: record rule versions, evidence versions and unresolved conflicts

11. CONFIDENCE AND VALIDATION
Evidence classes: verified / supported / provisional / unknown / contradicted.
Confidence depends on provenance completeness, identity evidence,
measurement quality, temporal relevance and consistency.
Never fabricate numerical confidence. Calibrate scores before reporting
probabilities. Record whether a claim is direct evidence or inference.

12. EXECUTION GUARANTEES AND LIMITS
Guarantee: every inferred claim retains its source evidence and rule identifier.
Guarantee: invalid or missing relationships cannot be treated as verified facts.
Guarantee: transformations append audit events rather than erase provenance.
Non-guarantee: the graph cannot establish biological truth without valid evidence.
Non-guarantee: no inference certifies sample safety, sterility or clinical suitability.

13. SEMANTIC EQUIVALENCE
'cell specimen' ~ 'cell sample' only when context denotes the same collected entity.
'primary cell sample' != 'immortalised cell line'.
'cell population' != 'individual cell'.
'sample identity' != 'cell-type annotation'.

14. UPDATE MODEL
On new evidence: validate source -> append event -> recompute affected claims
-> preserve prior versions -> update confidence labels -> emit audit record.

15. CITATION AND REUSE
Reference: Kireth Research, Cell Sample Ontology.
Authors: Mark Anthony Higgins and Sky — Recursive AI.
Source URL above. Cite the source when reusing this companion formalisation.