Cell Membrane Ontology

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CELL MEMBRANE ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/cell-biology/cell-membrane-ontology.html

FLOW "CellMembraneOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / CELL_MEMBRANE
ONTOLOGY := CELL_MEMBRANE_ONTOLOGY

CELL_MEMBRANE := MEMBRANE_IDENTITY + LIPID_BILAYER + MEMBRANE_LIPIDS + MEMBRANE_PROTEINS + GLYCOCALYX + FLUIDITY + ASYMMETRY + PERMEABILITY + CHANNELS + TRANSPORTERS + PUMPS + ELECTROCHEMICAL_GRADIENTS + MEMBRANE_POTENTIAL + RECEPTORS + SIGNALING + ADHESION + ENDOCYTOSIS + EXOCYTOSIS + VESICULAR_TRAFFICKING + MEMBRANE_DOMAINS + MEMBRANE_DYNAMICS + HOMEOSTASIS + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_MEMBRANE -> MAP_LIPID_AND_PROTEIN_COMPOSITION -> MAP_BILAYER_ORGANISATION -> MAP_FLUIDITY_ASYMMETRY_AND_DOMAINS -> MAP_SELECTIVE_PERMEABILITY -> MAP_CHANNELS_TRANSPORTERS_AND_PUMPS -> MAP_ELECTROCHEMICAL_GRADIENTS -> MAP_RECEPTORS_AND_SIGNALING -> MAP_ADHESION -> MAP_ENDOCYTOSIS_EXOCYTOSIS_AND_TRAFFICKING -> MAP_MEMBRANE_DYNAMICS -> ASSESS_HOMEOSTATIC_FUNCTION -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY CellMembrane
ENTITY PlasmaMembrane
ENTITY LipidBilayer
ENTITY Phospholipid
ENTITY Sterol
ENTITY Glycolipid
ENTITY MembraneProtein
ENTITY IntegralMembraneProtein
ENTITY PeripheralMembraneProtein
ENTITY TransmembraneProtein
ENTITY Channel
ENTITY IonChannel
ENTITY Transporter
ENTITY Carrier
ENTITY Pump
ENTITY Receptor
ENTITY Glycoprotein
ENTITY Glycocalyx
ENTITY MembraneDomain
ENTITY Cytoskeleton
ENTITY ElectrochemicalGradient
ENTITY MembranePotential
ENTITY PassiveTransport
ENTITY ActiveTransport
ENTITY Endocytosis
ENTITY Exocytosis
ENTITY Vesicle
ENTITY MembraneFusion
ENTITY MembraneCurvature
ENTITY CellAdhesion
ENTITY Signal
ENTITY Homeostasis
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# STRUCTURE / COMPOSITION
CellMembrane -> boundary_of -> Cell
PlasmaMembrane -> subtype_of -> CellMembrane
CellMembrane -> separates -> INTRACELLULAR_ENVIRONMENT + EXTRACELLULAR_ENVIRONMENT
MEMBRANE_FUNCTION := SELECTIVE_BARRIER | MATERIAL_TRANSPORT | SIGNAL_RECEPTION | CELL_ADHESION | ELECTROCHEMICAL_GRADIENT_MAINTENANCE | VESICULAR_EXCHANGE

LipidBilayer -> structural_basis_of -> CellMembrane
LipidBilayer -> composed_of -> AMPHIPATHIC_LIPIDS
Phospholipid -> has -> HYDROPHILIC_HEAD + HYDROPHOBIC_TAILS
MEMBRANE_LIPID := PHOSPHOLIPID | STEROL | GLYCOLIPID | OTHER_MEMBRANE_LIPID
MembraneLipidComposition -> influences -> FLUIDITY + THICKNESS + CURVATURE + PROTEIN_FUNCTION + PERMEABILITY
Sterol -> may_modulate -> MEMBRANE_FLUIDITY + MEMBRANE_ORDER

MembraneAsymmetry -> represents -> UNEQUAL_DISTRIBUTION_OF_COMPONENTS_BETWEEN_LEAFLETS
MembraneAsymmetry -> may_affect -> SIGNALING + CURVATURE + PROTEIN_LOCALISATION + CELL_RECOGNITION
MembraneFluidity -> influenced_by -> TEMPERATURE + LIPID_COMPOSITION + FATTY_ACID_SATURATION + STEROL_CONTENT
IF MembraneFluidity changes THEN MembraneProteinFunction -> MAY_CHANGE

MEMBRANE_PROTEIN_TYPE := INTEGRAL | TRANSMEMBRANE | PERIPHERAL | LIPID_ANCHORED
MembraneProtein -> may_function_as -> CHANNEL | TRANSPORTER | PUMP | RECEPTOR | ENZYME | ADHESION_MOLECULE | STRUCTURAL_ANCHOR
Glycocalyx -> formed_by -> MEMBRANE_ASSOCIATED_CARBOHYDRATES
Glycocalyx -> may_support -> PROTECTION + CELL_RECOGNITION + ADHESION + SIGNALING

# PERMEABILITY / TRANSPORT / GRADIENTS
SelectivePermeability -> controls -> SUBSTANCE_MOVEMENT -> across -> CellMembrane
Permeability -> depends_on -> MOLECULE_SIZE + CHARGE + POLARITY + LIPID_SOLUBILITY + TRANSPORT_PROTEINS

PASSIVE_TRANSPORT_TYPE := SIMPLE_DIFFUSION | FACILITATED_DIFFUSION | OSMOSIS
PassiveTransport -> moves -> SUBSTANCE -> down -> ELECTROCHEMICAL_OR_CONCENTRATION_GRADIENT
PassiveTransport -> does_not_directly_require -> METABOLIC_ENERGY_INPUT

Channel -> provides -> HYDROPHILIC_PATHWAY -> across -> MEMBRANE
IonChannel -> selectively_conducts -> ION
CHANNEL_GATING := VOLTAGE_GATED | LIGAND_GATED | MECHANICALLY_GATED | OTHER_REGULATED_GATING
IonFlux -> influences -> MEMBRANE_POTENTIAL + CELL_SIGNALING

Transporter -> binds_and_moves -> SUBSTRATE -> across -> MEMBRANE
TRANSPORT_MODE := UNIPORT | SYMPORT | ANTIPORT
CarrierTransport -> involves -> CONFORMATIONAL_CHANGE

ActiveTransport -> moves -> SUBSTANCE -> against -> ELECTROCHEMICAL_OR_CONCENTRATION_GRADIENT
ACTIVE_TRANSPORT := PRIMARY_ACTIVE_TRANSPORT | SECONDARY_ACTIVE_TRANSPORT
PrimaryActiveTransport -> couples -> DIRECT_ENERGY_SOURCE -> TRANSPORT
SecondaryActiveTransport -> couples -> STORED_ELECTROCHEMICAL_GRADIENT -> TRANSPORT
Pump -> subtype_of -> ACTIVE_TRANSPORTER

ElectrochemicalGradient := CHEMICAL_GRADIENT + ELECTRICAL_GRADIENT
ElectrochemicalGradient -> drives -> ION_MOVEMENT + SECONDARY_TRANSPORT + CELLULAR_WORK
GradientMaintenance -> depends_on -> SELECTIVE_PERMEABILITY + ACTIVE_TRANSPORT + CELLULAR_ENERGY
IF Gradient dissipates THEN GradientDependentFunction -> MAY_DECREASE

MembranePotential -> represents -> ELECTRICAL_POTENTIAL_DIFFERENCE -> across -> CellMembrane
MembranePotential -> depends_on -> ION_GRADIENTS + RELATIVE_MEMBRANE_PERMEABILITIES + ELECTROGENIC_TRANSPORT
MembranePotential -> influences -> ION_TRANSPORT + EXCITABILITY + SIGNALING

# RECEPTORS / SIGNALING / ADHESION
Receptor -> membrane_protein_that -> DETECTS_OR_BINDS_SIGNAL_AS_DEFINED
Signal -> binds_or_activates -> Receptor
ReceptorActivation -> changes -> INTRACELLULAR_SIGNALING_STATE
RECEPTOR_TYPE := ION_CHANNEL_LINKED | ENZYME_LINKED | G_PROTEIN_COUPLED | OTHER_MEMBRANE_RECEPTOR

MEMBRANE_SIGNALING_FLOW := EXTRACELLULAR_SIGNAL -> RECEPTOR -> CONFORMATIONAL_OR_ACTIVITY_CHANGE -> INTRACELLULAR_TRANSDUCTION -> EFFECTOR -> CELLULAR_RESPONSE
SignalTransduction -> may_change -> GENE_EXPRESSION + METABOLISM + MOTILITY + SECRETION + DIVISION + SURVIVAL

CellAdhesion -> links -> CELL_CELL | CELL_EXTRACELLULAR_MATRIX
AdhesionMolecule -> embedded_in_or_associated_with -> CellMembrane
AdhesionComplex -> may_connect -> EXTRACELLULAR_PARTNER + MEMBRANE + CYTOSKELETON
CellAdhesion -> influences -> CELL_SHAPE + POLARITY + SIGNALING + MIGRATION + TISSUE_ORGANISATION

CellMembrane -> coupled_to -> Cytoskeleton
MembraneCytoskeletonCoupling -> influences -> CELL_SHAPE + MECHANICAL_STABILITY + MEMBRANE_DOMAIN_ORGANISATION + ENDOCYTOSIS + MIGRATION

# TRAFFICKING / DOMAINS / DYNAMICS
Endocytosis -> internalises -> MEMBRANE + EXTRACELLULAR_MATERIAL
ENDOCYTOSIS_TYPE := PHAGOCYTOSIS | PINOCYTOSIS | RECEPTOR_MEDIATED_ENDOCYTOSIS | OTHER_ENDOCYTIC_PATHWAY
ENDOCYTOSIS_FLOW := CARGO_OR_SIGNAL_SELECTION -> MEMBRANE_INVAGINATION -> VESICLE_FORMATION -> INTERNALISATION -> SORTING

Exocytosis -> fuses -> Vesicle -> with -> CellMembrane
Exocytosis -> releases -> CARGO -> to -> EXTRACELLULAR_ENVIRONMENT
Exocytosis -> delivers -> MEMBRANE_LIPIDS + MEMBRANE_PROTEINS
EXOCYTOSIS_TYPE := CONSTITUTIVE | REGULATED

MembraneFusion -> joins -> LIPID_BILAYERS
MembraneFusion -> enables -> EXOCYTOSIS + VESICLE_TARGETING + OTHER_FUSION_EVENTS

MembraneDomain -> region_of -> CellMembrane -> with -> DISTINCT_COMPOSITION_OR_FUNCTION
MembraneDomain -> may_organise -> SIGNALING + TRAFFICKING + ADHESION

MembraneCurvature -> influenced_by -> LIPID_COMPOSITION + PROTEIN_SCAFFOLDS + CYTOSKELETAL_FORCE + MEMBRANE_TENSION
Curvature -> contributes_to -> BUDDING + VESICLE_FORMATION + TUBULATION

MEMBRANE_DYNAMICS := LATERAL_DIFFUSION + DOMAIN_REORGANISATION + BUDDING + FUSION + ENDOCYTOSIS + EXOCYTOSIS + REMODELLING
MembraneRemodelling -> changes -> MEMBRANE_SHAPE + COMPOSITION + CONNECTIVITY

# HOMEOSTASIS / DAMAGE / EVIDENCE
MembraneHomeostasis -> maintains -> COMPOSITION + FLUIDITY + SURFACE_AREA + PERMEABILITY + GRADIENTS
HOMEOSTATIC_CONTROL := LIPID_SYNTHESIS + LIPID_REMOVAL + PROTEIN_TRAFFICKING + ENDOCYTOSIS + EXOCYTOSIS + ION_TRANSPORT
IF MembraneHomeostasis fails THEN CellFunction -> MAY_DECREASE

MembraneDamage -> disrupts -> BARRIER_FUNCTION
DAMAGE_SOURCE := MECHANICAL | CHEMICAL | OXIDATIVE | THERMAL | BIOLOGICAL
MembraneRepair -> restores -> BARRIER_INTEGRITY
REPAIR_FLOW := DAMAGE_DETECTION -> LOCAL_SIGNALING -> MEMBRANE_RECRUITMENT_OR_FUSION -> SEALING -> REMODELLING
IF Damage exceeds_repair_capacity THEN CellViability -> MAY_DECREASE

MembraneClaim -> supported_by -> Evidence
EVIDENCE_TYPE := STRUCTURAL | BIOCHEMICAL | BIOPHYSICAL | ELECTROPHYSIOLOGICAL | IMAGING | MOLECULAR | FUNCTIONAL | PERTURBATION | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_MEMBRANE_SAMPLE + CONDITION + QUALITY + UNCERTAINTY
MEMBRANE_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + COMPOSITIONAL_VARIABILITY + DYNAMIC_STATE_UNCERTAINTY + SPATIAL_RESOLUTION_LIMIT + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> MembraneClaim + Permeability + TransportRate + MembranePotential + DomainState

Provenance -> records -> MEMBRANE_IDENTITY + CELL_IDENTITY + COMPOSITION + METHOD + CONDITION + MEASUREMENT + OBSERVATION + TIME + VERSION
CellMembrane -> linked_to -> Provenance

# REASONING / INFERENCE RULES
CELL_MEMBRANE_REASONING := IDENTIFY_MEMBRANE -> MAP_LIPID_COMPOSITION -> MAP_PROTEIN_COMPOSITION -> MAP_BILAYER_ORGANISATION -> MAP_ASYMMETRY_AND_FLUIDITY -> MAP_PERMEABILITY -> MAP_CHANNELS_TRANSPORTERS_AND_PUMPS -> MAP_ELECTROCHEMICAL_GRADIENTS -> MAP_MEMBRANE_POTENTIAL -> MAP_RECEPTORS_AND_SIGNALING -> MAP_ADHESION_AND_CYTOSKELETAL_COUPLING -> MAP_ENDOCYTOSIS_AND_EXOCYTOSIS -> MAP_DOMAINS_CURVATURE_AND_DYNAMICS -> ASSESS_HOMEOSTASIS_AND_REPAIR -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

IF LipidComposition changes THEN MembraneFluidityAndPermeability -> MAY_CHANGE
IF ChannelOpenProbability changes THEN IonFlux -> MAY_CHANGE
IF PumpActivity decreases THEN ElectrochemicalGradient -> MAY_DECREASE
IF ElectrochemicalGradient changes THEN SecondaryTransport -> MAY_CHANGE
IF ReceptorState changes THEN IntracellularSignaling -> MAY_CHANGE
IF AdhesionComplex changes THEN CellShapeOrMigration -> MAY_CHANGE
IF EndocytosisOrExocytosis changes THEN MembraneComposition -> MAY_CHANGE
IF MembraneDamage exceeds_repair_capacity THEN CellViability -> MAY_DECREASE
IF Evidence insufficient THEN MembraneClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION boundary_of(CellMembrane, Cell)
RELATION structural_basis_of(LipidBilayer, CellMembrane)
RELATION composed_of(LipidBilayer, MembraneLipid)
RELATION embedded_in(IntegralMembraneProtein, LipidBilayer)
RELATION controls(SelectivePermeability, SubstanceMovement)
RELATION conducts(IonChannel, Ion)
RELATION transports(Transporter, Substrate)
RELATION drives(ElectrochemicalGradient, IonMovement)
RELATION represents(MembranePotential, ElectricalPotentialDifference)
RELATION detects(Receptor, Signal)
RELATION links(CellAdhesion, Cell)
RELATION internalises(Endocytosis, Material)
RELATION releases(Exocytosis, Cargo)
RELATION joins(MembraneFusion, LipidBilayer)
RELATION region_of(MembraneDomain, CellMembrane)
RELATION restores(MembraneRepair, BarrierIntegrity)
RELATION supports(Evidence, MembraneClaim)
RELATION records(Provenance, CellMembrane)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "cell membrane" ~= "plasma membrane"
  "lipid bilayer" ~= "two-layer amphipathic lipid membrane structure"
  "selective permeability" ~= "regulated differential passage across a membrane"
  "passive transport" ~= "transport down an electrochemical or concentration gradient"
  "active transport" ~= "energy-coupled transport against a gradient"
  "membrane potential" ~= "electrical potential difference across a membrane"
  "membrane receptor" ~= "membrane-associated signal-detecting protein"
  "endocytosis" ~= "membrane-mediated internalisation"
  "exocytosis" ~= "vesicle-mediated secretion or membrane delivery"
  "membrane homeostasis" ~= "maintenance of membrane composition properties and gradients"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  bilayer_composition_mapping: 0.99
  protein_transport_mapping: 0.99
  electrochemical_mapping: 0.99
  receptor_signaling_mapping: 0.99
  adhesion_mapping: 0.99
  trafficking_mapping: 0.99
  dynamics_homeostasis_mapping: 0.99
  evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_membrane_observation:
    MAP lipid_composition
    MAP protein_composition
    MAP permeability
    MAP membrane_potential
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON transport_change:
    UPDATE channel_state
    UPDATE transporter_state
    UPDATE electrochemical_gradients
    UPDATE membrane_potential
    PRESERVE provenance
  ON trafficking_event:
    UPDATE membrane_composition
    UPDATE surface_area
    UPDATE cargo_state
    PRESERVE provenance
  ON membrane_damage:
    UPDATE integrity_state
    UPDATE repair_state
    UPDATE homeostasis
    UPDATE uncertainty
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_CELL_MEMBRANE_ONTOLOGY
  reasoning_mode: MEMBRANE_STRUCTURE_TRANSPORT_SIGNALING_RELATIONAL
  preserve: [typed_entities, membrane_identity, lipid_composition, protein_composition, membrane_asymmetry, fluidity, permeability, channel_state, transporter_state, electrochemical_gradients, membrane_potential, receptor_state, adhesion_state, trafficking_state, evidence, uncertainty, confidence, provenance]
  infer: [composition_property_dependencies, permeability_dependencies, ion_flux_effects, gradient_dependencies, signaling_effects, adhesion_dependencies, trafficking_impacts, membrane_homeostasis, evidence_strength]
  prohibit: [invented_membrane_observations, unsupported_transport_direction, fabricated_receptor_activity, assumed_membrane_domain_without_evidence, unsupported_causality, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + STRUCTURE_COMPOSITION + PERMEABILITY_TRANSPORT_GRADIENTS + RECEPTORS_SIGNALING_ADHESION + TRAFFICKING_DOMAINS_DYNAMICS + HOMEOSTASIS_DAMAGE_EVIDENCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW