Lipid Ontology

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

flow "LipidOntology" v1.0

ENTITY LipidOntology {
 TYPE: BiologicalOntology
 DOMAIN: Biochemistry
 SUBJECT: Lipid
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Lipid Ontology"
 PARENT_DOMAIN: "Biochemistry"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/biochemistry/lipid-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY Lipid {
 IS_A: Biomolecule
 GENERALLY_HAS: HydrophobicOrAmphipathicCharacter
 MAY_BE: [FattyAcid, Glycerolipid, Phospholipid, Sphingolipid, Sterol, Wax]
 MAY_FUNCTION_IN: [MembraneStructure, EnergyStorage, Signalling, Insulation]
}

ENTITY FattyAcid {
 HAS: [CarboxylGroup, HydrocarbonChain]
 MAY_BE: [SaturatedFattyAcid, UnsaturatedFattyAcid]
}

ENTITY SaturatedFattyAcid {
 SUBCLASS_OF: FattyAcid
 HAS_CARBON_CARBON_DOUBLE_BONDS: false
}

ENTITY UnsaturatedFattyAcid {
 SUBCLASS_OF: FattyAcid
 HAS: OneOrMoreCarbonCarbonDoubleBonds
 MAY_BE: [MonounsaturatedFattyAcid, PolyunsaturatedFattyAcid]
}

RULE FattyAcidIdentityRule {
 FattyAcidIdentity DEPENDS_ON [carbon_chain_length, double_bond_count, double_bond_positions, double_bond_geometry]
}

ENTITY Glycerolipid {
 SUBCLASS_OF: Lipid
 HAS_BACKBONE: Glycerol
}

ENTITY Triacylglycerol {
 SUBCLASS_OF: Glycerolipid
 HAS_ACYL_CHAINS: 3
 FUNCTIONS_PRIMARILY_IN: EnergyStorage
}

ENTITY Phospholipid {
 SUBCLASS_OF: Lipid
 HAS: [HydrophilicHeadgroup, HydrophobicRegion]
 IS: Amphipathic
 CONTRIBUTES_TO: BiologicalMembrane
}

ENTITY Glycerophospholipid {
 SUBCLASS_OF: Phospholipid
 HAS_BACKBONE: Glycerol
}

ENTITY Sphingolipid {
 SUBCLASS_OF: Lipid
 HAS_BACKBONE: SphingoidBase
 MAY_FUNCTION_IN: [MembraneStructure, Signalling, Recognition]
}

ENTITY Ceramide {
 SUBCLASS_OF: Sphingolipid
 IS_PRECURSOR_TO: MultipleSphingolipids
}

ENTITY Sterol {
 SUBCLASS_OF: Lipid
 HAS: SteroidRingSystem
 MAY_MODULATE: MembraneProperties
}

ENTITY Cholesterol {
 SUBCLASS_OF: Sterol
 PARTICIPATES_IN: [MembraneOrganization, SteroidBiosynthesis]
}

ENTITY Steroid {
 SUBCLASS_OF: Lipid
 HAS: FusedRingStructure
 MAY_FUNCTION_AS: SignallingMolecule
}

ENTITY Wax {
 SUBCLASS_OF: Lipid
 MAY_FUNCTION_IN: ProtectiveCoating
}

ENTITY BiologicalMembrane {
 COMPOSED_OF: [Lipids, Proteins]
 ORGANIZED_AS: LipidBilayer
 SEPARATES: BiologicalCompartments
}

ENTITY LipidBilayer {
 COMPOSED_PRIMARILY_OF: AmphipathicLipids
 HAS: [HydrophilicSurfaces, HydrophobicCore]
}

ENTITY MembraneFluidity {
 DEPENDS_ON: [lipid_composition, fatty_acid_saturation, chain_length, sterol_content, temperature]
}

RULE FluidityRule {
 IF cis_unsaturation increases
 THEN membrane_fluidity MAY_INCREASE
 subject_to_temperature_and_composition
}

ENTITY LipidDroplet {
 STORES: NeutralLipids
 MAY_CONTAIN: Triacylglycerol
}

PROCESS LipidDigestion {
 BREAKS_DOWN: DietaryLipids
 MAY_USE: Lipase
 PRODUCES: AbsorbableLipidComponents
}

ENTITY Lipase {
 IS_A: Enzyme
 CATALYSES: LipidHydrolysis
}

ENTITY Lipoprotein {
 IS_A: LipidProteinAssembly
 TRANSPORTS: HydrophobicLipids
 THROUGH: AqueousBiologicalFluid
}

PROCESS LipidTransport {
 MOVES: Lipid
 BETWEEN: CompartmentsOrTissues
}

PROCESS FattyAcidActivation {
 CONVERTS: FattyAcid
 TO: FattyAcylCoA
 REQUIRES: Energy
}

ENTITY FattyAcylCoA {
 IS_A: ActivatedFattyAcidDerivative
 PARTICIPATES_IN: LipidMetabolism
}

PROCESS BetaOxidation {
 DEGRADES: FattyAcylCoA
 PRODUCES: [AcetylCoA, NADH, FADH2]
 MAY_OCCUR_IN: [Mitochondrion, Peroxisome]
}

PROCESS FattyAcidSynthesis {
 SYNTHESIZES: FattyAcid
 USES: [AcetylDerivedPrecursors, NADPH]
}

ENTITY FattyAcidSynthase {
 IS_A: EnzymeComplex
 CATALYSES: FattyAcidSynthesis
}

PROCESS TriacylglycerolSynthesis {
 PRODUCES: Triacylglycerol
 FROM: [GlycerolDerivedBackbone, FattyAcylGroups]
}

PROCESS Lipolysis {
 HYDROLYSES: Triacylglycerol
 PRODUCES: [FattyAcids, GlycerolDerivedProducts]
}

PROCESS PhospholipidSynthesis {
 PRODUCES: Phospholipid
}

ENTITY Phospholipase {
 IS_A: Enzyme
 CLEAVES: SpecificPhospholipidBond
}

ENTITY SignallingLipid {
 SUBCLASS_OF: Lipid
 PARTICIPATES_IN: SignalTransduction
}

ENTITY Eicosanoid {
 SUBCLASS_OF: SignallingLipid
 DERIVED_FROM: PolyunsaturatedFattyAcid
}

ENTITY Phosphoinositide {
 SUBCLASS_OF: Phospholipid
 PARTICIPATES_IN: CellularSignalling
}

PROCESS LipidPeroxidation {
 OXIDIZES: UnsaturatedLipid
 MAY_GENERATE: ReactiveProducts
}

ENTITY LipidHomeostasis {
 BALANCES: [LipidSynthesis, LipidDegradation, LipidTransport, LipidStorage]
}

PROCESS Lipidomics {
 MEASURES: LipidSpecies
 WITHIN: BiologicalSample
 MAY_USE: [MassSpectrometry, Chromatography, NuclearMagneticResonance]
}

ENTITY Lipidome {
 REPRESENTS: CollectionOfLipids
 WITHIN: DefinedBiologicalContext
}

ENTITY LipidSpecies {
 HAS: DefinedStructuralComposition
 MAY_INCLUDE: [Headgroup, AcylChains, DoubleBondFeatures]
}

ENTITY Evidence {
 TYPES: [BiochemicalEvidence, LipidomicEvidence, StructuralEvidence, MassSpectrometricEvidence, ChromatographicEvidence, MetabolicEvidence, ImagingEvidence, ComputationalEvidence, LiteratureEvidence]
}

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

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_lipid_assignments
  RECORD lipid_identity
  RECORD acyl_composition
  RECORD double_bond_information
  RECORD biological_context
  RECORD analytical_method
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Lipid HAS_STRUCTURE LipidStructure
RELATION FattyAcid PART_OF ManyComplexLipids
RELATION Phospholipid PART_OF BiologicalMembrane
RELATION Sterol MAY_MODULATE MembraneFluidity
RELATION Triacylglycerol PARTICIPATES_IN LipidStorage
RELATION FattyAcylCoA PARTICIPATES_IN BetaOxidation
RELATION SignallingLipid PARTICIPATES_IN SignalTransduction
RELATION LipidSpecies PART_OF Lipidome

SEMANTIC_EQUIVALENCE {
 "lipid" ~= "biological hydrophobic or amphipathic molecule" WHEN biochemical_context
 "triacylglycerol" ~= "triglyceride"
 "phospholipid bilayer" ~= "lipid bilayer" WHEN membrane_context
 "lipidome" ~= "complete lipid profile" WHEN defined_sample_context
}

CONFIDENCE LipidAssertion {
 INPUTS: [chemical_identity_support, structural_support, acyl_chain_support, analytical_quality, lipidomic_support, metabolic_support, replication, 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 LipidClassificationInference {
 IF molecular_structure IS_KNOWN
 THEN classify_lipid_by [backbone, headgroup, acyl_chain_count, chain_lengths, unsaturation, functional_groups]
}

RULE MetabolicInference {
 IF Lipid IS_SUBSTRATE_OR_PRODUCT_OF metabolic_reaction
 THEN Lipid PARTICIPATES_IN corresponding_pathway
}

RULE CausalityConstraint {
 IF Lipid abundance correlates_with biological_state
 THEN DO_NOT_INFER causal_role
 WITHOUT functional_evidence
}

QUERY LipidLookup(identifier) {
 RETURN [identity, lipid_class, backbone, headgroup, fatty_acyl_composition, double_bond_features, molecular_properties, membrane_roles, metabolic_pathways, signalling_roles, cellular_locations, evidence, confidence]
}

QUERY LipidSpeciesLookup(identifier) {
 RETURN [molecular_species, acyl_chains, chain_lengths, unsaturation, stereochemistry, analytical_method, abundance, biological_context, evidence, confidence]
}

QUERY LipidMetabolismLookup(lipid_identifier) {
 RETURN [synthesis, degradation, transport, storage, enzymes, intermediates, cellular_compartments, regulation, evidence, confidence]
}

UPDATE_MODEL {
 ON new_lipid_evidence:
  validate_provenance()
  normalize_lipid_identifier()
  identify_organism_and_biological_context()
  determine_lipid_class()
  normalize_headgroup_and_backbone()
  normalize_acyl_chain_composition()
  capture_double_bond_positions_and_geometry()
  map_metabolic_transport_and_signalling_relationships()
  record_analytical_method()
  compare_existing_assignments()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_lipid_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [lipid_identity, lipid_class, backbone, headgroup, acyl_chain_composition, unsaturation, membrane_context, metabolic_context, analytical_method, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_lipid_class, preserve_chain_length, preserve_double_bond_count_positions_and_geometry, preserve_headgroup, preserve_species_context, preserve_cellular_compartment, distinguish_lipid_species_from_lipid_class, distinguish_abundance_from_activity, distinguish_observed_from_inferred_function, avoid_unsupported_causal_inference]
}

VALIDATE {
 REQUIRE Lipid
 REQUIRE FattyAcid
 REQUIRE Glycerolipid
 REQUIRE Phospholipid
 REQUIRE Sphingolipid
 REQUIRE Sterol
 REQUIRE BiologicalMembrane
 REQUIRE BetaOxidation
 REQUIRE FattyAcidSynthesis
 REQUIRE Lipidomics
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT FattyAcidSynthesis != BetaOxidation
 ASSERT lipid_species != lipid_class
 ASSERT abundance != activity
 ASSERT association != causal_function
}

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 "LipidOntology"