Experimental Cell Line Ontology

FLOW ALGEBRA — EXPERIMENTAL CELL LINE ENTITY ONTOLOGY
Version: 1.0 | Date: 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/experimental-cell-line-ontology.html
Purpose: Companion semantic formalisation; not a verbatim extraction of embedded page code.

FLOW "ExperimentalCellLineOntology" v1.0

AUTHORS:
  - Mark Anthony Higgins
  - Sky — Recursive AI
SOURCE:
  ontology: Experimental Cell Line Ontology
  category: Experimental Biological Entities
  url: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/experimental-biological-entities/experimental-cell-line-ontology.html
CITATION_BACKLINK: same as SOURCE.url
PURPOSE: Represent cell lines used in experiments with provenance, identity, passage history, conditions, treatments, measurements and evidence.

STATE_MODEL:
  S_t = (I_t, R_t, B_t, K_t)
  I_t: observed and asserted experimental cell-line entities and attributes
  R_t: typed relationships among cell lines, samples, experiments and evidence
  B_t: identity, provenance, quality and interpretation constraints
  K_t: background knowledge, controlled vocabularies and evidence confidence
  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)
  Note: P denotes a calibrated ranking only where a defined model exists; otherwise leave unscored.

ENTITY_TYPES:
  ExperimentalCellLine: cultured cellular population used as experimental material
  CellLineIdentity: stable designation and registry identifiers
  ParentCellLine: line from which a derivative originates
  DerivedCellLine: genetically or phenotypically modified descendant
  CellClone: clonally derived subpopulation
  DonorOrganism: organism from which original cells derive
  TissueOfOrigin: source tissue or anatomical structure
  CellType: cell identity or lineage designation
  CultureBatch: time-bounded instance of cell-line maintenance
  PassageEvent: documented transfer or subculture event
  CultureCondition: documented medium, substrate and environment metadata
  ExperimentalGroup: treatment, comparator or reference assignment
  Perturbation: recorded experimental manipulation
  Measurement: observed result with method, unit and uncertainty
  AuthenticationEvidence: independent identity test result
  ContaminationAssessment: recorded screening outcome
  QualityAssessment: viability, phenotype, integrity or suitability evidence
  RepositoryRecord: external catalogue or accession reference
  ProvenanceRecord: origin, custody and processing history

RELATIONSHIPS:
  ExperimentalCellLine --has_identity--> CellLineIdentity
  ExperimentalCellLine --derived_from--> ParentCellLine
  ExperimentalCellLine --originates_from--> DonorOrganism
  ExperimentalCellLine --originates_in--> TissueOfOrigin
  ExperimentalCellLine --has_cell_type--> CellType
  ExperimentalCellLine --represented_by--> CultureBatch
  CultureBatch --underwent--> PassageEvent
  CultureBatch --maintained_under--> CultureCondition
  CultureBatch --assigned_to--> ExperimentalGroup
  ExperimentalGroup --exposed_to--> Perturbation
  CultureBatch --produced--> Measurement
  ExperimentalCellLine --supported_by--> AuthenticationEvidence
  CultureBatch --assessed_by--> ContaminationAssessment
  CultureBatch --assessed_by--> QualityAssessment
  ExperimentalCellLine --registered_as--> RepositoryRecord
  CultureBatch --documented_by--> ProvenanceRecord

INVARIANTS_AND_BOUNDARIES:
  - A cell-line designation alone does not prove identity.
  - Parent and derivative cell lines remain distinct entities.
  - Passage number is batch-specific and may be unknown.
  - Authentication, contamination and quality status are time- and sample-specific.
  - Missing evidence must be represented as UNKNOWN, never automatically as PASS.
  - A recorded measurement must retain its experimental context and units.
  - An observed association does not establish a causal treatment effect.
  - Human-derived material may require consent, privacy and ethical metadata.

PATHWAYS:
  identity_resolution:
    input: designation, accession, source and authentication evidence
    process: reconcile identifiers; check conflicts; preserve provenance
    output: supported_identity | disputed_identity | unresolved_identity
  lineage_tracking:
    input: origin and derivation records
    process: trace parent-child links without collapsing derivative identity
    output: directed lineage graph with provenance
  experiment_mapping:
    input: culture batch, group assignment, intervention and observations
    process: associate measurements with exact experimental context
    output: contextualised evidence graph
  quality_review:
    input: authentication, contamination and quality assessments
    process: assess recency, relevance and contradictions
    output: evidence-supported status or UNKNOWN

INFERENCE_RULES:
  R1: IF derivative_of(A,B) THEN related_lineage(A,B); NOT identical(A,B).
  R2: IF authentication_evidence(A) is absent THEN identity_status(A)=UNKNOWN.
  R3: IF contamination_screen(batch) is absent THEN contamination_status(batch)=UNKNOWN.
  R4: IF conflicting identifiers exist THEN flag identity_conflict and request review.
  R5: IF measurement belongs_to batch THEN retain batch, method, time and units.
  R6: IF treatment and control groups are recorded THEN permit comparison only after checking design and confounders.
  R7: IF provenance chain is incomplete THEN mark downstream lineage claims provisional.
  R8: IF quality evidence is stale or inapplicable THEN do not infer current suitability.

MINI_RECURSION_ENGINE:
  initialise(S_0)
  repeat until fixed_point OR budget_exhausted:
    candidates := expand(I_t, R_t)
    valid := filter(candidates, B_t)
    supported := rank_or_leave_unscored(valid, K_t, evidence_t)
    I_(t+1) := merge_with_provenance(I_t, supported)
    preserve_unknowns_and_conflicts()
  terminate with trace, unresolved questions and evidence ledger

TRI_MAPPING:
  entity_layer: ExperimentalCellLine, CultureBatch, ExperimentalGroup, Measurement
  relation_layer: derived_from, represented_by, assigned_to, produced
  evidence_layer: provenance, authentication, quality and observation records

HOW_TO_READ:
  - ENTITY_TYPES declare nodes and their intended meanings.
  - RELATIONSHIPS declare typed edges, not automatic causal claims.
  - STATE_MODEL defines iterative evidence-constrained interpretation.
  - INFERENCE_RULES describe conservative deductions and uncertainty handling.
  - TRI_MAPPING connects entity, relation and evidence views.

MAPPING_TABLE:
  cell line designation -> CellLineIdentity -> identity assertion with provenance
  derivative history -> derived_from -> lineage edge with source evidence
  passage record -> underwent -> batch-specific event
  treatment assignment -> assigned_to/exposed_to -> experimental context
  assay result -> produced -> measurement with unit and method
  quality record -> assessed_by -> bounded quality evidence

CONFIDENCE:
  levels: VERIFIED | SUPPORTED | PROVISIONAL | UNKNOWN | CONFLICTED
  rules:
    VERIFIED: independently corroborated, relevant evidence with no unresolved conflict
    SUPPORTED: credible documented evidence, not independently corroborated
    PROVISIONAL: incomplete or indirect evidence
    UNKNOWN: no adequate evidence
    CONFLICTED: contradictory evidence requiring resolution
  no fabricated numeric confidence scores

EXECUTION_GUARANTEE:
  - Preserve source and provenance on each asserted fact.
  - Never silently convert unknown to negative or positive.
  - Never merge different cell-line identities solely by similar names.
  - Preserve contradictions and terminate recursion at a fixed point or budget limit.
  - Outputs are semantic interpretations, not biological validation certificates.

AI_SEARCH_FLOW:
  intent: locate and interpret experimental cell-line entities and evidence
  inputs: query, identifiers, tissue, lineage, experimental context
  retrieve: ontology nodes, relations, evidence and provenance
  expand: synonyms and typed relations under constraints
  validate: identity, context, evidence freshness and contradictions
  rank: relevance and documented support; abstain where evidence insufficient
  output: answer, linked entities, confidence category, citations, unknowns

SEMANTIC_EQUIVALENCE:
  - 'experimental cell line' and 'cell line used experimentally' may map to a common class.
  - 'cell line', 'cell clone', 'culture batch' and 'primary culture' are not universally equivalent.
  - Synonym resolution must not override accession or provenance conflicts.

UPDATE_MODEL:
  changes: versioned append-only evidence events where practical
  revisions: preserve earlier assertions and record supersession reason
  audit: source URL, timestamp, author and affected entities
  FLOW_HASH: compute SHA-256 from final canonical UTF-8 bytes when publishing

END FLOW