Biological Process Ontology

AI SEARCH FLOW ALGEBRA
BIOLOGICAL PROCESS ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/foundations-of-biology/biological-process-ontology.html

FLOW "BiologicalProcessOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY / BIOLOGICAL_PROCESS
ONTOLOGY := BIOLOGICAL_PROCESS_ONTOLOGY

BIOLOGICAL_PROCESS :=
  PROCESS_IDENTITY + PARTICIPANTS + INPUTS + OUTPUTS
  + TRANSFORMATION + STATE_CHANGE + LOCATION + TIME
  + REGULATION + SIGNALING + METABOLISM + TRANSPORT
  + GROWTH + DEVELOPMENT + REPRODUCTION + PHYSIOLOGY
  + ECOLOGICAL_PROCESS + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE :=
  IDENTIFY_PROCESS -> IDENTIFY_PARTICIPANTS
  -> DEFINE_INPUTS_AND_OUTPUTS -> MAP_TRANSFORMATION
  -> MAP_STATE_TRANSITIONS -> MAP_LOCATION_AND_TIMING
  -> MAP_DEPENDENCIES -> MAP_REGULATION_AND_FEEDBACK
  -> CLASSIFY_PROCESS_TYPE -> ASSESS_EVIDENCE
  -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY BiologicalProcess
ENTITY ProcessType
ENTITY Participant
ENTITY Input
ENTITY Output
ENTITY BiologicalEntity
ENTITY Biomolecule
ENTITY Gene
ENTITY Protein
ENTITY Cell
ENTITY Tissue
ENTITY Organ
ENTITY Organism
ENTITY Population
ENTITY Ecosystem
ENTITY State
ENTITY StateVariable
ENTITY StateTransition
ENTITY Transformation
ENTITY Location
ENTITY Time
ENTITY Duration
ENTITY Rate
ENTITY Regulation
ENTITY Feedback
ENTITY Signal
ENTITY MetabolicProcess
ENTITY TransportProcess
ENTITY GrowthProcess
ENTITY DevelopmentalProcess
ENTITY ReproductiveProcess
ENTITY PhysiologicalProcess
ENTITY EcologicalProcess
ENTITY EvolutionaryProcess
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# PROCESS IDENTITY / PARTICIPANTS / FLOW
BiologicalProcess ->
  has -> PROCESS_ID + ProcessType + PARTICIPANTS
  + TEMPORAL_EXTENT + CONTEXT

PROCESS_SCOPE :=
  MOLECULAR | SUBCELLULAR | CELLULAR | TISSUE
  | ORGAN | ORGANISMAL | POPULATION | ECOLOGICAL

Participant -> participates_in -> BiologicalProcess

PARTICIPANT_ROLE :=
  INPUT | OUTPUT | CATALYST | REGULATOR
  | CARRIER | SIGNAL | RECEPTOR | EFFECTOR
  | SUBSTRATE | PRODUCT

PROCESS_FLOW :=
  INPUT_STATE -> BIOLOGICAL_MECHANISM -> OUTPUT_STATE

Transformation -> maps -> INPUT -> OUTPUT

TRANSFORMATION_TYPE :=
  CHEMICAL | PHYSICAL | INFORMATIONAL | STRUCTURAL
  | DEVELOPMENTAL | PHYSIOLOGICAL | ECOLOGICAL

STATE_TRANSITION :=
  STATE_t + PROCESS + INPUT + REGULATION -> STATE_t_plus_1

IF Process occurs
THEN RelevantStateVariables -> MAY_CHANGE

# LOCATION / TIME / DEPENDENCIES / REGULATION
BiologicalProcess -> occurs_at -> Location
BiologicalProcess -> occurs_over -> Duration

LOCATION_TYPE :=
  MOLECULAR_SITE | ORGANELLE | CELL | TISSUE
  | ORGAN | ORGANISM | HABITAT | ECOSYSTEM

TemporalRelation :=
  BEFORE | AFTER | OVERLAPS | DURING | SIMULTANEOUS_WITH

Rate -> measures -> PROCESS_CHANGE_PER_TIME

ProcessRate ->
  influenced_by -> TEMPERATURE + SUBSTRATE_AVAILABILITY
  + REGULATORS + ENERGY + ENVIRONMENT + SYSTEM_STATE

DEPENDENCY_TYPE :=
  REQUIRES | ENABLES | PRECEDES | INHIBITS
  | ACTIVATES | PROVIDES_INPUT_TO | CONSUMES_OUTPUT_OF

IF ProcessA provides_required_input_to ProcessB
AND ProcessA fails
THEN ProcessB -> MAY_BE_IMPAIRED

REGULATION_TYPE :=
  ACTIVATION | INHIBITION | MODULATION
  | FEEDBACK | FEEDFORWARD

PositiveRegulation -> increases -> PROCESS_ACTIVITY_AS_DEFINED
NegativeRegulation -> decreases -> PROCESS_ACTIVITY_AS_DEFINED

FEEDBACK_TYPE := NEGATIVE_FEEDBACK | POSITIVE_FEEDBACK
NegativeFeedback -> tends_to_stabilise -> SYSTEM_VARIABLE
PositiveFeedback -> tends_to_amplify -> PROCESS_OR_STATE_CHANGE

# SIGNALING / METABOLISM / TRANSPORT
SIGNALING_PROCESS :=
  SIGNAL_GENERATION -> SIGNAL_TRANSPORT
  -> RECEPTOR_BINDING -> TRANSDUCTION
  -> EFFECTOR_ACTIVATION -> RESPONSE

Signal -> carries -> BIOLOGICAL_INFORMATION
SignalTransduction -> converts -> SIGNAL -> BIOLOGICAL_RESPONSE

METABOLIC_PROCESS :=
  CATABOLIC_PROCESS | ANABOLIC_PROCESS
  | ENERGY_TRANSFER_PROCESS | BIOSYNTHETIC_PROCESS
  | DEGRADATIVE_PROCESS

Substrate -> consumed_by -> MetabolicProcess
Product -> produced_by -> MetabolicProcess
Enzyme -> catalyses -> MetabolicProcess
MetabolicPathway -> contains -> ORDERED_METABOLIC_PROCESSES

TransportProcess ->
  moves -> MATERIAL_OR_ENTITY
  -> from -> SOURCE_LOCATION
  -> to -> DESTINATION_LOCATION

TRANSPORT_TYPE :=
  DIFFUSION | FACILITATED_DIFFUSION | ACTIVE_TRANSPORT
  | VESICULAR_TRANSPORT | BULK_FLOW | CIRCULATORY_TRANSPORT

# GENE EXPRESSION / CELLULAR / GROWTH / DEVELOPMENT
GENE_EXPRESSION_PROCESS :=
  TRANSCRIPTION -> RNA_PROCESSING_IF_APPLICABLE
  -> TRANSLATION -> PRODUCT_MATURATION

Gene -> provides -> INFORMATION_TEMPLATE
Transcription -> produces -> RNA
Translation -> produces -> Protein
GeneRegulation -> controls -> GENE_EXPRESSION_PROCESS

CELLULAR_PROCESS :=
  CELL_CYCLE | CELL_DIVISION | CELL_DIFFERENTIATION
  | APOPTOSIS | CELL_SIGNALING | CELL_MIGRATION
  | CELLULAR_HOMEOSTASIS

CellularProcess -> changes -> CELL_STATE

GrowthProcess ->
  increases -> SIZE | MASS | CELL_NUMBER | BIOMASS

GrowthProcess -> requires -> MATERIAL + ENERGY + REGULATION

DEVELOPMENTAL_PROCESS :=
  CLEAVAGE | DIFFERENTIATION | MORPHOGENESIS
  | ORGANOGENESIS | MATURATION
  | METAMORPHOSIS_WHERE_APPLICABLE

DevelopmentalProcess ->
  regulated_by -> GENETIC_INFORMATION + SIGNALING + ENVIRONMENT

# REPRODUCTION / PHYSIOLOGY / ECOLOGY / EVOLUTION
REPRODUCTIVE_PROCESS :=
  GAMETOGENESIS | FERTILISATION
  | ASEXUAL_REPRODUCTION | SEXUAL_REPRODUCTION
  | SPORE_FORMATION | OTHER_LINEAGE_SPECIFIC_PROCESS

ReproductiveProcess ->
  produces -> OFFSPRING | REPRODUCTIVE_CELL | PROPAGULE

ReproductiveProcess -> transmits -> HERITABLE_INFORMATION

PHYSIOLOGICAL_PROCESS :=
  RESPIRATION | CIRCULATION | DIGESTION | EXCRETION
  | OSMOREGULATION | THERMOREGULATION
  | IMMUNE_RESPONSE | NEURAL_SIGNALING
  | ENDOCRINE_REGULATION | LOCOMOTION

PhysiologicalProcess ->
  contributes_to -> ORGANISM_FUNCTION + HOMEOSTASIS

ECOLOGICAL_PROCESS :=
  PREDATION | COMPETITION | MUTUALISM | PARASITISM
  | HERBIVORY | DECOMPOSITION | PRIMARY_PRODUCTION
  | NUTRIENT_CYCLING | SUCCESSION

EcologicalProcess ->
  changes -> POPULATION + COMMUNITY + ECOSYSTEM_STATE

EVOLUTIONARY_PROCESS :=
  MUTATION | NATURAL_SELECTION | GENETIC_DRIFT
  | GENE_FLOW | RECOMBINATION

EvolutionaryProcess ->
  changes -> HERITABLE_POPULATION_PROPERTIES
  -> across -> GENERATIONS

# NETWORKS / RESOURCES / ENVIRONMENT / FAILURE
ProcessNetwork ->
  contains -> INTERCONNECTED_BIOLOGICAL_PROCESSES

ProcessEdge ->
  represents -> DEPENDENCY + REGULATION
  + MATERIAL_FLOW + INFORMATION_FLOW

Pathway ->
  ordered_or_networked_set_of -> BiologicalProcess

PATHWAY_TYPE :=
  METABOLIC | SIGNALING | DEVELOPMENTAL
  | REGULATORY | PHYSIOLOGICAL

COUPLING_TYPE :=
  ENERGY_COUPLING | MATERIAL_COUPLING
  | SIGNAL_COUPLING | REGULATORY_COUPLING

RESOURCE_TYPE :=
  ENERGY | NUTRIENT | SUBSTRATE | OXYGEN
  | WATER | SPACE | COFACTOR

IF RequiredResource below_threshold
THEN ProcessRate -> MAY_DECREASE

Environment -> influences -> BiologicalProcess

ENVIRONMENTAL_FACTOR :=
  TEMPERATURE | LIGHT | WATER | PH | SALINITY
  | PRESSURE | NUTRIENT_AVAILABILITY | OTHER_ORGANISMS

FAILURE_MODE :=
  MISSING_INPUT | COMPONENT_FAILURE | REGULATORY_FAILURE
  | ENERGY_LIMITATION | TRANSPORT_FAILURE
  | ENVIRONMENTAL_INHIBITION

ProcessFailure ->
  may_affect -> DOWNSTREAM_PROCESSES + SYSTEM_FUNCTION

RobustnessMechanism :=
  REDUNDANCY | ALTERNATIVE_PATHWAY
  | FEEDBACK | RESERVE_CAPACITY | COMPENSATION

# EVIDENCE / UNCERTAINTY / PROVENANCE
ProcessClaim -> supported_by -> Evidence

EVIDENCE_TYPE :=
  OBSERVATIONAL | EXPERIMENTAL | BIOCHEMICAL
  | MOLECULAR | CELLULAR | PHYSIOLOGICAL
  | ECOLOGICAL | COMPUTATIONAL

Evidence ->
  has -> SOURCE + METHOD + PARTICIPANTS
  + LOCATION + TIME + CONTEXT + QUALITY + UNCERTAINTY

PROCESS_EXPERIMENT_FLOW :=
  DEFINE_PROCESS -> IDENTIFY_BASELINE
  -> ALTER_INPUT_OR_REGULATOR -> MEASURE_OUTPUT
  -> MEASURE_STATE_CHANGE -> ANALYSE_DEPENDENCY
  -> REPLICATE -> UPDATE_MODEL

Correlation ->
  does_not_by_itself_establish -> PROCESS_CAUSATION

PROCESS_UNCERTAINTY :=
  MEASUREMENT_UNCERTAINTY + TIMING_UNCERTAINTY
  + PARTICIPANT_UNCERTAINTY + RATE_UNCERTAINTY
  + MODEL_UNCERTAINTY + BIOLOGICAL_VARIABILITY

Uncertainty ->
  qualifies -> ProcessClaim + Rate + StateTransition + Dependency

Provenance ->
  records -> PROCESS_ID + PARTICIPANTS
  + INPUTS + OUTPUTS + LOCATION + TIME
  + METHOD + EVIDENCE + VERSION

BiologicalProcess -> linked_to -> Provenance

# REASONING / INFERENCE RULES
BIOLOGICAL_PROCESS_REASONING :=
  IDENTIFY_PROCESS -> CLASSIFY_PROCESS_TYPE
  -> IDENTIFY_PARTICIPANTS -> ASSIGN_PARTICIPANT_ROLES
  -> DEFINE_INPUTS_AND_OUTPUTS -> MAP_TRANSFORMATION
  -> MAP_STATE_TRANSITIONS -> MAP_LOCATION
  -> MAP_TIMING_AND_RATE -> MAP_PROCESS_DEPENDENCIES
  -> MAP_REGULATION_AND_FEEDBACK
  -> MAP_SIGNALING_OR_INFORMATION_FLOW
  -> MAP_MATERIAL_AND_ENERGY_FLOW
  -> MAP_ENVIRONMENTAL_CONTEXT
  -> IDENTIFY_FAILURE_AND_ROBUSTNESS
  -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY
  -> PRESERVE_PROVENANCE

IF RequiredInput unavailable
THEN ProcessFeasibility -> DECREASES

IF PositiveRegulator increases
THEN ProcessActivity -> MAY_INCREASE

IF NegativeRegulator increases
THEN ProcessActivity -> MAY_DECREASE

IF UpstreamProcess fails
THEN DependentDownstreamProcess -> MAY_BE_IMPAIRED

IF ProcessRate changes
THEN SystemStateTrajectory -> MAY_CHANGE

IF Environment changes
THEN ProcessRateOrOutcome -> MAY_CHANGE

IF PrimaryPathway impaired
AND AlternativePathway available
THEN ProcessFunction -> MAY_BE_MAINTAINED

IF Evidence insufficient
THEN ProcessClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION participates_in(Participant, BiologicalProcess)
RELATION enters(Input, BiologicalProcess)
RELATION produced_by(Output, BiologicalProcess)
RELATION transforms(Transformation, Input, Output)
RELATION changes(StateTransition, State)
RELATION occurs_at(BiologicalProcess, Location)
RELATION occurs_over(BiologicalProcess, Duration)
RELATION regulates(Regulator, BiologicalProcess)
RELATION carries(Signal, BiologicalInformation)
RELATION catalyses(Enzyme, MetabolicProcess)
RELATION moves(TransportProcess, Material)
RELATION controls(GeneRegulation, GeneExpressionProcess)
RELATION changes(CellularProcess, CellState)
RELATION produces(ReproductiveProcess, Offspring)
RELATION contributes_to(PhysiologicalProcess, Homeostasis)
RELATION changes(EcologicalProcess, EcosystemState)
RELATION changes(EvolutionaryProcess, PopulationProperties)
RELATION supports(Evidence, ProcessClaim)
RELATION records(Provenance, BiologicalProcess)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "biological process" ~= "ordered biological activity producing state change"
  "biological pathway" ~= "linked sequence or network of biological processes"
  "process participant" ~= "entity participating in a biological process"
  "process regulation" ~= "control of biological process activity"
  "signal transduction" ~= "conversion of biological signal into response"
  "metabolic process" ~= "biochemical transformation process"
  "transport process" ~= "biological movement of material between locations"
  "developmental process" ~= "biological process changing form or organisation over time"
  "physiological process" ~= "process contributing to organism function"
  "ecological process" ~= "process changing populations communities or ecosystems"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  process_identity_mapping: 0.99
  participant_flow_mapping: 0.99
  regulation_signaling_mapping: 0.99
  metabolic_transport_mapping: 0.99
  development_reproduction_mapping: 0.99
  physiology_ecology_mapping: 0.99
  dependency_network_mapping: 0.99
  evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_biological_process:
    MAP process_type
    MAP participants
    MAP inputs
    MAP outputs
    MAP location
    MAP timing
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON new_process_evidence:
    UPDATE participant_roles
    UPDATE transformation
    UPDATE dependencies
    UPDATE regulation
    UPDATE uncertainty
    PRESERVE provenance

  ON process_state_change:
    UPDATE state_variables
    UPDATE process_rate
    UPDATE downstream_dependencies
    PRESERVE provenance

  ON ontology_revision:
    PRESERVE process_identity
    UPDATE relationships
    UPDATE inference_rules
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_BIOLOGICAL_PROCESS_ONTOLOGY
  reasoning_mode: TEMPORAL_PROCESS_RELATIONAL

  preserve:
    - typed_entities
    - process_identity
    - process_type
    - participants
    - participant_roles
    - inputs_outputs
    - transformations
    - state_transitions
    - location
    - timing
    - regulation
    - dependencies
    - evidence
    - uncertainty
    - confidence
    - provenance

  infer:
    - process_feasibility
    - participant_dependencies
    - state_transition_dependencies
    - regulatory_effects
    - pathway_dependencies
    - environmental_effects
    - downstream_impacts
    - evidence_strength

  prohibit:
    - invented_process_observations
    - fabricated_participant_roles
    - assumed_causal_mechanisms_without_evidence
    - unsupported_process_rates
    - conflating_correlation_with_process_causation
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + PROCESS_IDENTITY_PARTICIPANTS_FLOW
  + LOCATION_TIME_DEPENDENCIES_REGULATION
  + SIGNALING_METABOLISM_TRANSPORT
  + GENE_EXPRESSION_CELLULAR_GROWTH_DEVELOPMENT
  + REPRODUCTION_PHYSIOLOGY_ECOLOGY_EVOLUTION
  + NETWORKS_RESOURCES_ENVIRONMENT_FAILURE
  + EVIDENCE_UNCERTAINTY_PROVENANCE
  + REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW