Biological System Ontology

AI SEARCH FLOW ALGEBRA
BIOLOGICAL SYSTEM 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-system-ontology.html

FLOW "BiologicalSystemOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY / BIOLOGICAL_SYSTEM
ONTOLOGY := BIOLOGICAL_SYSTEM_ONTOLOGY

BIOLOGICAL_SYSTEM :=
  SYSTEM_BOUNDARY + COMPONENTS + ORGANISATION
  + STRUCTURE + FUNCTION + BIOLOGICAL_PROCESSES
  + INFORMATION_FLOW + MATTER_FLOW + ENERGY_FLOW
  + INTERACTIONS + REGULATION + FEEDBACK
  + STATE + DYNAMICS + EMERGENT_PROPERTIES
  + ENVIRONMENT + ADAPTATION + EVIDENCE + PROVENANCE

PURPOSE :=
  IDENTIFY_SYSTEM -> DEFINE_BOUNDARY -> IDENTIFY_COMPONENTS
  -> MAP_ORGANISATION -> MAP_STRUCTURE_AND_FUNCTION
  -> MAP_PROCESSES_AND_FLOWS -> MAP_INTERACTIONS
  -> MAP_REGULATION_AND_FEEDBACK -> MAP_STATE_AND_DYNAMICS
  -> IDENTIFY_EMERGENT_PROPERTIES -> MAP_ENVIRONMENT
  -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY BiologicalSystem
ENTITY SystemBoundary
ENTITY BiologicalComponent
ENTITY BiologicalStructure
ENTITY BiologicalFunction
ENTITY BiologicalProcess
ENTITY BiologicalState
ENTITY StateVariable
ENTITY Biomolecule
ENTITY Gene
ENTITY Protein
ENTITY Cell
ENTITY Tissue
ENTITY Organ
ENTITY OrganSystem
ENTITY Organism
ENTITY Population
ENTITY Community
ENTITY Ecosystem
ENTITY Interaction
ENTITY Network
ENTITY Signal
ENTITY InformationFlow
ENTITY MatterFlow
ENTITY EnergyFlow
ENTITY RegulatoryProcess
ENTITY Feedback
ENTITY Homeostasis
ENTITY Perturbation
ENTITY Response
ENTITY EmergentProperty
ENTITY Environment
ENTITY Adaptation
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# SYSTEM / ORGANISATION
BiologicalSystem -> has -> SystemBoundary + COMPONENT_SET + ORGANISATION
SystemBoundary -> separates -> INTERNAL_SYSTEM + EXTERNAL_ENVIRONMENT
BiologicalSystem -> exchanges_with -> Environment

BIOLOGICAL_SYSTEM_LEVEL :=
  MOLECULAR_SYSTEM | CELLULAR_SYSTEM | TISSUE_SYSTEM
  | ORGAN_SYSTEM | ORGANISMAL_SYSTEM | POPULATION_SYSTEM
  | COMMUNITY_SYSTEM | ECOSYSTEM_SYSTEM

HigherLevelSystem -> contains_or_organises -> LowerLevelSystem
BiologicalComponent -> part_of -> BiologicalSystem

SYSTEM_ORGANISATION :=
  HIERARCHICAL | NETWORKED | MODULAR
  | DISTRIBUTED | COMPARTMENTALISED

Organisation -> influences -> SYSTEM_FUNCTION + SYSTEM_DYNAMICS

# STRUCTURE / FUNCTION / PROCESS
BiologicalStructure -> enables_or_constrains -> BiologicalFunction
BiologicalFunction -> contributes_to -> SYSTEM_BEHAVIOUR + SYSTEM_MAINTENANCE

IF Structure changes
THEN Function -> MAY_CHANGE

BiologicalProcess -> transforms -> SYSTEM_STATE

PROCESS_TYPE :=
  METABOLIC | SIGNALING | TRANSPORT | GENE_EXPRESSION
  | CELL_DIVISION | DEVELOPMENT | PHYSIOLOGICAL
  | ECOLOGICAL | EVOLUTIONARY

BiologicalProcess -> has -> INPUT + MECHANISM + OUTPUT + CONTEXT

# INFORMATION / MATTER / ENERGY
InformationFlow -> transfers -> BIOLOGICAL_INFORMATION

BIOLOGICAL_INFORMATION_FLOW :=
  STORAGE -> TRANSMISSION -> INTERPRETATION
  -> REGULATION -> RESPONSE

DNA -> stores -> GENETIC_INFORMATION
GeneExpression -> transfers -> GENETIC_INFORMATION_TO_FUNCTION
Signal -> carries -> REGULATORY_INFORMATION

SIGNALING_FLOW :=
  SIGNAL -> RECEPTOR -> TRANSDUCTION -> EFFECTOR -> RESPONSE

MatterFlow -> transfers -> MATERIAL -> through -> BiologicalSystem

MATTER_FLOW :=
  INPUT -> TRANSPORT -> TRANSFORMATION
  -> INCORPORATION -> OUTPUT_OR_WASTE

EnergyFlow -> transfers -> ENERGY -> through -> BiologicalSystem

ENERGY_FLOW :=
  SOURCE -> CAPTURE_OR_UPTAKE -> TRANSFORMATION
  -> BIOLOGICAL_WORK -> DISSIPATION

EnergyAvailability -> influences -> PROCESS_RATE + SYSTEM_FUNCTION

# INTERACTIONS / NETWORKS / REGULATION
Interaction -> connects -> BiologicalComponent + BiologicalComponent

INTERACTION_TYPE :=
  BINDING | CATALYSIS | SIGNALING | REGULATION
  | TRANSPORT | COMPETITION | COOPERATION
  | PREDATION | MUTUALISM | OTHER_CONTEXTUAL_RELATION

Network -> represents -> INTERACTING_COMPONENTS

BIOLOGICAL_NETWORK :=
  GENE_REGULATORY_NETWORK | PROTEIN_INTERACTION_NETWORK
  | METABOLIC_NETWORK | SIGNALING_NETWORK
  | NEURAL_NETWORK | ECOLOGICAL_NETWORK

Node -> represents -> BiologicalComponent
Edge -> represents -> Interaction

RegulatoryProcess -> controls -> BiologicalProcess + StateVariable

REGULATION_TYPE :=
  ACTIVATION | INHIBITION | FEEDBACK | FEEDFORWARD
  | ALLOSTERIC | TRANSCRIPTIONAL
  | POST_TRANSLATIONAL | PHYSIOLOGICAL

FEEDBACK_TYPE := NEGATIVE_FEEDBACK | POSITIVE_FEEDBACK
NegativeFeedback -> tends_to_reduce -> DEVIATION
PositiveFeedback -> tends_to_amplify -> CHANGE

Homeostasis -> maintains -> StateVariable -> within -> FUNCTIONAL_RANGE

# STATE / DYNAMICS / PERTURBATION
BiologicalState -> describes -> CONDITION_OF_BIOLOGICAL_SYSTEM
BiologicalState -> defined_by -> StateVariable

STATE_VARIABLE_TYPE :=
  CONCENTRATION | EXPRESSION_LEVEL | CELL_NUMBER
  | MEMBRANE_POTENTIAL | METABOLIC_RATE
  | PHYSIOLOGICAL_VALUE | POPULATION_SIZE
  | ENVIRONMENTAL_VALUE

SystemState(t) := SET_OF(StateVariables_at_time_t)

SystemDynamics -> describes -> CHANGE_OF_STATE_OVER_TIME

STATE_TRANSITION :=
  CURRENT_STATE + PROCESS + INPUT + ENVIRONMENT -> NEXT_STATE

DynamicBehaviour :=
  STEADY_STATE | TRANSIENT | OSCILLATORY
  | CYCLIC | BISTABLE | CHAOTIC | ADAPTIVE

Perturbation -> changes -> INPUT | COMPONENT | PARAMETER | ENVIRONMENT

PERTURBATION_TYPE :=
  GENETIC | CHEMICAL | PHYSICAL | ENVIRONMENTAL | ECOLOGICAL

PERTURBATION_RESPONSE :=
  BASELINE -> PERTURBATION -> TRANSIENT_RESPONSE
  -> RECOVERY_OR_NEW_STATE

# ROBUSTNESS / EMERGENCE / ENVIRONMENT
Robustness ->
  represents -> MAINTENANCE_OF_FUNCTION_UNDER_PERTURBATION

Robustness ->
  may_arise_from -> REDUNDANCY + FEEDBACK
  + MODULARITY + ALTERNATIVE_PATHWAYS

Resilience ->
  represents -> CAPACITY_TO_RECOVER_AFTER_DISTURBANCE

EmergentProperty ->
  arises_from -> COMPONENT_INTERACTIONS + ORGANISATION

EMERGENT_PROPERTY_TYPE :=
  HOMEOSTASIS | COLLECTIVE_BEHAVIOUR | PATTERN_FORMATION
  | ROBUSTNESS | OSCILLATION | ADAPTATION | ECOSYSTEM_FUNCTION

EmergentProperty -> not_reducible_to -> SINGLE_COMPONENT_ALONE

Environment ->
  provides -> INPUTS + CONDITIONS + CONSTRAINTS + PERTURBATIONS

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

BiologicalSystem -> generally_operates_as -> OPEN_SYSTEM
OpenSystem -> exchanges -> MATTER + ENERGY + INFORMATION -> with -> Environment

MULTISCALE_BIOLOGY :=
  MOLECULAR <-> CELLULAR <-> TISSUE <-> ORGAN
  <-> ORGANISM <-> POPULATION <-> ECOSYSTEM

# MODELLING / EVIDENCE / UNCERTAINTY
BiologicalModel -> represents -> BiologicalSystem

MODEL_TYPE :=
  CONCEPTUAL | NETWORK | MATHEMATICAL
  | STATISTICAL | COMPUTATIONAL | MECHANISTIC

Model -> includes -> VARIABLES + PARAMETERS + RELATIONSHIPS + ASSUMPTIONS
ModelPrediction -> compared_with -> Observation

SystemClaim -> supported_by -> Evidence

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

Evidence -> has -> SOURCE + METHOD + SYSTEM_CONTEXT + QUALITY + UNCERTAINTY
Correlation -> does_not_by_itself_establish -> CAUSATION

SYSTEM_EXPERIMENT_FLOW :=
  DEFINE_SYSTEM -> DEFINE_BASELINE -> APPLY_PERTURBATION
  -> MEASURE_RESPONSE -> MODEL_RELATIONSHIPS
  -> TEST_PREDICTIONS -> REFINE_MODEL

BIOLOGICAL_SYSTEM_UNCERTAINTY :=
  MEASUREMENT_UNCERTAINTY + PARAMETER_UNCERTAINTY
  + BIOLOGICAL_VARIABILITY + MODEL_UNCERTAINTY
  + ENVIRONMENTAL_UNCERTAINTY

Uncertainty -> qualifies -> StateVariable + Interaction + ModelPrediction + SystemClaim

# PROVENANCE / REASONING
Provenance ->
  records -> SYSTEM_IDENTITY + COMPONENT_IDENTITY
  + ORGANISATION_LEVEL + METHOD + MEASUREMENT
  + MODEL_VERSION + ENVIRONMENTAL_CONTEXT
  + TIME + VERSION

BiologicalSystem -> linked_to -> Provenance

BIOLOGICAL_SYSTEM_REASONING :=
  IDENTIFY_SYSTEM -> DEFINE_SYSTEM_BOUNDARY
  -> IDENTIFY_ORGANISATION_LEVEL -> IDENTIFY_COMPONENTS
  -> MAP_COMPONENT_RELATIONSHIPS -> MAP_STRUCTURE_FUNCTION
  -> MAP_BIOLOGICAL_PROCESSES -> MAP_INFORMATION_FLOW
  -> MAP_MATTER_AND_ENERGY_FLOW
  -> MAP_REGULATION_AND_FEEDBACK
  -> DEFINE_STATE_VARIABLES -> MAP_SYSTEM_DYNAMICS
  -> IDENTIFY_PERTURBATIONS_AND_RESPONSES
  -> IDENTIFY_ROBUSTNESS_AND_RESILIENCE
  -> IDENTIFY_EMERGENT_PROPERTIES
  -> MAP_ENVIRONMENTAL_COUPLING
  -> MAP_CROSS_SCALE_EFFECTS
  -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY
  -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF ComponentState changes
THEN SystemState -> MAY_CHANGE

IF InteractionStrength changes
THEN NetworkDynamics -> MAY_CHANGE

IF RegulatoryFeedback weakens
THEN HomeostaticStability -> MAY_DECREASE

IF EnergyAvailability decreases
THEN BiologicalProcessRate -> MAY_DECREASE

IF SystemBoundary changes
THEN MatterEnergyInformationExchange -> MAY_CHANGE

IF Perturbation exceeds_robustness_capacity
THEN SystemFunction -> MAY_DEGRADE

IF ComponentInteractions reorganise
THEN EmergentProperties -> MAY_CHANGE

IF Evidence insufficient
THEN SystemClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION has(BiologicalSystem, SystemBoundary)
RELATION contains(BiologicalSystem, BiologicalComponent)
RELATION part_of(BiologicalComponent, BiologicalSystem)
RELATION enables(BiologicalStructure, BiologicalFunction)
RELATION transforms(BiologicalProcess, BiologicalState)
RELATION transfers(InformationFlow, BiologicalInformation)
RELATION transfers(MatterFlow, Matter)
RELATION transfers(EnergyFlow, Energy)
RELATION connects(Interaction, BiologicalComponent)
RELATION represents(Network, InteractingComponents)
RELATION controls(RegulatoryProcess, StateVariable)
RELATION regulates(Feedback, BiologicalProcess)
RELATION maintains(Homeostasis, StateVariable)
RELATION changes(Perturbation, BiologicalSystem)
RELATION describes(Response, SystemChange)
RELATION arises_from(EmergentProperty, ComponentInteractions)
RELATION influences(Environment, BiologicalSystem)
RELATION represents(BiologicalModel, BiologicalSystem)
RELATION supports(Evidence, SystemClaim)
RELATION records(Provenance, BiologicalSystem)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "biological system" ~= "organised interacting biological components"
  "systems biology" ~= "study of interacting biological systems and networks"
  "system boundary" ~= "defined separation between biological system and environment"
  "biological network" ~= "network of interacting biological entities"
  "biological regulation" ~= "control of biological state or process"
  "homeostatic feedback" ~= "feedback maintaining biological variables within functional ranges"
  "system dynamics" ~= "change of biological system state over time"
  "emergent property" ~= "system-level property arising from component interactions"
  "biological robustness" ~= "maintenance of biological function under perturbation"
  "biological resilience" ~= "recovery of biological function after disturbance"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  system_boundary_mapping: 0.99
  component_organisation_mapping: 0.99
  structure_function_mapping: 0.99
  process_flow_mapping: 0.99
  network_regulation_mapping: 0.99
  state_dynamics_mapping: 0.99
  emergence_environment_mapping: 0.99
  evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_biological_system:
    MAP boundary
    MAP organisation_level
    MAP components
    MAP interactions
    MAP state_variables
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON new_measurement:
    UPDATE state_variables
    UPDATE system_state
    UPDATE uncertainty
    PRESERVE provenance

  ON perturbation_event:
    UPDATE perturbation
    UPDATE response
    UPDATE robustness_state
    UPDATE resilience_state
    PRESERVE provenance

  ON model_revision:
    UPDATE model_version
    UPDATE parameters
    UPDATE relationships
    REASSESS predictions
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_BIOLOGICAL_SYSTEM_ONTOLOGY
  reasoning_mode: MULTISCALE_SYSTEMS_BIOLOGY_RELATIONAL

  preserve:
    - typed_entities
    - system_boundary
    - organisation_level
    - component_identity
    - interaction_networks
    - biological_processes
    - information_flows
    - matter_and_energy_flows
    - state_variables
    - regulatory_relationships
    - environmental_context
    - evidence
    - confidence
    - provenance

  infer:
    - component_system_dependencies
    - structure_function_dependencies
    - flow_dependencies
    - regulatory_dependencies
    - state_transitions
    - robustness_and_resilience
    - emergent_properties
    - cross_scale_effects
    - evidence_strength

  prohibit:
    - invented_system_observations
    - fabricated_component_relationships
    - assumed_causality_from_correlation
    - unsupported_emergent_properties
    - assumed_system_state_without_evidence
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + SYSTEM_ORGANISATION + STRUCTURE_FUNCTION_PROCESS
  + INFORMATION_MATTER_ENERGY
  + INTERACTIONS_NETWORKS_REGULATION
  + STATE_DYNAMICS_PERTURBATION
  + ROBUSTNESS_EMERGENCE_ENVIRONMENT
  + MODELLING_EVIDENCE_UNCERTAINTY
  + PROVENANCE_REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW