Organelle Ontology

AI SEARCH FLOW ALGEBRA
ORGANELLE ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "OrganelleOntology" v4.0
DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / ORGANELLE
ONTOLOGY := ORGANELLE_ONTOLOGY

ORGANELLE := ORGANELLE_IDENTITY + ORGANELLE_TYPE + MEMBRANE_STATE + COMPARTMENT + COMPOSITION + STRUCTURE + FUNCTION + NUCLEUS + MITOCHONDRION + CHLOROPLAST + ENDOPLASMIC_RETICULUM + GOLGI_APPARATUS + LYSOSOME + PEROXISOME + ENDOSOME + VESICLE + VACUOLE + BIOGENESIS + PROTEIN_TARGETING + TRAFFICKING + ORGANELLE_CONTACTS + DYNAMICS + FUSION + FISSION + QUALITY_CONTROL + TURNOVER + INHERITANCE + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_ORGANELLE -> CLASSIFY_ORGANELLE_TYPE -> MAP_BOUNDARY_AND_COMPARTMENT -> MAP_COMPOSITION_AND_STRUCTURE -> MAP_ORGANELLE_FUNCTION -> MAP_BIOGENESIS_AND_PROTEIN_TARGETING -> MAP_TRAFFICKING_AND_CONTACT_SITES -> MAP_FUSION_FISSION_AND_POSITIONING -> MAP_QUALITY_CONTROL_AND_TURNOVER -> MAP_CELL_DIVISION_INHERITANCE -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Organelle
ENTITY OrganelleType
ENTITY OrganelleMembrane
ENTITY OrganelleCompartment
ENTITY Nucleus
ENTITY Mitochondrion
ENTITY Chloroplast
ENTITY EndoplasmicReticulum
ENTITY GolgiApparatus
ENTITY Lysosome
ENTITY Peroxisome
ENTITY Endosome
ENTITY Vesicle
ENTITY Vacuole
ENTITY Ribosome
ENTITY Centrosome
ENTITY Protein
ENTITY Lipid
ENTITY Metabolite
ENTITY Genome
ENTITY ProteinTargeting
ENTITY VesicularTrafficking
ENTITY OrganelleContactSite
ENTITY OrganelleBiogenesis
ENTITY OrganelleFusion
ENTITY OrganelleFission
ENTITY OrganellePositioning
ENTITY OrganelleQualityControl
ENTITY Autophagy
ENTITY Mitophagy
ENTITY OrganelleInheritance
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# IDENTITY / COMPARTMENTALISATION
Organelle -> part_of -> Cell
Organelle -> has -> OrganelleType + STRUCTURE + COMPOSITION + FUNCTION + CELLULAR_LOCATION
ORGANELLE_CLASS := MEMBRANE_BOUND | NON_MEMBRANE_BOUND_AS_DEFINED
MembraneBoundOrganelle -> enclosed_by -> ONE_OR_MORE_MEMBRANES
OrganelleIdentity -> depends_on -> STRUCTURE + MOLECULAR_MARKERS + FUNCTION + CELLULAR_CONTEXT

OrganelleCompartment -> creates -> DISTINCT_INTRACELLULAR_ENVIRONMENT
Compartment -> may_have -> SPECIFIC_PH + ION_COMPOSITION + REDOX_STATE + METABOLITE_COMPOSITION + ENZYME_SET
Compartmentalisation -> enables -> PROCESS_SPECIALISATION + SPATIAL_REGULATION + CHEMICAL_SEPARATION
IF OrganelleMembraneIntegrity decreases THEN CompartmentFunction -> MAY_CHANGE

OrganelleMembrane -> separates -> ORGANELLE_LUMEN_OR_MATRIX + SURROUNDING_CELLULAR_REGION
OrganelleMembrane -> regulates -> MATERIAL_EXCHANGE + SIGNALING + GRADIENTS

# MAJOR ORGANELLES
Nucleus -> contains -> NUCLEAR_GENOME + CHROMATIN + NUCLEOLUS
Nucleus -> supports -> GENOME_STORAGE + DNA_REPLICATION + TRANSCRIPTION + RNA_PROCESSING + GENE_REGULATION

Mitochondrion -> contains -> MATRIX + INNER_MEMBRANE + INTERMEMBRANE_SPACE + MITOCHONDRIAL_GENOME_AS_APPLICABLE
Mitochondrion -> participates_in -> ATP_PRODUCTION + CENTRAL_METABOLISM + REDOX_REGULATION + CELL_SIGNALING + CELL_DEATH_REGULATION
MITOCHONDRIAL_ENERGY_FLOW := REDUCING_EQUIVALENTS -> ELECTRON_TRANSPORT -> PROTON_GRADIENT -> ATP_SYNTHESIS

Chloroplast -> organelle_of -> PHOTOSYNTHETIC_EUKARYOTIC_CELL_AS_APPLICABLE
Chloroplast -> contains -> STROMA + THYLAKOID_SYSTEM + CHLOROPLAST_GENOME_AS_APPLICABLE
Chloroplast -> participates_in -> PHOTOSYNTHESIS + CARBON_FIXATION + BIOSYNTHESIS

EndoplasmicReticulum -> participates_in -> PROTEIN_SYNTHESIS + PROTEIN_FOLDING + LIPID_SYNTHESIS
GolgiApparatus -> modifies_and_sorts -> PROTEINS_AND_LIPIDS
Endosome -> participates_in -> ENDOCYTIC_TRAFFICKING
Lysosome -> participates_in -> DEGRADATION + RECYCLING
Peroxisome -> participates_in -> OXIDATIVE_METABOLISM + LIPID_METABOLISM
Vacuole -> may_support -> STORAGE + DEGRADATION + ION_HOMEOSTASIS + OSMOTIC_REGULATION
Ribosome -> performs -> TRANSLATION
Centrosome -> may_organise -> MICROTUBULES

# BIOGENESIS / TARGETING / TRAFFICKING
OrganelleBiogenesis -> creates_or_expands -> Organelle
BIOGENESIS_INPUT := PROTEINS + LIPIDS + NUCLEIC_ACIDS_AS_APPLICABLE + METABOLITES
OrganelleBiogenesis -> depends_on -> GENE_EXPRESSION + PROTEIN_TARGETING + MEMBRANE_SYNTHESIS + ASSEMBLY_PROCESSES

ProteinTargeting -> directs -> Protein -> to -> CORRECT_ORGANELLE_OR_COMPARTMENT
TargetingSignal -> recognised_by -> TARGETING_MACHINERY
PROTEIN_TARGET := NUCLEUS | MITOCHONDRION | CHLOROPLAST | ENDOPLASMIC_RETICULUM | PEROXISOME | OTHER_DESTINATION
IF TargetingSignalOrMachinery fails THEN ProteinLocalization -> MAY_BE_ABNORMAL

OrganelleProteinImport -> moves -> Protein -> across -> ORGANELLE_MEMBRANE
ProteinImport -> may_require -> RECEPTOR + TRANSLOCON + ENERGY + TARGETING_SIGNAL

Vesicle -> membrane_bound_carrier_of -> CARGO
VESICLE_FLOW := CARGO_SELECTION -> BUDDING -> TRANSPORT -> TETHERING -> DOCKING -> FUSION
VesicularTrafficking -> maintains -> ORGANELLE_COMPOSITION + CARGO_DISTRIBUTION

LipidTransport -> occurs_via -> VESICULAR_TRAFFICKING | LIPID_TRANSFER_PROTEIN | MEMBRANE_CONTACT_SITE | OTHER_MECHANISM

# CONTACTS / POSITIONING / DYNAMICS
OrganelleContactSite -> region_of_close_apposition_between -> ORGANELLE_MEMBRANES
ContactSite -> may_enable -> LIPID_TRANSFER + ION_TRANSFER + METABOLITE_TRANSFER + SIGNALING + ORGANELLE_DYNAMICS
ContactSite -> does_not_require -> MEMBRANE_FUSION

OrganellePositioning -> determines -> SPATIAL_DISTRIBUTION_OF_ORGANELLES
Positioning -> depends_on -> CYTOSKELETON + MOTOR_PROTEINS + TETHERING_FACTORS + CELL_POLARITY
OrganellePosition -> influences -> LOCAL_METABOLISM + SIGNALING + TRANSPORT_EFFICIENCY

OrganelleFusion -> joins -> ORGANELLE_MEMBRANES_OR_COMPARTMENTS
Fusion -> may_change -> ORGANELLE_SIZE + CONTENT + CONNECTIVITY
OrganelleFission -> divides -> ORGANELLE -> into -> MULTIPLE_ORGANELLE_UNITS
Fission -> may_support -> ORGANELLE_NUMBER_CONTROL + DISTRIBUTION + CELL_DIVISION_INHERITANCE
FusionFissionBalance -> influences -> ORGANELLE_MORPHOLOGY

ORGANELLE_DYNAMICS := MOVEMENT + FUSION + FISSION + GROWTH + REMODELLING + TURNOVER
OrganelleMorphology -> changes_with -> FUNCTION + CELL_STATE + STRESS + CELL_CYCLE

# COMMUNICATION / QUALITY CONTROL / INHERITANCE
OrganelleCommunication -> coordinates -> CELLULAR_FUNCTION
COMMUNICATION_MODE := VESICULAR_TRAFFICKING | CONTACT_SITE_TRANSFER | METABOLITE_EXCHANGE | ION_SIGNALING | PROTEIN_SIGNALING
CrossOrganelleCommunication -> contributes_to -> CELLULAR_HOMEOSTASIS

OrganelleQualityControl -> detects_or_manages -> DAMAGED_OR_DYSFUNCTIONAL_ORGANELLE
QUALITY_CONTROL := PROTEIN_QUALITY_CONTROL | MEMBRANE_REPAIR | SELECTIVE_COMPONENT_REMOVAL | ORGANELLE_FUSION_FISSION | SELECTIVE_AUTOPHAGY
IF OrganelleDamage exceeds_repair_capacity THEN OrganelleTurnover -> MAY_INCREASE

Autophagy -> delivers -> CELLULAR_COMPONENT -> to -> DEGRADATIVE_COMPARTMENT
SelectiveAutophagy -> targets -> SPECIFIC_ORGANELLE_OR_COMPONENT
Mitophagy -> selective_autophagy_of -> MITOCHONDRIA
OrganelleTurnover -> balances -> BIOGENESIS + DEGRADATION

OrganelleInheritance -> distributes -> ORGANELLES -> to -> DAUGHTER_CELLS
Inheritance -> may_require -> ORGANELLE_REPLICATION_OR_GROWTH + POSITIONING + CYTOSKELETAL_TRANSPORT + CELL_DIVISION_COORDINATION
IF OrganelleInheritance fails THEN DaughterCellFunction -> MAY_BE_AFFECTED

OrganelleGenome -> present_in -> MITOCHONDRIA_AS_APPLICABLE + CHLOROPLASTS_AS_APPLICABLE
OrganelleFunction -> depends_on -> NUCLEAR_GENOME + ORGANELLE_GENOME_AS_APPLICABLE

# EVIDENCE / UNCERTAINTY / PROVENANCE
OrganelleClaim -> supported_by -> Evidence
EVIDENCE_TYPE := MICROSCOPIC | ULTRASTRUCTURAL | MOLECULAR | BIOCHEMICAL | GENETIC | PROTEOMIC | METABOLOMIC | IMAGING | FUNCTIONAL | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_SAMPLE + ORGANELLE_TYPE + CONDITION + QUALITY + UNCERTAINTY
ORGANELLE_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + ORGANELLE_IDENTITY_UNCERTAINTY + SPATIAL_RESOLUTION_LIMIT + DYNAMIC_STATE_UNCERTAINTY + CELL_TO_CELL_VARIABILITY + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> OrganelleIdentity + OrganelleFunction + OrganellePosition + OrganelleClaim

Provenance -> records -> CELL_IDENTITY + ORGANELLE_IDENTITY + ORGANELLE_TYPE + MOLECULAR_MARKERS + METHOD + CONDITION + OBSERVATION + TIME + VERSION
Organelle -> linked_to -> Provenance

# REASONING
ORGANELLE_REASONING := IDENTIFY_ORGANELLE -> CLASSIFY_ORGANELLE_TYPE -> MAP_MEMBRANE_AND_COMPARTMENT -> MAP_STRUCTURE_AND_COMPOSITION -> MAP_FUNCTION -> MAP_BIOGENESIS -> MAP_PROTEIN_TARGETING_AND_IMPORT -> MAP_LIPID_AND_VESICULAR_TRAFFICKING -> MAP_CONTACT_SITES -> MAP_POSITIONING_AND_MOVEMENT -> MAP_FUSION_AND_FISSION -> MAP_ORGANELLE_COMMUNICATION -> MAP_QUALITY_CONTROL_AND_TURNOVER -> MAP_INHERITANCE -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF OrganelleMembraneIntegrity decreases THEN OrganelleFunction -> MAY_DECREASE
IF ProteinTargeting fails THEN OrganelleProteinComposition -> MAY_CHANGE
IF VesicularTrafficking changes THEN OrganelleComposition -> MAY_CHANGE
IF ContactSiteState changes THEN InterOrganelleTransfer -> MAY_CHANGE
IF FusionFissionBalance changes THEN OrganelleMorphology -> MAY_CHANGE
IF OrganellePosition changes THEN LocalCellularFunction -> MAY_CHANGE
IF QualityControl fails THEN DamagedOrganelleAccumulation -> MAY_INCREASE
IF OrganelleInheritance fails THEN DaughterCellFunction -> MAY_BE_AFFECTED
IF Evidence insufficient THEN OrganelleClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS / EQUIVALENCE
RELATION part_of(Organelle, Cell)
RELATION enclosed_by(MembraneBoundOrganelle, OrganelleMembrane)
RELATION contains(Nucleus, NuclearGenome)
RELATION participates_in(Mitochondrion, EnergyMetabolism)
RELATION participates_in(Chloroplast, Photosynthesis)
RELATION participates_in(EndoplasmicReticulum, ProteinProcessing)
RELATION modifies_and_sorts(GolgiApparatus, CellularCargo)
RELATION degrades(Lysosome, CellularMaterial)
RELATION participates_in(Peroxisome, OxidativeMetabolism)
RELATION transports(Vesicle, Cargo)
RELATION performs(Ribosome, Translation)
RELATION creates(OrganelleBiogenesis, Organelle)
RELATION directs(ProteinTargeting, Protein)
RELATION connects(OrganelleContactSite, Organelle)
RELATION joins(OrganelleFusion, Organelle)
RELATION divides(OrganelleFission, Organelle)
RELATION targets(Mitophagy, Mitochondrion)
RELATION distributes(OrganelleInheritance, Organelle)
RELATION supports(Evidence, OrganelleClaim)
RELATION records(Provenance, Organelle)

SEMANTIC_EQUIVALENCE:
  "organelle" ~= "specialised cellular structure or compartment"
  "membrane-bound organelle" ~= "cellular compartment enclosed by one or more membranes"
  "organelle biogenesis" ~= "formation growth or assembly of an organelle"
  "protein targeting" ~= "directed delivery of proteins to cellular compartments"
  "organelle contact site" ~= "close apposition between organelle membranes enabling communication or transfer"
  "organelle fusion" ~= "joining of organelle membranes or compartments"
  "organelle fission" ~= "division of an organelle into multiple units"
  "organelle quality control" ~= "cellular processes maintaining organelle integrity and function"
  "organelle turnover" ~= "balance of organelle formation and degradation"
  "organelle inheritance" ~= "distribution of organelles to daughter cells"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  identity_compartment_mapping: 0.99
  major_organelle_mapping: 0.99
  biogenesis_targeting_mapping: 0.99
  trafficking_contact_mapping: 0.99
  dynamics_mapping: 0.99
  quality_control_mapping: 0.99
  inheritance_mapping: 0.99
  evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_organelle_observation:
    MAP organelle_identity
    MAP organelle_type
    MAP membrane_state
    MAP composition
    MAP position
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON trafficking_change:
    UPDATE cargo_state
    UPDATE organelle_composition
    UPDATE contact_relationships
    PRESERVE provenance
  ON dynamic_event:
    UPDATE fusion_state
    UPDATE fission_state
    UPDATE morphology
    UPDATE position
    PRESERVE provenance
  ON quality_control_event:
    UPDATE damage_state
    UPDATE repair_or_turnover_state
    UPDATE organelle_function
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_ORGANELLE_ONTOLOGY
  reasoning_mode: ORGANELLE_STRUCTURE_FUNCTION_DYNAMICS_RELATIONAL
  preserve: [typed_entities, organelle_identity, organelle_type, membrane_state, compartment_state, composition, function, targeting_state, trafficking_state, contact_sites, position, fusion_fission_state, quality_control_state, inheritance_state, evidence, uncertainty, confidence, provenance]
  infer: [structure_function_dependencies, targeting_dependencies, trafficking_impacts, contact_site_transfer, dynamic_state, quality_control_response, turnover_state, inheritance_dependencies, evidence_strength]
  prohibit: [invented_organelle_observations, assuming_all_organelles_are_membrane_bound, fabricated_targeting_signals, unsupported_organelle_contacts, unsupported_function_assignment, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + IDENTITY_COMPARTMENTALISATION + MAJOR_ORGANELLES + BIOGENESIS_TARGETING_TRAFFICKING + CONTACTS_POSITIONING_DYNAMICS + COMMUNICATION_QUALITY_CONTROL_INHERITANCE + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW