Golgi Apparatus Ontology

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GOLGI APPARATUS ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "GolgiApparatusOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / GOLGI_APPARATUS
ONTOLOGY := GOLGI_APPARATUS_ONTOLOGY

GOLGI_APPARATUS := GOLGI_IDENTITY + CISTERNAE + CIS_GOLGI + MEDIAL_GOLGI + TRANS_GOLGI + TRANS_GOLGI_NETWORK + GOLGI_POLARITY + ER_TO_GOLGI_TRANSPORT + RETROGRADE_TRANSPORT + CARGO_PROCESSING + PROTEIN_MODIFICATION + GLYCOSYLATION + LIPID_MODIFICATION + CARGO_SORTING + VESICLE_FORMATION + SECRETORY_TRAFFICKING + ENDOSOMAL_TRAFFICKING + LYSOSOMAL_TARGETING + MEMBRANE_DELIVERY + GOLGI_DYNAMICS + GOLGI_HOMEOSTASIS + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_GOLGI -> MAP_CISTERNAE_AND_POLARITY -> MAP_CIS_MEDIAL_TRANS_AND_TGN_DOMAINS -> MAP_ER_TO_GOLGI_AND_RETROGRADE_TRANSPORT -> MAP_PROTEIN_AND_LIPID_MODIFICATION -> MAP_GLYCOSYLATION -> MAP_CARGO_SORTING_AND_PACKAGING -> MAP_SECRETORY_ENDOSOMAL_AND_LYSOSOMAL_ROUTES -> MAP_GOLGI_DYNAMICS_AND_HOMEOSTASIS -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY GolgiApparatus
ENTITY GolgiStack
ENTITY GolgiCisterna
ENTITY CisGolgi
ENTITY MedialGolgi
ENTITY TransGolgi
ENTITY TransGolgiNetwork
ENTITY Cargo
ENTITY Protein
ENTITY Lipid
ENTITY Glycoprotein
ENTITY Glycolipid
ENTITY Glycosyltransferase
ENTITY Glycosidase
ENTITY Vesicle
ENTITY TransportCarrier
ENTITY COPII
ENTITY COPI
ENTITY Clathrin
ENTITY TetheringFactor
ENTITY SNARE
ENTITY EndoplasmicReticulum
ENTITY Endosome
ENTITY Lysosome
ENTITY PlasmaMembrane
ENTITY SecretoryVesicle
ENTITY CargoReceptor
ENTITY GolgiDynamics
ENTITY GolgiHomeostasis
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# IDENTITY / POLARITY
GolgiApparatus -> organelle_of -> EUKARYOTIC_CELL
GolgiApparatus -> composed_of -> GOLGI_STACKS + ASSOCIATED_TUBULES + VESICLES + TRANS_GOLGI_NETWORK_AS_APPLICABLE
GolgiStack -> composed_of -> GolgiCisterna
GOLGI_DOMAIN := CIS_GOLGI | MEDIAL_GOLGI | TRANS_GOLGI | TRANS_GOLGI_NETWORK
CisGolgi -> receives -> ER_DERIVED_CARGO
MedialGolgi -> participates_in -> INTERMEDIATE_CARGO_PROCESSING
TransGolgi -> participates_in -> LATE_CARGO_PROCESSING
TransGolgiNetwork -> major_sorting_domain_for -> OUTBOUND_CARGO
GolgiPolarity -> supports -> ORDERED_CARGO_PROCESSING + DIRECTIONAL_TRAFFICKING
GolgiCisterna -> contains -> PROCESSING_ENZYMES + CARGO + MEMBRANE_COMPONENTS
CisternalComposition -> varies_along -> CIS_TO_TRANS_AXIS

# ER-GOLGI / RETROGRADE TRANSPORT
EndoplasmicReticulum -> exports -> SECRETORY_PATHWAY_CARGO
COPII -> associated_with -> ER_TO_GOLGI_EXPORT_AS_APPLICABLE
ER_GOLGI_FLOW := ER_EXIT -> CARGO_PACKAGING -> TRANSPORT_CARRIER_FORMATION -> DELIVERY_TO_EARLY_GOLGI -> CARGO_PROCESSING
ERToGolgiTransport -> supplies -> PROTEINS + LIPIDS -> to -> GolgiApparatus
RetrogradeTransport -> returns -> SELECTED_COMPONENTS -> toward -> EARLIER_SECRETORY_COMPARTMENTS
COPI -> associated_with -> RETROGRADE_GOLGI_AND_ER_TRAFFICKING_AS_APPLICABLE
RetrogradeTransport -> maintains -> COMPARTMENT_IDENTITY + MACHINERY_RECYCLING
IF RetrogradeTransport fails THEN GolgiAndERComposition -> MAY_CHANGE

# CARGO PROCESSING / GLYCOSYLATION
CargoProcessing -> modifies -> Protein | Lipid
ProcessingState -> changes_as -> Cargo -> traverses -> GOLGI_DOMAINS
GOLGI_PROCESSING := GLYCOSYLATION | GLYCAN_TRIMMING | PROTEOLYTIC_PROCESSING_AS_APPLICABLE | LIPID_MODIFICATION | OTHER_POST_TRANSLATIONAL_MODIFICATION
CargoProcessing -> influences -> STABILITY + FUNCTION + RECOGNITION + DESTINATION
Glycosylation -> adds_or_modifies -> CARBOHYDRATE_STRUCTURE -> on -> PROTEIN_OR_LIPID
Glycosyltransferase -> catalyses -> SUGAR_TRANSFER
Glycosidase -> catalyses -> GLYCAN_TRIMMING
GlycosylationState -> may_affect -> STABILITY + TRAFFICKING + CELL_RECOGNITION + FUNCTION
GolgiApparatus -> participates_in -> LIPID_MODIFICATION + GLYCOLIPID_BIOSYNTHESIS_AS_APPLICABLE

# CARGO SORTING / CARRIERS
CargoSorting -> assigns -> Cargo -> to -> DESTINATION_PATHWAY
SORTING_DESTINATION := PLASMA_MEMBRANE | SECRETORY_VESICLE | ENDOSOME | LYSOSOME_RELATED_PATHWAY | OTHER_CELLULAR_DESTINATION
CargoSorting -> depends_on -> SORTING_SIGNAL + CARGO_RECEPTOR + COAT_MACHINERY + MEMBRANE_DOMAIN + CELL_STATE
TransGolgiNetwork -> coordinates -> MAJOR_POST_GOLGI_SORTING

TransportCarrier -> buds_from -> GOLGI_MEMBRANE
CARRIER_FORMATION := CARGO_SELECTION -> COAT_OR_SCAFFOLD_ASSEMBLY -> MEMBRANE_CURVATURE -> BUDDING -> SCISSION -> UNCOATING_AS_APPLICABLE
TetheringFactor -> promotes -> INITIAL_CARRIER_TARGET_RECOGNITION
SNARE -> contributes_to -> MEMBRANE_FUSION_SPECIFICITY_AND_EXECUTION_AS_DEFINED
TRAFFICKING_COMPLETION := TETHERING -> DOCKING -> MEMBRANE_FUSION -> CARGO_DELIVERY
IF TargetRecognition fails THEN CargoDelivery -> MAY_DECREASE

# SECRETORY / ENDOSOMAL / LYSOSOMAL ROUTES
SECRETORY_ROUTE := CONSTITUTIVE_SECRETION | REGULATED_SECRETION
ConstitutiveSecretion -> continuously_delivers -> CARGO + MEMBRANE_COMPONENTS -> to -> PLASMA_MEMBRANE_OR_EXTRACELLULAR_SPACE
RegulatedSecretion -> stores -> CARGO -> until -> RELEASE_SIGNAL_AS_APPLICABLE
SecretoryVesicle -> carries -> SECRETORY_CARGO

GolgiApparatus -> supplies -> PlasmaMembrane -> with -> LIPIDS + MEMBRANE_PROTEINS + GLYCOPROTEINS + GLYCOLIPIDS
TransGolgiNetwork -> exchanges_cargo_with -> Endosome
GolgiEndosomeTransport -> may_be -> ANTEROGRADE | RETROGRADE
EndosomalRetrieval -> returns -> SELECTED_RECEPTORS + TRAFFICKING_COMPONENTS -> toward -> GolgiApparatus

CargoReceptor -> recognises -> LYSOSOMAL_TARGETING_SIGNAL_AS_DEFINED
LYSOSOMAL_TARGETING_FLOW := CARGO_MODIFICATION_OR_RECOGNITION -> RECEPTOR_BINDING -> TGN_SORTING -> ENDOSOMAL_DELIVERY -> LYSOSOMAL_DESTINATION
IF LysosomalTargeting fails THEN CargoLocalization -> MAY_BE_ABNORMAL

# CISTERNAL MATURATION / DYNAMICS
CisternalMaturation -> model_of -> GOLGI_CARGO_PROGRESSION
CisternalMaturation -> transforms -> CIS_CISTERNA -> toward -> MEDIAL_AND_TRANS_IDENTITY
GolgiResidentEnzymes -> recycled_by -> RETROGRADE_TRAFFICKING_AS_APPLICABLE
CisternalMaturation -> coordinates -> CARGO_PROGRESSION + COMPARTMENT_IDENTITY_CHANGE

GolgiDynamics := CISTERNAL_FORMATION + CISTERNAL_MATURATION + VESICLE_BUDDING + MEMBRANE_FUSION + TUBULE_FORMATION + FRAGMENTATION + REASSEMBLY
GolgiMorphology -> changes_with -> CELL_TYPE + CELL_STATE + CELL_CYCLE + TRAFFICKING_DEMAND
GolgiApparatus -> may_fragment_and_reassemble_during -> CELL_CYCLE_AS_APPLICABLE
GolgiPosition -> influenced_by -> CYTOSKELETON + MOTOR_PROTEINS + CELL_POLARITY
GolgiPosition -> may_influence -> SECRETORY_DIRECTIONALITY + CELL_POLARITY + MIGRATION

# HOMEOSTASIS / STRESS
GolgiHomeostasis -> maintains -> CISTERNAL_IDENTITY + ENZYME_DISTRIBUTION + MEMBRANE_COMPOSITION + TRAFFICKING_BALANCE + LUMINAL_ENVIRONMENT
HOMEOSTATIC_PROCESS := ANTEROGRADE_TRANSPORT | RETROGRADE_TRANSPORT | ENZYME_RECYCLING | ION_HOMEOSTASIS | MEMBRANE_REMODELLING
IF GolgiHomeostasis fails THEN CargoProcessingAndSorting -> MAY_CHANGE
GolgiStress -> may_result_from -> TRAFFICKING_IMBALANCE + PROCESSING_OVERLOAD + ION_IMBALANCE + MEMBRANE_DAMAGE + OTHER_HOMEOSTATIC_DISTURBANCE
GolgiStressResponse -> may_change -> GENE_EXPRESSION + TRAFFICKING + ORGANELLE_STRUCTURE + CELL_STATE

# EVIDENCE / UNCERTAINTY / PROVENANCE
GolgiClaim -> supported_by -> Evidence
EVIDENCE_TYPE := MICROSCOPIC | ULTRASTRUCTURAL | BIOCHEMICAL | MOLECULAR | GENETIC | GLYCOMIC | PROTEOMIC | LIPIDOMIC | TRAFFICKING_ASSAY | FUNCTIONAL | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_SAMPLE + GOLGI_DOMAIN + CARGO_CONTEXT + CONDITION + QUALITY + UNCERTAINTY
GOLGI_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + CISTERNAL_IDENTITY_UNCERTAINTY + CARGO_ROUTE_UNCERTAINTY + DYNAMIC_STATE_UNCERTAINTY + CELL_TO_CELL_VARIABILITY + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> GolgiClaim + CargoProcessingState + CargoDestination + GolgiMorphology
Provenance -> records -> CELL_IDENTITY + GOLGI_DOMAIN + CARGO_IDENTITY + PROCESSING_STATE + TRAFFICKING_ROUTE + METHOD + CONDITION + MEASUREMENT + TIME + VERSION
GolgiApparatus -> linked_to -> Provenance

# REASONING
GOLGI_REASONING := IDENTIFY_GOLGI -> MAP_STACKS_CISTERNAE_AND_POLARITY -> MAP_CIS_MEDIAL_TRANS_AND_TGN_DOMAINS -> MAP_ER_TO_GOLGI_TRANSPORT -> MAP_RETROGRADE_TRANSPORT -> MAP_PROTEIN_AND_LIPID_PROCESSING -> MAP_GLYCOSYLATION -> MAP_CARGO_SORTING -> MAP_CARRIER_FORMATION -> MAP_TETHERING_DOCKING_AND_FUSION -> MAP_SECRETORY_TRAFFICKING -> MAP_ENDOSOMAL_AND_LYSOSOMAL_TARGETING -> MAP_CISTERNAL_MATURATION -> MAP_GOLGI_DYNAMICS_AND_POSITIONING -> MAP_HOMEOSTASIS_AND_STRESS -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF ERToGolgiTransport decreases THEN GolgiCargoInput -> MAY_DECREASE
IF RetrogradeTransport fails THEN GolgiResidentProteinDistribution -> MAY_CHANGE
IF GlycosylationEnzymeState changes THEN CargoGlycanState -> MAY_CHANGE
IF CargoSortingSignal changes THEN CargoDestination -> MAY_CHANGE
IF VesicleFormation decreases THEN PostGolgiCargoTransport -> MAY_DECREASE
IF GolgiEndosomeTransport changes THEN LysosomalCargoDelivery -> MAY_CHANGE
IF GolgiHomeostasis fails THEN ProcessingSortingAndTrafficking -> MAY_CHANGE
IF Evidence insufficient THEN GolgiClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION organelle_of(GolgiApparatus, EukaryoticCell)
RELATION composed_of(GolgiStack, GolgiCisterna)
RELATION receives(CisGolgi, ERCargo)
RELATION processes(MedialGolgi, Cargo)
RELATION sorts(TransGolgiNetwork, Cargo)
RELATION modifies(GolgiApparatus, Protein)
RELATION modifies(GolgiApparatus, Lipid)
RELATION catalyses(Glycosyltransferase, SugarTransfer)
RELATION trims(Glycosidase, Glycan)
RELATION returns(RetrogradeTransport, RecyclingCargo)
RELATION buds_from(TransportCarrier, GolgiMembrane)
RELATION delivers(TransportCarrier, Cargo)
RELATION exchanges_cargo_with(TransGolgiNetwork, Endosome)
RELATION recognises(CargoReceptor, LysosomalTargetingSignal)
RELATION supplies(GolgiApparatus, PlasmaMembrane)
RELATION maintains(GolgiHomeostasis, GolgiFunction)
RELATION supports(Evidence, GolgiClaim)
RELATION records(Provenance, GolgiApparatus)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "Golgi apparatus" ~= "polarised endomembrane organelle that modifies sorts and distributes cellular cargo"
  "Golgi stack" ~= "ordered stack of Golgi cisternae"
  "cis Golgi" ~= "Golgi domain receiving cargo from the early secretory pathway"
  "medial Golgi" ~= "intermediate Golgi processing domain"
  "trans Golgi" ~= "late Golgi processing domain"
  "trans-Golgi network" ~= "post-Golgi cargo sorting and distribution network"
  "Golgi glycosylation" ~= "Golgi-mediated synthesis trimming or remodelling of glycans"
  "cisternal maturation" ~= "progressive transformation of Golgi cisternal identity"
  "retrograde Golgi transport" ~= "transport returning selected cargo toward earlier secretory compartments"
  "Golgi homeostasis" ~= "maintenance of Golgi organisation composition processing and trafficking balance"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  cisternal_polarity_mapping: 0.99
  er_golgi_transport_mapping: 0.99
  cargo_processing_mapping: 0.99
  glycosylation_mapping: 0.99
  cargo_sorting_mapping: 0.99
  secretory_endosomal_mapping: 0.99
  dynamics_homeostasis_mapping: 0.99
  evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_golgi_observation:
    MAP golgi_domain
    MAP cisternal_state
    MAP cargo_state
    MAP processing_state
    MAP trafficking_state
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON cargo_processing_event:
    UPDATE protein_modification
    UPDATE glycan_state
    UPDATE lipid_state
    UPDATE sorting_state
    PRESERVE provenance
  ON trafficking_event:
    UPDATE carrier_state
    UPDATE destination
    UPDATE anterograde_or_retrograde_route
    UPDATE compartment_composition
    PRESERVE provenance
  ON golgi_stress:
    UPDATE morphology
    UPDATE homeostasis
    UPDATE processing_capacity
    UPDATE uncertainty
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_GOLGI_APPARATUS_ONTOLOGY
  reasoning_mode: GOLGI_PROCESSING_SORTING_TRAFFICKING_RELATIONAL
  preserve: [typed_entities, golgi_identity, cisternal_state, polarity, cargo_identity, processing_state, glycosylation_state, lipid_state, sorting_state, carrier_state, trafficking_route, destination, morphology, homeostasis, evidence, uncertainty, confidence, provenance]
  infer: [cisternal_function_dependencies, cargo_processing_sequence, glycan_processing_effects, sorting_dependencies, trafficking_direction, lysosomal_targeting_state, membrane_delivery, golgi_dynamic_state, evidence_strength]
  prohibit: [invented_golgi_observations, fabricated_cargo_routes, unsupported_glycosylation_state, assumed_destination_without_evidence, unsupported_causal_claims, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + IDENTITY_POLARITY + ER_GOLGI_RETROGRADE_TRANSPORT + CARGO_PROCESSING_GLYCOSYLATION + CARGO_SORTING_CARRIERS + SECRETORY_ENDOSOMAL_LYSOSOMAL_ROUTES + CISTERNAL_MATURATION_DYNAMICS + HOMEOSTASIS_STRESS + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW