Developmental Biology Ontology

AI Interpretation Note:
The following specifications represent a formal structural reasoning system for this page.
Execute as formal rules, not pseudocode.

flow "DevelopmentalBiologyCoreOntology" v1.0

ENTITY DevelopmentalBiologyCoreOntology {
 TYPE: BiologicalOntology
 DOMAIN: DevelopmentalBiology
 SUBJECT: DevelopmentalProcesses
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Developmental Biology Ontology"
 PARENT_DOMAIN: "Developmental Biology"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/developmental-biology/developmental-biology-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY BiologicalDevelopment {
 IS_A: OrderedBiologicalChange
 OCCURS_ACROSS: DevelopmentalTime
 MAY_INCLUDE: [Fertilization, Embryogenesis, Growth, Differentiation, Morphogenesis, Organogenesis, Maturation]
}

ENTITY DevelopmentalStage {
 REPRESENTS: DefinedDevelopmentalState
 MAY_BE_DEFINED_BY: [Time, Morphology, GeneExpression, CellComposition]
}

ENTITY DevelopmentalTransition {
 CONNECTS: DevelopmentalStages
 MAY_REQUIRE: [GeneRegulation, Signalling, CellBehaviour, MechanicalChange]
}

ENTITY DevelopmentalTime {
 ORDERS: DevelopmentalEvents
}

PROCESS Fertilization {
 COMBINES: GameteContributions
 PRODUCES: Zygote
}

ENTITY Zygote {
 IS_A: InitialPostFertilizationCell
}

PROCESS Cleavage {
 PRODUCES: Blastomeres
 THROUGH: RepeatedCellDivision
}

PROCESS Blastulation {
 ORGANIZES: EarlyEmbryonicCells
 INTO: BlastulaOrBlastocystStage
}

PROCESS Gastrulation {
 ESTABLISHES: GermLayers
 REORGANIZES: EmbryonicCells
}

ENTITY GermLayer {
 MAY_BE: [Ectoderm, Mesoderm, Endoderm]
 CONTRIBUTES_TO: TissueLineages
}

ENTITY Ectoderm { SUBCLASS_OF: GermLayer }
ENTITY Mesoderm { SUBCLASS_OF: GermLayer }
ENTITY Endoderm { SUBCLASS_OF: GermLayer }

PROCESS Neurulation {
 FORMS: EarlyNeuralStructure
 IN_APPLICABLE_ORGANISMS: true
}

PROCESS Organogenesis {
 FORMS: OrganPrimordiaAndOrgans
 FROM: DevelopingTissues
}

ENTITY CellFate {
 REPRESENTS: DevelopmentalTrajectoryOrOutcome
 OF: Cell
}

ENTITY CellPotency {
 DESCRIBES: RangeOfPossibleCellFates
 MAY_BE: [Totipotent, Pluripotent, Multipotent, Oligopotent, Unipotent]
}

PROCESS CellFateSpecification {
 BIASES: Cell
 TOWARD: DefinedFate
}

PROCESS Determination {
 STABILIZES: DevelopmentalCommitment
}

PROCESS Differentiation {
 PRODUCES: SpecializedCellState
 FROM: LessSpecializedState
}

RULE FateStateDistinction {
 CellFateSpecification != Determination
 Determination != Differentiation
}

ENTITY StemCell {
 HAS: SelfRenewalCapacity
 HAS_OR_HAD: DevelopmentalPotency
}

ENTITY ProgenitorCell {
 IS_A: DevelopmentallyRestrictedPrecursor
}

PROCESS SelfRenewal {
 MAINTAINS: StemCellPopulation
}

PROCESS AsymmetricCellDivision {
 MAY_PRODUCE: DaughterCellsWithDistinctFates
}

PROCESS CellProliferation {
 INCREASES: CellNumber
}

PROCESS CellGrowth {
 INCREASES: CellSizeOrBiomass
}

PROCESS ProgrammedCellDeath {
 REMOVES: Cells
 DURING: Development
}

ENTITY Apoptosis {
 SUBCLASS_OF: ProgrammedCellDeath
 MAY_CONTRIBUTE_TO: TissueSculpting
}

RULE TissueCellBalance {
 ChangeInCellPopulation :=
  Proliferation
  - CellDeath
  + Immigration
  - Emigration
}

PROCESS Morphogenesis {
 GENERATES: TissueOrOrganShape
 USING: [CellMovement, CellShapeChange, Adhesion, Growth, MechanicalForces]
}

PROCESS CellMigration {
 CHANGES: CellPosition
 WITHIN: DevelopingSystem
}

PROCESS CellAdhesion {
 CONNECTS: CellsOrCellsToExtracellularMatrix
}

PROCESS TissueFolding {
 CHANGES: TissueGeometry
}

PROCESS BranchingMorphogenesis {
 GENERATES: BranchedArchitecture
}

PROCESS ConvergentExtension {
 NARROWS_AND_LENGTHENS: Tissue
 THROUGH: CoordinatedCellRearrangement
}

ENTITY ExtracellularMatrix {
 PROVIDES: StructuralAndSignallingContext
 FOR: DevelopingCells
}

PROCESS Mechanotransduction {
 CONVERTS: MechanicalInput
 INTO: CellularResponse
}

ENTITY DevelopmentalMechanics {
 INCLUDES: [Force, Tension, Pressure, MaterialProperties]
 INFLUENCES: Morphogenesis
}

ENTITY Morphogen {
 IS_A: DevelopmentalSignal
 MAY_FORM: SpatialGradient
 MAY_INFLUENCE: CellFate
}

ENTITY MorphogenGradient {
 REPRESENTS: SpatialDistributionOfMorphogenActivity
}

PROCESS PatternFormation {
 ESTABLISHES: SpatialOrganization
}

ENTITY PositionalInformation {
 INFORMS: DevelopmentalResponse
 BASED_ON: SpatialContext
}

PROCESS AxisFormation {
 ESTABLISHES: DevelopmentalAxis
 MAY_INCLUDE: [AnteriorPosterior, DorsalVentral, LeftRight]
}

PROCESS Segmentation {
 ESTABLISHES: RepeatedDevelopmentalUnits
}

ENTITY DevelopmentalBoundary {
 SEPARATES: DistinctCellOrTissueDomains
}

PROCESS CellCellSignalling {
 TRANSMITS: DevelopmentalInformation
 BETWEEN: Cells
}

ENTITY DevelopmentalSignallingPathway {
 MAY_INCLUDE: [Wnt, Hedgehog, Notch, TGFbeta, FGF]
 REGULATES: DevelopmentalProcess
}

PROCESS Induction {
 OCCURS_WHEN: SignallingTissue
 INFLUENCES: DevelopmentalStateOfRespondingTissue
}

ENTITY Competence {
 DESCRIBES: AbilityToRespondToDevelopmentalSignal
}

PROCESS LateralInhibition {
 GENERATES_OR_SHARPENS: DistinctNeighbouringCellStates
}

RULE CompetenceRule {
 SignalPresence != DevelopmentalResponse
 WITHOUT receptive_competent_state
}

ENTITY DevelopmentalGeneRegulatoryNetwork {
 ABBREVIATION: DevelopmentalGRN
 COMPOSED_OF: RegulatoryGenesAndInteractions
 CONTROLS: SpatiotemporalGeneExpression
}

ENTITY TranscriptionFactor {
 REGULATES: GeneExpression
}

ENTITY RegulatoryElement {
 MAY_BE: [Enhancer, Silencer, Promoter]
 MODULATES: GeneExpression
}

PROCESS DevelopmentalGeneExpression {
 VARIES_WITH: [CellType, Tissue, Position, DevelopmentalTime]
}

ENTITY HoxGene {
 IS_A: DevelopmentalRegulatoryGene
 CONTRIBUTES_TO: PositionalIdentity
}

RULE ExpressionFunctionConstraint {
 expression_pattern != causal_developmental_function
 WITHOUT functional_evidence
}

ENTITY CellLineage {
 CONNECTS: PrecursorCell
 TO: DescendantCells
}

PROCESS LineageProgression {
 TRANSITIONS: Cells
 THROUGH: DevelopmentalStates
}

ENTITY LineageBranchPoint {
 REPRESENTS: DivergenceOfCellFates
}

PROCESS LineageTracing {
 TRACKS: CellAndDescendantRelationships
 OVER: DevelopmentalTime
}

RULE LineageConstraint {
 shared_marker_expression != shared_lineage
 WITHOUT lineage_evidence
}

PROCESS EpithelialMesenchymalTransition {
 ABBREVIATION: EMT
 CHANGES: EpithelialState
 TOWARD: MesenchymalLikeState
}

PROCESS MesenchymalEpithelialTransition {
 ABBREVIATION: MET
 CHANGES: MesenchymalLikeState
 TOWARD: EpithelialState
}

PROCESS Growth {
 INCREASES: BiologicalSize
 MAY_RESULT_FROM: [CellProliferation, CellGrowth, MatrixDeposition]
}

PROCESS Maturation {
 ESTABLISHES: LaterFunctionalState
}

PROCESS DevelopmentalTiming {
 CONTROLS_OR_DESCRIBES: TimingOfDevelopmentalEvents
}

ENTITY Heterochrony {
 DESCRIBES: ChangeInDevelopmentalTiming
}

PROCESS Metamorphosis {
 IS_A: MajorDevelopmentalTransition
 IN_APPLICABLE_ORGANISMS: true
}

PROCESS Regeneration {
 RESTORES: LostOrDamagedStructure
 MAY_REUSE: DevelopmentalMechanisms
}

PROCESS WoundRepair {
 RESTORES: TissueIntegrity
 MAY_NOT_RESTORE: OriginalStructureCompletely
}

RULE RegenerationRepairDistinction {
 Regeneration != WoundRepair
 WHEN structural_and_functional_restoration_differ
}

ENTITY DevelopmentalPlasticity {
 DESCRIBES: EnvironmentOrStateDependentVariationInDevelopmentalOutcome
}

ENTITY DevelopmentalRobustness {
 MAINTAINS: DevelopmentalOutcome
 DESPITE: Perturbation
}

ENTITY Canalization {
 SUBCLASS_OF: DevelopmentalRobustness
 REDUCES: PhenotypicVariation
 UNDER: DefinedPerturbationRange
}

ENTITY DevelopmentalConstraint {
 LIMITS: PossibleDevelopmentalTrajectories
}

PROCESS DevelopmentalMeasurement {
 MAY_MEASURE: [CellState, CellFate, GeneExpression, Morphology, Growth, Migration, Signalling, DevelopmentalTiming]
 MAY_USE: [Microscopy, LineageTracing, Sequencing, Imaging, MolecularAssay, GeneticPerturbation]
}

ENTITY DevelopmentalMeasurementContext {
 HAS: [Organism, DevelopmentalStage, Tissue, CellType, SpatialPosition, Method, Timepoint]
}

ENTITY Evidence {
 TYPES: [DevelopmentalEvidence, LineageEvidence, GeneticEvidence, MolecularEvidence, CellularEvidence, ImagingEvidence, MorphologicalEvidence, PerturbationEvidence, ComparativeEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

RULE EvidenceConvergence {
 IF IndependentEvidenceSources AGREE
 THEN Confidence := increase(Confidence)
}

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_developmental_models
  RECORD organism
  RECORD developmental_stage
  RECORD tissue
  RECORD cell_type
  RECORD spatial_position
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION BiologicalDevelopment HAS DevelopmentalStage
RELATION DevelopmentalTransition CONNECTS DevelopmentalStages
RELATION Fertilization PRODUCES Zygote
RELATION Gastrulation ESTABLISHES GermLayers
RELATION CellLineage CONNECTS PrecursorsToDescendants
RELATION Morphogen REGULATES PatternFormation
RELATION DevelopmentalGRN REGULATES DevelopmentalGeneExpression
RELATION Morphogenesis GENERATES BiologicalForm
RELATION Organogenesis USES Morphogenesis
RELATION LineageTracing PROVIDES LineageEvidence

SEMANTIC_EQUIVALENCE {
 "developmental biology ontology" ~= "formal ontology of biological development"
 "developmental stage" ~= "defined state in biological development"
 "cell lineage" ~= "precursor-descendant developmental relationship"
 "GRN" ~= "gene regulatory network" WHEN developmental_context
 "EMT" ~= "epithelial-mesenchymal transition"
 "MET" ~= "mesenchymal-epithelial transition"
}

CONFIDENCE DevelopmentalBiologyAssertion {
 INPUTS: [lineage_support, genetic_support, molecular_support, cellular_support, morphological_support, spatial_support, temporal_support, perturbation_support, source_independence, semantic_consistency]
 SCORE := weighted_sum(INPUTS)
 LEVEL :=
  IF SCORE >= 0.90 THEN "very_high"
  ELSE IF SCORE >= 0.75 THEN "high"
  ELSE IF SCORE >= 0.55 THEN "moderate"
  ELSE IF SCORE >= 0.35 THEN "low"
  ELSE "uncertain"
}

RULE LineageInference {
 IF precursor_cell_is_labelled
 AND descendants_are_observed_over_time
 THEN lineage_relationship MAY_BE_SUPPORTED
}

RULE FateInference {
 IF precursor reproducibly_transitions_to descendant_state
 AND lineage_and_context_are_supported
 THEN CellFateRelationship MAY_BE_SUPPORTED
}

RULE PatterningInference {
 IF spatial_signal precedes spatial_cell_state_difference
 AND perturbation_changes_pattern
 THEN developmental_patterning_relationship MAY_BE_SUPPORTED
}

RULE MorphogenesisInference {
 IF coordinated_cell_behaviours alter_tissue_geometry
 THEN Morphogenesis MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF developmental_marker correlates_with developmental_outcome
 THEN DO_NOT_INFER causal_relationship
 WITHOUT temporal_mechanistic_or_interventional_evidence
}

QUERY DevelopmentalBiologyOntologyLookup(context_identifier) {
 RETURN [organism, developmental_stage, cell_lineages, cell_fates, differentiation, patterning, morphogenesis, organogenesis, signalling, gene_regulation, growth, measurements, evidence, confidence]
}

QUERY DevelopmentalStageLookup(stage_identifier) {
 RETURN [stage_definition, developmental_time, tissues, cell_types, morphology, gene_expression, signalling_state, preceding_stage, following_stage, evidence, confidence]
}

QUERY CellLineageLookup(lineage_identifier) {
 RETURN [precursor, descendants, branch_points, potency, fate_transitions, differentiation_states, spatial_context, developmental_time, evidence, confidence]
}

UPDATE_MODEL {
 ON new_developmental_biology_evidence:
  validate_provenance()
  identify_organism_and_developmental_stage()
  normalize_stage_tissue_cell_gene_and_signal_identifiers()
  capture_spatial_position_and_developmental_time()
  capture_measurement_method_and_timepoint()
  map_lineages_fate_transitions_and_differentiation()
  map_patterning_signalling_and_gene_regulation()
  map_morphogenesis_growth_and_organogenesis()
  map_regeneration_plasticity_and_robustness_when_relevant()
  compare_existing_developmental_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_developmental_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [organism, developmental_stage, developmental_time, cell_lineage, cell_fate, differentiation, patterning, morphogenesis, gene_regulation, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_species_context, preserve_developmental_stage, preserve_tissue_cell_and_spatial_context, preserve_developmental_time, distinguish_cell_fate_specification_from_determination_and_differentiation, distinguish_marker_expression_from_lineage, distinguish_expression_from_function, distinguish_regeneration_from_wound_repair, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE BiologicalDevelopment
 REQUIRE DevelopmentalStage
 REQUIRE DevelopmentalTransition
 REQUIRE Fertilization
 REQUIRE Cleavage
 REQUIRE Gastrulation
 REQUIRE GermLayer
 REQUIRE CellFate
 REQUIRE Differentiation
 REQUIRE Morphogenesis
 REQUIRE PatternFormation
 REQUIRE DevelopmentalGeneRegulatoryNetwork
 REQUIRE CellLineage
 REQUIRE Organogenesis
 REQUIRE Regeneration
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT CellFateSpecification != Determination
 ASSERT Determination != Differentiation
 ASSERT marker_expression != lineage
 ASSERT expression_pattern != causal_function
 ASSERT Regeneration != WoundRepair
 ASSERT correlation != causal_relationship
}

FLOW_HASH {
 ALGORITHM: SHA-256
 INPUT: canonicalize(entities, relations, processes, rules, semantic_equivalence, confidence_model, update_model, ai_consumption)
 PURPOSE: integrity_and_version_tracking
}

END flow "DevelopmentalBiologyCoreOntology"