Prokaryotic Cell Ontology

AI SEARCH FLOW ALGEBRA
PROKARYOTIC CELL ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

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

FLOW "ProkaryoticCellOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / CELL_BIOLOGY / PROKARYOTIC_CELL
ONTOLOGY := PROKARYOTIC_CELL_ONTOLOGY

PROKARYOTIC_CELL := CELL_IDENTITY + CELL_ENVELOPE + CELL_MEMBRANE + CELL_WALL + CYTOPLASM + NUCLEOID + CHROMOSOME + PLASMID + RIBOSOME + APPENDAGES + TRANSPORT + METABOLISM + ENERGY_CONSERVATION + GENE_EXPRESSION + REGULATION + BINARY_FISSION + HORIZONTAL_GENE_TRANSFER + ENVIRONMENTAL_RESPONSE + HOMEOSTASIS + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_PROKARYOTIC_CELL -> CLASSIFY_CELLULAR_FEATURES -> MAP_CELL_ENVELOPE -> MAP_NUCLEOID_AND_GENOME -> MAP_PLASMIDS_AND_RIBOSOMES -> MAP_APPENDAGES -> MAP_TRANSPORT_AND_METABOLISM -> MAP_ENERGY_CONSERVATION -> MAP_GENE_EXPRESSION_AND_REGULATION -> MAP_BINARY_FISSION -> MAP_HORIZONTAL_GENE_TRANSFER -> MAP_ENVIRONMENTAL_RESPONSE_AND_HOMEOSTASIS -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY ProkaryoticCell
ENTITY Bacterium
ENTITY Archaeon
ENTITY CellEnvelope
ENTITY CellMembrane
ENTITY CellWall
ENTITY OuterMembrane
ENTITY Periplasm
ENTITY Capsule
ENTITY Cytoplasm
ENTITY Nucleoid
ENTITY Chromosome
ENTITY DNA
ENTITY Gene
ENTITY Operon
ENTITY Plasmid
ENTITY Ribosome
ENTITY Flagellum
ENTITY Pilus
ENTITY Fimbria
ENTITY Transporter
ENTITY Metabolism
ENTITY EnergyConservation
ENTITY GeneExpression
ENTITY GeneRegulation
ENTITY BinaryFission
ENTITY HorizontalGeneTransfer
ENTITY Transformation
ENTITY Transduction
ENTITY Conjugation
ENTITY EnvironmentalSignal
ENTITY StressResponse
ENTITY Homeostasis
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# IDENTITY AND ORGANISATION
ProkaryoticCell -> subtype_of -> Cell
ProkaryoticCell -> lacks -> MEMBRANE_BOUND_NUCLEUS
PROKARYOTIC_DOMAIN := BACTERIA | ARCHAEA
Bacterium -> subtype_of -> ProkaryoticCell
Archaeon -> subtype_of -> ProkaryoticCell
ProkaryoticCell -> contains -> CELL_MEMBRANE + CYTOPLASM + NUCLEOID + RIBOSOMES
ProkaryoticCell -> may_contain -> CELL_WALL + OUTER_MEMBRANE + CAPSULE + PLASMIDS + STORAGE_INCLUSIONS + APPENDAGES
ProkaryoticOrganisation -> generally_lacks -> MEMBRANE_BOUND_ORGANELLES_TYPICAL_OF_EUKARYOTES

# CELL ENVELOPE
CellEnvelope -> includes -> CellMembrane + CELL_WALL_WHERE_PRESENT + OUTER_MEMBRANE_WHERE_PRESENT
CellEnvelope -> provides -> BOUNDARY + PROTECTION + SHAPE + TRANSPORT_INTERFACE + ENVIRONMENTAL_INTERACTION
CellMembrane -> supports -> SELECTIVE_TRANSPORT + SIGNALING + ENERGY_CONSERVATION + HOMEOSTASIS
CellWall -> provides -> SHAPE + MECHANICAL_SUPPORT + OSMOTIC_PROTECTION
BacterialCellWall -> may_contain -> PEPTIDOGLYCAN
ArchaealCellWall -> may_use -> DISTINCT_NON_PEPTIDOGLYCAN_STRUCTURES
IF MembraneIntegrity decreases THEN CellularViability -> MAY_DECREASE

# NUCLEOID GENOME PLASMIDS
Nucleoid -> contains -> PRIMARY_CHROMOSOMAL_DNA_AS_DEFINED
Nucleoid -> not_bounded_by -> NUCLEAR_MEMBRANE
Chromosome -> contains -> GENES + REGULATORY_REGIONS
Genome := CHROMOSOMAL_DNA + EXTRACHROMOSOMAL_GENETIC_ELEMENTS_AS_APPLICABLE
DNA -> stores -> GENETIC_INFORMATION
Gene -> region_of -> DNA
Plasmid -> extrachromosomal_genetic_element_of -> ProkaryoticCell
Plasmid -> may_carry -> METABOLIC_GENES + RESISTANCE_GENES + TRANSFER_GENES + OTHER_ACCESSORY_GENES

# RIBOSOMES AND GENE EXPRESSION
Ribosome -> performs -> TRANSLATION
GENETIC_INFORMATION_FLOW := DNA -> TRANSCRIPTION -> RNA -> TRANSLATION -> PROTEIN
InManyProkaryotes: TRANSCRIPTION -> may_be_spatially_and_temporally_coupled_with -> TRANSLATION
Operon -> groups -> FUNCTIONALLY_RELATED_GENES_AS_DEFINED
Operon -> controlled_by -> SHARED_REGULATORY_ELEMENTS
GeneRegulation -> changes -> TRANSCRIPTION_RATE + RNA_STABILITY + TRANSLATION + PROTEIN_ACTIVITY
EnvironmentalSignal -> may_change -> REGULATORY_STATE
IF RegulatoryState changes THEN GeneExpressionPattern -> MAY_CHANGE

# TRANSPORT METABOLISM ENERGY
MEMBRANE_TRANSPORT := SIMPLE_DIFFUSION | FACILITATED_TRANSPORT | ACTIVE_TRANSPORT | GROUP_TRANSLOCATION_AS_APPLICABLE
Transporter -> moves -> ION | NUTRIENT | METABOLITE | WASTE
ActiveTransport -> requires -> ENERGY_COUPLING
Metabolism -> transforms -> MATTER + ENERGY
PROKARYOTIC_METABOLIC_MODE := AEROBIC_RESPIRATION | ANAEROBIC_RESPIRATION | FERMENTATION | PHOTOSYNTHESIS_AS_APPLICABLE | CHEMOLITHOTROPHY_AS_APPLICABLE | OTHER_METABOLIC_STRATEGY
MetabolicPathway -> contains -> BIOCHEMICAL_REACTIONS
Enzyme -> catalyses -> BIOCHEMICAL_REACTION
EnergyConservation -> converts -> ENERGY_SOURCE -> CELLULARLY_USABLE_ENERGY
ProtonMotiveForce -> may_drive -> ATP_SYNTHESIS + TRANSPORT + MOTILITY
ElectronTransportChain -> may_generate -> ELECTROCHEMICAL_GRADIENT
ATP -> supports -> BIOSYNTHESIS + TRANSPORT + MOTILITY + HOMEOSTASIS

# APPENDAGES MOTILITY BIOFILMS
APPENDAGE_TYPE := FLAGELLUM | PILUS | FIMBRIA | OTHER_SURFACE_APPENDAGE
Flagellum -> may_enable -> MOTILITY
Pilus -> may_support -> ADHESION + DNA_TRANSFER_AS_APPLICABLE
Fimbria -> may_support -> SURFACE_ATTACHMENT
Chemotaxis -> biases -> MOTILITY -> in_response_to -> CHEMICAL_GRADIENT
CHEMOTAXIS_FLOW := CHEMICAL_SIGNAL -> RECEPTOR -> SIGNALING_NETWORK -> MOTOR_CONTROL -> ALTERED_MOVEMENT
Biofilm -> community_of -> SURFACE_ASSOCIATED_CELLS_AS_DEFINED
BIOFILM_DEVELOPMENT := ATTACHMENT -> MICROCOLONY_FORMATION -> MATRIX_PRODUCTION -> MATURATION -> DISPERSAL_AS_APPLICABLE
BiofilmState -> may_change -> GENE_EXPRESSION + METABOLISM + STRESS_TOLERANCE

# BINARY FISSION
BinaryFission -> common_reproductive_division_process_of -> MANY_PROKARYOTES
BINARY_FISSION_FLOW := CELL_GROWTH -> DNA_REPLICATION -> CHROMOSOME_SEGREGATION -> DIVISION_SITE_FORMATION -> SEPTATION -> DAUGHTER_CELL_SEPARATION
BinaryFission -> produces -> DAUGHTER_CELLS
DNAReplication -> copies -> CHROMOSOMAL_DNA
ReplicationAccuracy -> supports -> GENOME_STABILITY
IF ReplicationError persists THEN MutationRisk -> INCREASES
ChromosomeSegregation -> distributes -> REPLICATED_CHROMOSOMES -> into -> DAUGHTER_CELLS
IF Segregation fails THEN DaughterGenomeIntegrity -> MAY_DECREASE

# HORIZONTAL GENE TRANSFER
HorizontalGeneTransfer -> transfers -> GENETIC_INFORMATION -> between -> CELLS_OR_LINEAGES
HGT_MODE := TRANSFORMATION | TRANSDUCTION | CONJUGATION
HorizontalGeneTransfer -> contributes_to -> GENETIC_VARIATION + RAPID_TRAIT_ACQUISITION
Transformation -> imports -> EXTRACELLULAR_DNA
Competence -> enables -> DNA_UPTAKE
Transduction -> transfers -> DNA -> via -> VIRAL_OR_PHAGE_VECTOR
Conjugation -> transfers -> DNA -> through -> CELL_TO_CELL_TRANSFER_SYSTEM
Conjugation -> may_transfer -> PLASMID + OTHER_MOBILE_GENETIC_ELEMENT
MOBILE_ELEMENT_TYPE := PLASMID | TRANSPOSON | INTEGRATIVE_ELEMENT | PHAGE_ASSOCIATED_ELEMENT | OTHER_MOBILE_ELEMENT
MobileGeneticElement -> may_carry -> ACCESSORY_GENES

# ENVIRONMENTAL RESPONSE HOMEOSTASIS
ENVIRONMENTAL_SIGNAL_TYPE := NUTRIENT | TEMPERATURE | PH | OSMOLARITY | OXYGEN | LIGHT | TOXIN | CELL_DENSITY_SIGNAL
Sensor -> detects -> EnvironmentalSignal
SignalTransduction -> changes -> GENE_EXPRESSION + ENZYME_ACTIVITY + MOTILITY + CELL_STATE
QuorumSensing -> responds_to -> CELL_DENSITY_ASSOCIATED_SIGNAL_AS_DEFINED
QUORUM_FLOW := SIGNAL_PRODUCTION -> SIGNAL_ACCUMULATION -> SIGNAL_DETECTION -> REGULATORY_RESPONSE
Homeostasis -> maintains -> INTERNAL_VARIABLE -> within -> FUNCTIONAL_RANGE
HOMEOSTATIC_VARIABLE := PH | ION_BALANCE | OSMOTIC_STATE | REDOX_STATE | ENERGY_STATE | PROTEIN_QUALITY
STRESS_TYPE := OXIDATIVE | HEAT | COLD | OSMOTIC | NUTRIENT_LIMITATION | ACID | ALKALINE | DNA_DAMAGE | TOXIC_COMPOUND
StressResponse -> may_change -> GENE_EXPRESSION + METABOLISM + PROTEIN_STATE + MEMBRANE_STATE
IF Stress exceeds_tolerance THEN CellViability -> MAY_DECREASE

# EVIDENCE UNCERTAINTY PROVENANCE
ProkaryoticCellClaim -> supported_by -> Evidence
EVIDENCE_TYPE := MICROSCOPIC | CULTURE_BASED | BIOCHEMICAL | MOLECULAR | GENETIC | GENOMIC | PHYSIOLOGICAL | EXPERIMENTAL | COMPUTATIONAL
Evidence -> has -> SOURCE + METHOD + CELL_OR_STRAIN + ENVIRONMENT + QUALITY + UNCERTAINTY
PROKARYOTIC_UNCERTAINTY := MEASUREMENT_UNCERTAINTY + STRAIN_VARIATION + CULTURE_CONDITION_VARIATION + TAXONOMIC_UNCERTAINTY + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> CellIdentity + MetabolicState + GeneFunction + CellClaim
Provenance -> records -> CELL_OR_STRAIN_IDENTITY + TAXONOMIC_CONTEXT + GENOME_OR_PLASMID_CONTEXT + METHOD + ENVIRONMENT + OBSERVATION + EXPERIMENT + TIME + VERSION
ProkaryoticCell -> linked_to -> Provenance

# REASONING
PROKARYOTIC_CELL_REASONING := IDENTIFY_CELL -> CLASSIFY_DOMAIN_OR_TAXON -> MAP_CELL_ENVELOPE -> MAP_CELL_WALL -> MAP_CYTOPLASM_AND_NUCLEOID -> MAP_CHROMOSOME_AND_PLASMIDS -> MAP_RIBOSOMES_AND_GENE_EXPRESSION -> MAP_TRANSPORT -> MAP_METABOLIC_STRATEGY -> MAP_ENERGY_CONSERVATION -> MAP_APPENDAGES_AND_MOTILITY -> MAP_BINARY_FISSION -> MAP_HORIZONTAL_GENE_TRANSFER -> MAP_ENVIRONMENTAL_SIGNALING -> MAP_HOMEOSTASIS_AND_STRESS -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF MembraneIntegrity decreases THEN CellularHomeostasis -> MAY_DECREASE
IF CellWallIntegrity decreases THEN OsmoticVulnerability -> MAY_INCREASE
IF Plasmid acquired THEN AccessoryTraitSet -> MAY_CHANGE
IF HorizontalGeneTransfer occurs THEN GeneticVariation -> MAY_INCREASE
IF NutrientAvailability changes THEN MetabolicState -> MAY_CHANGE
IF EnvironmentalSignal changes THEN GeneExpressionPattern -> MAY_CHANGE
IF ReplicationOrSegregation fails THEN DaughterGenomeIntegrity -> MAY_DECREASE
IF Evidence insufficient THEN ProkaryoticCellClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION subtype_of(ProkaryoticCell, Cell)
RELATION subtype_of(Bacterium, ProkaryoticCell)
RELATION subtype_of(Archaeon, ProkaryoticCell)
RELATION includes(CellEnvelope, CellMembrane)
RELATION separates(CellMembrane, Cytoplasm, Environment)
RELATION contains(Nucleoid, ChromosomalDNA)
RELATION contains(Chromosome, Gene)
RELATION extrachromosomal_element_of(Plasmid, ProkaryoticCell)
RELATION performs(Ribosome, Translation)
RELATION controls(Operon, GeneExpression)
RELATION mediates(Transporter, MembraneTransport)
RELATION transforms(Metabolism, Matter, Energy)
RELATION drives(ProtonMotiveForce, ATP_Synthesis)
RELATION enables(Flagellum, Motility)
RELATION produces(BinaryFission, DaughterCell)
RELATION transfers(HorizontalGeneTransfer, GeneticInformation)
RELATION imports(Transformation, ExtracellularDNA)
RELATION transfers(Transduction, DNA)
RELATION transfers(Conjugation, DNA)
RELATION detects(Sensor, EnvironmentalSignal)
RELATION maintains(Homeostasis, InternalVariable)
RELATION supports(Evidence, ProkaryoticCellClaim)
RELATION records(Provenance, ProkaryoticCell)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "prokaryotic cell" ~= "cell lacking a membrane-bound nucleus"
  "nucleoid" ~= "non-membrane-bound chromosome-containing region"
  "plasmid" ~= "extrachromosomal replicating genetic element"
  "binary fission" ~= "common prokaryotic cell division process"
  "horizontal gene transfer" ~= "genetic transfer between cells or lineages outside direct descent"
  "transformation" ~= "uptake of extracellular DNA"
  "transduction" ~= "virus-mediated genetic transfer"
  "conjugation" ~= "cell-to-cell DNA transfer"
  "proton motive force" ~= "transmembrane electrochemical proton gradient"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  cell_identity_mapping: 0.99
  envelope_mapping: 0.99
  genome_plasmid_mapping: 0.99
  metabolism_energy_mapping: 0.99
  appendage_motility_mapping: 0.99
  division_mapping: 0.99
  horizontal_transfer_mapping: 0.99
  environmental_response_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_prokaryotic_cell:
    MAP taxonomic_context
    MAP envelope_features
    MAP chromosome
    MAP plasmids
    MAP metabolic_state
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON new_genomic_evidence:
    UPDATE genes
    UPDATE operons
    UPDATE mobile_elements
    UPDATE plasmid_state
    PRESERVE provenance
  ON environmental_change:
    UPDATE signaling_state
    UPDATE gene_expression_state
    UPDATE metabolic_state
    UPDATE stress_state
    PRESERVE provenance
  ON horizontal_gene_transfer_event:
    UPDATE genetic_content
    UPDATE accessory_traits
    UPDATE lineage_relationships
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_PROKARYOTIC_CELL_ONTOLOGY
  reasoning_mode: PROKARYOTIC_CELLULAR_RELATIONAL
  preserve: [typed_entities, cell_identity, taxonomic_context, envelope_structure, chromosome, plasmids, operons, metabolic_state, transport_state, division_state, horizontal_transfer_state, environmental_context, evidence, uncertainty, confidence, provenance]
  infer: [envelope_function_dependencies, genome_expression_dependencies, plasmid_trait_dependencies, metabolic_dependencies, energy_conservation_dependencies, division_dependencies, horizontal_transfer_impacts, environmental_response, evidence_strength]
  prohibit: [invented_cell_observations, assuming_all_prokaryotes_share_identical_envelope_structure, fabricated_plasmid_content, unsupported_horizontal_transfer_events, unsupported_metabolic_capabilities, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + IDENTITY_ENVELOPE_CYTOPLASM + NUCLEOID_GENOME_PLASMIDS_RIBOSOMES + TRANSPORT_METABOLISM_ENERGY + APPENDAGES_MOTILITY_BIOFILMS + BINARY_FISSION_GENOME_REPLICATION + HORIZONTAL_GENE_TRANSFER + ENVIRONMENTAL_RESPONSE_HOMEOSTASIS + EVIDENCE_UNCERTAINTY_PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW