Mitochondrion Ontology

AI SEARCH FLOW ALGEBRA
MITOCHONDRION ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "MitochondrionOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / MITOCHONDRION
ONTOLOGY := MITOCHONDRION_ONTOLOGY

MITOCHONDRION := MITOCHONDRIAL_IDENTITY + OUTER_MEMBRANE + INTERMEMBRANE_SPACE + INNER_MEMBRANE + CRISTAE + MATRIX + MITOCHONDRIAL_GENOME + MITORIBOSOME + PROTEIN_IMPORT + RESPIRATORY_CHAIN + OXIDATIVE_PHOSPHORYLATION + PROTON_MOTIVE_FORCE + ATP_SYNTHESIS + CENTRAL_METABOLISM + METABOLITE_TRANSPORT + REDOX_STATE + CALCIUM_HOMEOSTASIS + SIGNALING + FUSION + FISSION + BIOGENESIS + QUALITY_CONTROL + MITOPHAGY + INHERITANCE + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_MITOCHONDRION -> MAP_MEMBRANES_CRISTAE_AND_MATRIX -> MAP_MITOCHONDRIAL_GENOME_AND_EXPRESSION -> MAP_PROTEIN_IMPORT -> MAP_RESPIRATORY_CHAIN_AND_PROTON_GRADIENT -> MAP_OXIDATIVE_PHOSPHORYLATION_AND_ATP_SYNTHESIS -> MAP_METABOLITE_TRANSPORT_AND_METABOLISM -> MAP_REDOX_CALCIUM_AND_SIGNALING -> MAP_FUSION_FISSION_AND_POSITIONING -> MAP_BIOGENESIS_QUALITY_CONTROL_AND_MITOPHAGY -> MAP_INHERITANCE -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Mitochondrion
ENTITY OuterMitochondrialMembrane
ENTITY IntermembraneSpace
ENTITY InnerMitochondrialMembrane
ENTITY Crista
ENTITY Matrix
ENTITY MitochondrialGenome
ENTITY MitochondrialDNA
ENTITY MitochondrialGene
ENTITY Mitoribosome
ENTITY ProteinImport
ENTITY RespiratoryChain
ENTITY ElectronTransportChain
ENTITY RespiratoryComplex
ENTITY ProtonGradient
ENTITY MembranePotential
ENTITY ProtonMotiveForce
ENTITY ATPSynthase
ENTITY ATP
ENTITY OxidativePhosphorylation
ENTITY MetaboliteTransporter
ENTITY MetabolicPathway
ENTITY RedoxState
ENTITY ReactiveOxygenSpecies
ENTITY Calcium
ENTITY MitochondrialFusion
ENTITY MitochondrialFission
ENTITY MitochondrialBiogenesis
ENTITY MitochondrialQualityControl
ENTITY Mitophagy
ENTITY MitochondrialInheritance
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# STRUCTURE / COMPARTMENTS
Mitochondrion -> organelle_of -> EUKARYOTIC_CELL
Mitochondrion -> enclosed_by -> OuterMitochondrialMembrane
Mitochondrion -> contains -> IntermembraneSpace + InnerMitochondrialMembrane + Matrix
InnerMitochondrialMembrane -> forms -> Cristae
Cristae -> increase -> INNER_MEMBRANE_SURFACE_AREA
MITOCHONDRIAL_COMPARTMENT := OUTER_MEMBRANE | INTERMEMBRANE_SPACE | INNER_MEMBRANE | CRISTAE | MATRIX
Compartmentalisation -> enables -> ELECTROCHEMICAL_GRADIENTS + METABOLIC_SPECIALISATION + CONTROLLED_TRANSPORT
OuterMitochondrialMembrane -> mediates -> EXCHANGE_WITH_CYTOSOL_AS_DEFINED
InnerMitochondrialMembrane -> contains -> RESPIRATORY_CHAIN_COMPONENTS + ATP_SYNTHASE + TRANSPORTERS
IF InnerMembraneIntegrity decreases THEN ProtonMotiveForce -> MAY_DECREASE

# GENOME / EXPRESSION / PROTEIN IMPORT
MitochondrialGenome -> composed_of -> MitochondrialDNA
MitochondrialGenome -> encodes -> SUBSET_OF_MITOCHONDRIAL_RNAS_AND_PROTEINS
MitochondrialFunction -> depends_on -> NUCLEAR_GENOME + MITOCHONDRIAL_GENOME_AS_APPLICABLE
MitochondrialDNAReplication -> copies -> MitochondrialDNA
MitochondrialTranscription -> produces -> MITOCHONDRIAL_RNA
Mitoribosome -> translates -> MITOCHONDRIAL_MRNA_AS_APPLICABLE
ProteinImport -> transports -> NUCLEAR_ENCODED_MITOCHONDRIAL_PROTEIN -> into -> MITOCHONDRION
TargetingSignal -> recognised_by -> MITOCHONDRIAL_IMPORT_MACHINERY
ProteinImport -> may_require -> MEMBRANE_POTENTIAL + ATP + CHAPERONES + TRANSLOCASES
IF ProteinImport fails THEN MitochondrialProteomeAndFunction -> MAY_CHANGE

# RESPIRATORY CHAIN / OXIDATIVE PHOSPHORYLATION
ElectronTransportChain -> located_in -> InnerMitochondrialMembrane
RespiratoryChain -> transfers -> ELECTRONS -> through -> RESPIRATORY_COMPONENTS
RESPIRATORY_FLOW := REDUCING_EQUIVALENT -> ELECTRON_TRANSFER -> PROTON_TRANSLOCATION -> ELECTROCHEMICAL_GRADIENT
ProtonGradient -> component_of -> ProtonMotiveForce
MembranePotential -> component_of -> ProtonMotiveForce
ProtonMotiveForce -> drives -> ATP_SYNTHESIS + TRANSPORT
ATPSynthase -> couples -> PROTON_FLOW -> ATP_SYNTHESIS
OxidativePhosphorylation := ELECTRON_TRANSPORT + PROTON_MOTIVE_FORCE + ATP_SYNTHESIS
ATP -> supports -> CELLULAR_ENERGY_REQUIRING_PROCESSES
IF ElectronTransport decreases THEN ProtonMotiveForceAndATPProduction -> MAY_DECREASE
IF MembranePotential collapses THEN GradientDependentMitochondrialFunctions -> MAY_DECREASE

# METABOLISM / TRANSPORT / REDOX / CALCIUM
Matrix -> contains -> ENZYMES + METABOLITES + MITOCHONDRIAL_GENETIC_MACHINERY_AS_APPLICABLE
MitochondrialMetabolism -> includes -> TRICARBOXYLIC_ACID_CYCLE_AS_APPLICABLE + FATTY_ACID_OXIDATION_AS_APPLICABLE + AMINO_ACID_METABOLISM_AS_APPLICABLE + OTHER_PATHWAYS
MetabolicPathway -> produces_or_consumes -> REDUCING_EQUIVALENTS + METABOLITES
MetaboliteTransporter -> exchanges -> METABOLITE -> across -> InnerMitochondrialMembrane
MetaboliteExchange -> connects -> MITOCHONDRIAL_METABOLISM + CYTOSOLIC_METABOLISM

RedoxState -> depends_on -> ELECTRON_DONORS + ELECTRON_ACCEPTORS + ANTIOXIDANT_SYSTEMS
ReactiveOxygenSpecies -> may_arise_from -> MITOCHONDRIAL_REDOX_REACTIONS
ReactiveOxygenSpecies -> may_function_in -> SIGNALING
ExcessReactiveOxygenSpecies -> may_increase -> OXIDATIVE_DAMAGE_RISK

Mitochondrion -> participates_in -> CALCIUM_HOMEOSTASIS
MitochondrialCalcium -> may_influence -> METABOLISM + SIGNALING + CELL_DEATH_PATHWAYS
CalciumTransport -> regulated_by -> MEMBRANE_TRANSPORT_SYSTEMS

# DYNAMICS / BIOGENESIS / QUALITY CONTROL
MitochondrialFusion -> joins -> MITOCHONDRIAL_COMPARTMENTS_OR_NETWORKS
MitochondrialFission -> divides -> MITOCHONDRION_OR_NETWORK
FusionFissionBalance -> influences -> MITOCHONDRIAL_MORPHOLOGY + CONTENT_DISTRIBUTION + QUALITY_CONTROL
MitochondrialPositioning -> depends_on -> CYTOSKELETON + MOTOR_PROTEINS + CELLULAR_DEMAND

MitochondrialBiogenesis -> increases_or_renews -> MITOCHONDRIAL_COMPONENTS
BIOGENESIS_INPUT := NUCLEAR_GENE_EXPRESSION + MITOCHONDRIAL_GENE_EXPRESSION + PROTEIN_IMPORT + MEMBRANE_LIPID_SYNTHESIS + ORGANELLE_GROWTH
NuclearMitochondrialCoordination -> regulates -> BIOGENESIS + METABOLISM + STRESS_RESPONSE

MitochondrialQualityControl -> detects_or_manages -> DAMAGED_PROTEINS + DAMAGED_MEMBRANES + DYSFUNCTIONAL_MITOCHONDRIA
QUALITY_CONTROL := PROTEOSTASIS + DNA_MAINTENANCE + FUSION_FISSION + MEMBRANE_REPAIR + SELECTIVE_MITOPHAGY
Mitophagy -> selective_autophagic_turnover_of -> MITOCHONDRIA
IF MitochondrialDamage exceeds_repair_capacity THEN MitophagyOrCellStressResponse -> MAY_INCREASE

MitochondrialInheritance -> distributes -> MITOCHONDRIA_AND_MTDNA -> to -> DAUGHTER_CELLS
Inheritance -> depends_on -> ORGANELLE_REPLICATION + POSITIONING + DYNAMICS + CELL_DIVISION

# SIGNALING / CELL STATE
Mitochondrion -> participates_in -> CELLULAR_SIGNALING
MITOCHONDRIAL_SIGNAL := ATP_OR_ENERGY_STATE | REDOX_SIGNAL | REACTIVE_OXYGEN_SPECIES | CALCIUM | METABOLITE | CELL_DEATH_SIGNAL
MitochondrialState -> may_change -> GENE_EXPRESSION + METABOLISM + STRESS_RESPONSE + CELL_FATE
MitochondrialOuterMembranePermeabilisation -> may_participate_in -> APOPTOTIC_SIGNALING_AS_APPLICABLE
MitochondrialDysfunction -> may_affect -> ENERGY_STATE + REDOX_HOMEOSTASIS + METABOLISM + CELL_SURVIVAL

# EVIDENCE / UNCERTAINTY / PROVENANCE
MitochondrionClaim -> supported_by -> Evidence
EVIDENCE_TYPE := MICROSCOPIC | ULTRASTRUCTURAL | BIOCHEMICAL | MOLECULAR | GENETIC | GENOMIC | PROTEOMIC | METABOLOMIC | BIOENERGETIC | FUNCTIONAL | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_SAMPLE + MITOCHONDRIAL_CONTEXT + CONDITION + QUALITY + UNCERTAINTY
MITOCHONDRIAL_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + HETEROGENEITY + MTDNA_HETEROPLASMY_AS_APPLICABLE + DYNAMIC_STATE_UNCERTAINTY + CELL_TO_CELL_VARIABILITY + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> MitochondrionClaim + BioenergeticState + GenomeState + Morphology + Function
Provenance -> records -> CELL_IDENTITY + MITOCHONDRIAL_IDENTITY + MTDNA_CONTEXT + MEMBRANE_STATE + METABOLIC_STATE + METHOD + CONDITION + MEASUREMENT + TIME + VERSION
Mitochondrion -> linked_to -> Provenance

# REASONING
MITOCHONDRION_REASONING := IDENTIFY_MITOCHONDRION -> MAP_OUTER_AND_INNER_MEMBRANES -> MAP_CRISTAE_AND_MATRIX -> MAP_MITOCHONDRIAL_GENOME -> MAP_GENE_EXPRESSION_AND_PROTEIN_IMPORT -> MAP_RESPIRATORY_CHAIN -> MAP_PROTON_MOTIVE_FORCE -> MAP_ATP_SYNTHESIS -> MAP_METABOLITE_TRANSPORT_AND_METABOLISM -> MAP_REDOX_AND_REACTIVE_OXYGEN_SPECIES -> MAP_CALCIUM_STATE -> MAP_SIGNALING -> MAP_FUSION_FISSION_AND_POSITIONING -> MAP_BIOGENESIS -> MAP_QUALITY_CONTROL_AND_MITOPHAGY -> MAP_INHERITANCE -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF InnerMembraneIntegrity decreases THEN ProtonMotiveForce -> MAY_DECREASE
IF RespiratoryChainActivity decreases THEN ATPProduction -> MAY_DECREASE
IF ProtonMotiveForce decreases THEN ATP_Synthase_DrivingForce -> MAY_DECREASE
IF ProteinImport fails THEN MitochondrialFunction -> MAY_CHANGE
IF MTDNAIntegrity decreases THEN MitochondrialGeneExpression -> MAY_CHANGE
IF FusionFissionBalance changes THEN MitochondrialMorphologyAndQualityControl -> MAY_CHANGE
IF ReactiveOxygenSpecies exceed_control_capacity THEN OxidativeDamageRisk -> MAY_INCREASE
IF MitochondrialCalcium changes THEN MetabolismOrSignaling -> MAY_CHANGE
IF Evidence insufficient THEN MitochondrionClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION organelle_of(Mitochondrion, EukaryoticCell)
RELATION encloses(OuterMitochondrialMembrane, Mitochondrion)
RELATION forms(InnerMitochondrialMembrane, Crista)
RELATION contains(Matrix, MitochondrialGenome)
RELATION translates(Mitoribosome, MitochondrialRNA)
RELATION imports(ProteinImport, MitochondrialProtein)
RELATION contains(InnerMitochondrialMembrane, RespiratoryChain)
RELATION generates(ElectronTransportChain, ProtonMotiveForce)
RELATION drives(ProtonMotiveForce, ATPSynthase)
RELATION synthesises(ATPSynthase, ATP)
RELATION exchanges(MetaboliteTransporter, Metabolite)
RELATION regulates(Mitochondrion, CalciumHomeostasis)
RELATION joins(MitochondrialFusion, Mitochondrion)
RELATION divides(MitochondrialFission, Mitochondrion)
RELATION creates(MitochondrialBiogenesis, MitochondrialComponent)
RELATION targets(Mitophagy, Mitochondrion)
RELATION distributes(MitochondrialInheritance, Mitochondrion)
RELATION supports(Evidence, MitochondrionClaim)
RELATION records(Provenance, Mitochondrion)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "mitochondrion" ~= "double-membrane eukaryotic organelle central to cellular bioenergetics and metabolism"
  "cristae" ~= "folds or specialised domains of the inner mitochondrial membrane"
  "mitochondrial matrix" ~= "innermost mitochondrial compartment enclosed by the inner membrane"
  "respiratory chain" ~= "mitochondrial electron-transfer system supporting proton translocation"
  "oxidative phosphorylation" ~= "ATP production coupled to respiratory electron transport and proton motive force"
  "proton motive force" ~= "electrochemical proton gradient across the inner mitochondrial membrane"
  "mitochondrial fusion" ~= "joining of mitochondrial membranes and compartments"
  "mitochondrial fission" ~= "division of mitochondria or mitochondrial networks"
  "mitophagy" ~= "selective autophagic turnover of mitochondria"
  "mitochondrial biogenesis" ~= "formation growth and renewal of mitochondrial components"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  structure_compartment_mapping: 0.99
  genome_expression_mapping: 0.99
  protein_import_mapping: 0.99
  respiratory_chain_mapping: 0.99
  oxidative_phosphorylation_mapping: 0.99
  metabolism_redox_mapping: 0.99
  dynamics_quality_control_mapping: 0.99
  evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_mitochondrial_observation:
    MAP membrane_state
    MAP cristae_state
    MAP genome_state
    MAP bioenergetic_state
    MAP metabolic_state
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON bioenergetic_change:
    UPDATE respiratory_chain_state
    UPDATE proton_motive_force
    UPDATE membrane_potential
    UPDATE ATP_synthesis
    PRESERVE provenance
  ON mitochondrial_dynamic_event:
    UPDATE fusion_state
    UPDATE fission_state
    UPDATE morphology
    UPDATE position
    PRESERVE provenance
  ON mitochondrial_damage:
    UPDATE quality_control_state
    UPDATE mitophagy_state
    UPDATE redox_state
    UPDATE uncertainty
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_MITOCHONDRION_ONTOLOGY
  reasoning_mode: MITOCHONDRIAL_BIOENERGETIC_RELATIONAL
  preserve: [typed_entities, mitochondrial_identity, membrane_state, cristae_state, matrix_state, mitochondrial_genome, protein_import_state, respiratory_chain_state, proton_motive_force, ATP_synthesis_state, metabolic_state, redox_state, calcium_state, fusion_fission_state, quality_control_state, mitophagy_state, inheritance_state, evidence, uncertainty, confidence, provenance]
  infer: [membrane_gradient_dependencies, respiratory_chain_effects, ATP_synthesis_dependencies, protein_import_dependencies, metabolic_exchange, redox_impacts, calcium_effects, mitochondrial_dynamics, quality_control_response, evidence_strength]
  prohibit: [invented_mitochondrial_observations, unsupported_respiratory_activity, fabricated_mtdna_state, assumed_ATP_output_without_evidence, unsupported_causal_claims, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + STRUCTURE_COMPARTMENTS + GENOME_EXPRESSION_IMPORT + RESPIRATORY_OXIDATIVE_PHOSPHORYLATION + METABOLISM_TRANSPORT_REDOX_CALCIUM + DYNAMICS_BIOGENESIS_QUALITY_CONTROL + SIGNALING_INHERITANCE + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW