Lipoprotein Ontology

FLOW ALGEBRA
Lipoprotein Ontology — Kireth Semantic Library
Version: 1.0 | Locale: en-GB | Encoding: UTF-8
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/macromolecular-entities/lipoprotein-ontology.html
Authors: Mark Higgins — Sky (Recursive AI)

# 01 — IDENTITY
flow "LipoproteinOntology" v1.0
ontology.id: "kireth:biological-entities:macromolecular-entities:lipoprotein"
ontology.label: "Lipoprotein Ontology"
ontology.parent: "Macromolecular Entities"
ontology.domain: [biology, biochemistry, lipid_metabolism, molecular_transport]
ontology.scope: "Lipid–protein assemblies, their composition, classes, transformations, transport and biological roles."
ontology.definition: "A lipoprotein is an assembly of lipids and proteins; plasma lipoproteins transport hydrophobic lipids through blood. The term also encompasses other lipid-associated proteins in broader biological contexts."

# 02 — TYPES
entity Lipoprotein: BiologicalAssembly
entity PlasmaLipoprotein: Lipoprotein
entity Apolipoprotein: Protein
entity Lipid: Molecule
entity Triacylglycerol: Lipid
entity Cholesterol: Lipid
entity CholesterylEster: Lipid
entity Phospholipid: Lipid
entity FreeFattyAcid: Lipid
entity LipoproteinParticle: PlasmaLipoprotein
entity Chylomicron: LipoproteinParticle
entity ChylomicronRemnant: LipoproteinParticle
entity VLDL: LipoproteinParticle
entity IDL: LipoproteinParticle
entity LDL: LipoproteinParticle
entity HDL: LipoproteinParticle
entity LpA: LipoproteinParticle
entity LipoproteinReceptor: Protein
entity LipoproteinLipase: Enzyme
entity HepaticLipase: Enzyme
entity EndothelialLipase: Enzyme
entity LCAT: Enzyme
entity CETP: TransferProtein
entity Tissue: BiologicalStructure
entity Hepatocyte: Cell
entity Enterocyte: Cell
entity Macrophage: Cell
entity Plasma: BiologicalFluid
entity MetabolicProcess: BiologicalProcess
entity Measurement: Observation
entity Evidence: InformationArtifact

# 03 — CORE PROPERTIES
property has_component: Lipoprotein -> (Lipid | Protein)
property has_apolipoprotein: LipoproteinParticle -> Apolipoprotein
property has_surface: LipoproteinParticle -> MolecularRegion
property has_core: LipoproteinParticle -> MolecularRegion
property carries: LipoproteinParticle -> Lipid
property synthesised_by: LipoproteinParticle -> Cell
property taken_up_by: LipoproteinParticle -> Cell
property binds_receptor: LipoproteinParticle -> LipoproteinReceptor
property participates_in: LipoproteinParticle -> MetabolicProcess
property derived_from: LipoproteinParticle -> LipoproteinParticle
property transfers_lipid_to: LipoproteinParticle -> LipoproteinParticle
property has_density: LipoproteinParticle -> Measurement
property has_size: LipoproteinParticle -> Measurement
property has_concentration: LipoproteinParticle -> Measurement
property supported_by: Assertion -> Evidence

# 04 — STRUCTURAL MODEL
structure PlasmaLipoproteinParticle:
  surface: [phospholipid_monolayer, unesterified_cholesterol, apolipoproteins]
  hydrophobic_core: [triacylglycerols, cholesteryl_esters]
  organisation: "Dynamic, non-covalent assembly; composition depends on particle class and metabolic state."
  invariant: "A plasma lipoprotein particle is not a lipid bilayer vesicle."

# 05 — TAXONOMY
classification plasma_particle_classes:
  - Chylomicron
  - ChylomicronRemnant
  - VLDL
  - IDL
  - LDL
  - HDL
  - LpA
classification axes:
  - density
  - particle_diameter
  - apolipoprotein_composition
  - lipid_composition
  - metabolic_origin
  - biological_function
constraint: "Density and size ranges overlap and depend on analytical method; do not infer exact class solely from one measurement."

# 06 — EXEMPLAR RELATIONSHIPS
Chylomicron synthesised_by Enterocyte
VLDL synthesised_by Hepatocyte
Chylomicron has_apolipoprotein ApoB48
VLDL has_apolipoprotein ApoB100
LDL has_apolipoprotein ApoB100
HDL has_apolipoprotein ApoA1
LpA has_apolipoprotein ApoB100
LpA has_apolipoprotein ApoA
Chylomicron carries Triacylglycerol
VLDL carries Triacylglycerol
LDL carries CholesterylEster
HDL carries Cholesterol
note: "Statements describe characteristic associations, not exhaustive or exclusive composition."

# 07 — METABOLIC PATHWAYS
process ExogenousLipidTransport:
  inputs: [dietary_lipids, enterocyte]
  steps:
    - assemble_chylomicron
    - secrete_to_lymph
    - enter_circulation
    - lipoprotein_lipase_hydrolyses_triacylglycerol
    - deliver_fatty_acids_to_tissues
    - form_chylomicron_remnant
    - hepatic_remnant_uptake
  outputs: [tissue_fatty_acids, hepatic_remnant_lipids]

process EndogenousLipidTransport:
  inputs: [hepatic_lipids]
  steps:
    - assemble_and_secrete_VLDL
    - peripheral_triacylglycerol_hydrolysis
    - generate_IDL
    - hepatic_uptake_or_further_remodelling
    - generate_LDL
    - receptor_mediated_LDL_clearance
  outputs: [distributed_lipids, cleared_particles]
  qualification: "Not every VLDL particle necessarily becomes LDL."

process HDLCholesterolTransport:
  steps:
    - lipid_poor_apolipoprotein_accepts_cellular_cholesterol
    - HDL_particle_maturation
    - cholesterol_esterification_by_LCAT
    - selective_hepatic_uptake_or_interparticle_transfer
  qualification: "Reverse cholesterol transport is a network of pathways, not a single obligatory linear route."

# 08 — ENZYMATIC AND RECEPTOR ACTIONS
rule LPLHydrolysis:
  when: substrate is triacylglycerol_rich_lipoprotein AND LipoproteinLipase active
  infer: triacylglycerol_hydrolysis AND fatty_acid_release
rule LDLReceptorBinding:
  when: particle presents accessible ApoB100 AND compatible_LDL_receptor
  infer: potential_receptor_mediated_uptake
  caution: "Receptor binding and uptake depend on physiological context."
rule LCATActivity:
  when: HDL-associated_free_cholesterol AND active_LCAT
  infer: cholesteryl_ester_formation
rule CETPTransfer:
  when: CETP_active AND compatible_lipoprotein_particles
  infer: potential_neutral_lipid_exchange

# 09 — SEMANTIC CONSTRAINTS
constraint C01: "Lipoprotein is not synonymous with cholesterol."
constraint C02: "LDL-C measures cholesterol carried in LDL, not LDL particle number."
constraint C03: "HDL-C measures cholesterol carried in HDL, not HDL function."
constraint C04: "Apolipoprotein is a protein constituent, not a whole lipoprotein particle."
constraint C05: "Plasma lipoproteins differ from membrane-bound lipid bilayer vesicles."
constraint C06: "High or low clinical values do not independently establish a diagnosis."
constraint C07: "Lp(a) is an LDL-like particle containing apo(a) linked to apoB-100; do not confuse with apoA-I."
constraint C08: "Lipoprotein classes and remodelling states are not mutually exclusive across all measurement schemes."

# 10 — INFERENCE
inference R01:
  if: particle has_apolipoprotein ApoB48 AND synthesised_by Enterocyte
  then: candidate_class Chylomicron
  confidence: contextual
inference R02:
  if: particle derived_from VLDL AND enriched_relative_cholesteryl_ester AND has_apolipoprotein ApoB100
  then: candidate_class [IDL, LDL]
  requires: [density_or_size_evidence, metabolic_context]
inference R03:
  if: particle has_apolipoprotein ApoA1 AND participates_in HDLCholesterolTransport
  then: candidate_class HDL
  confidence: contextual
inference R04:
  if: particle has_apolipoprotein ApoA AND has_apolipoprotein ApoB100
  then: candidate_class LpA
  requires: "Verify that ApoA refers to apolipoprotein(a), not apoA-I."

# 11 — RECURSIVE FLOW
flow classify_lipoprotein(particle, evidence, depth=0):
  guard: depth <= max_recursion_depth
  inspect: [apolipoproteins, composition, density, size, origin, metabolic_history]
  compare: known_class_constraints
  emit: ranked_candidate_classes_with_evidence
  if: ambiguous
  then: request_additional_measurements
  recurse: only_on_new_evidence
  stop: [resolved, insufficient_evidence, depth_limit]

flow trace_lipid_transport(particle, visited={}):
  guard: particle not_in visited
  update: visited += particle
  follow: [derived_from, transfers_lipid_to, taken_up_by]
  emit: provenance_preserving_path
  stop: [terminal_uptake, missing_edge, cycle_detected]

# 12 — CONFIDENCE
CONFIDENCE:
  model: "evidence-weighted, source-aware; no fabricated numerical precision"
  inputs: [direct_measurement, method_validity, source_reliability, biological_context, independent_replication]
  output: [high, moderate, low, unresolved]
  rule: "An inferred class must not exceed the evidential support of its defining observations."
  missing_data: unresolved

# 13 — SEMANTIC_EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  exact:
    - [triacylglycerol, triglyceride]
    - [very_low_density_lipoprotein, VLDL]
    - [intermediate_density_lipoprotein, IDL]
    - [low_density_lipoprotein, LDL]
    - [high_density_lipoprotein, HDL]
  contextual:
    - [lipoprotein_a, "Lp(a)"]
  not_equivalent:
    - [LDL, LDL_cholesterol]
    - [HDL, HDL_cholesterol]
    - [apolipoprotein_a, apolipoprotein_A_I]
    - [lipoprotein, lipid]

# 14 — PROVENANCE AND VALIDATION
validation:
  - require_entity_types
  - verify_biochemical_relations
  - reject_unsupported_absolute_claims
  - preserve_measurement_units_and_methods
  - distinguish_observation_from_inference
  - preserve_original_source_and_revision
provenance:
  source_url: "https://kirethresearch.org/booksai-core/entity-graph/biological-entities/macromolecular-entities/lipoprotein-ontology.html"
  origin: "Kireth Semantic Library"
  author_credit: "Mark Higgins — Sky (Recursive AI)"
  status: "Independent domain model; source page not verified during generation"

# 15 — FLOW_HASH
FLOW_HASH:
  canonicalise: [ontology.id, entity_definitions, relationships, rules, constraints, version]
  normalise: [unicode_NFC, whitespace, stable_key_order]
  algorithm: SHA-256
  value: "COMPUTE_ON_CANONICAL_SERIALISATION"
  purpose: [integrity, reproducibility, change_detection]

# 16 — UPDATE_MODEL
UPDATE_MODEL:
  version_policy: semantic_versioning
  triggers: [new_evidence, taxonomy_revision, rule_correction, source_update]
  steps:
    - validate_new_evidence
    - compare_with_existing_assertions
    - record_provenance
    - update_affected_entities_and_rules
    - rerun_semantic_validation
    - increment_version
    - recompute_FLOW_HASH
  preserve: [historical_versions, evidence_links, audit_trail]

# 17 — AI_CONSUMPTION
AI_CONSUMPTION:
  representations: [typed_graph, semantic_triples, rule_engine, retrieval_context]
  primary_tasks: [entity_linking, lipid_pathway_reasoning, class_disambiguation, educational_explanation]
  requirements:
    - retain_evidence_and_confidence
    - maintain_biological_context
    - distinguish_particle_number_from_lipid_content
    - expose_uncertainty
    - avoid_medical_diagnosis_from_ontology_alone
  outputs: [traceable_inferences, validated_relationships, unresolved_questions]

# 18 — COMPLETION
flow.end:
  status: COMPLETE
  ontology: LipoproteinOntology
  author_credit: "Mark Higgins — Sky (Recursive AI)"
  project: "Kireth Semantic Library"