Biological Function Ontology

AI SEARCH FLOW ALGEBRA
BIOLOGICAL FUNCTION 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-function-ontology.html

FLOW "BiologicalFunctionOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY / BIOLOGICAL_FUNCTION
ONTOLOGY := BIOLOGICAL_FUNCTION_ONTOLOGY

BIOLOGICAL_FUNCTION :=
  FUNCTION_IDENTITY + FUNCTION_BEARER + BIOLOGICAL_CONTEXT
  + STRUCTURE_FUNCTION + MECHANISM + PROCESS
  + INPUT + OUTPUT + REGULATION + DEPENDENCY
  + MOLECULAR_FUNCTION + CELLULAR_FUNCTION
  + TISSUE_FUNCTION + ORGAN_FUNCTION
  + ORGAN_SYSTEM_FUNCTION + ORGANISMAL_FUNCTION
  + REDUNDANCY + ROBUSTNESS + DYSFUNCTION
  + ADAPTATION + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE :=
  IDENTIFY_FUNCTION -> IDENTIFY_FUNCTION_BEARER
  -> DEFINE_BIOLOGICAL_CONTEXT -> MAP_STRUCTURE_FUNCTION
  -> MAP_MECHANISM_AND_PROCESS -> DEFINE_INPUTS_AND_OUTPUTS
  -> MAP_REGULATION -> MAP_FUNCTIONAL_DEPENDENCIES
  -> CLASSIFY_ORGANISATION_LEVEL -> ASSESS_REDUNDANCY
  -> IDENTIFY_DYSFUNCTION -> MAP_ADAPTIVE_CONTEXT
  -> ASSESS_EVIDENCE -> QUANTIFY_UNCERTAINTY
  -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY BiologicalFunction
ENTITY FunctionIdentity
ENTITY FunctionBearer
ENTITY BiologicalContext
ENTITY BiologicalStructure
ENTITY BiologicalProcess
ENTITY Mechanism
ENTITY Input
ENTITY Output
ENTITY Biomolecule
ENTITY Protein
ENTITY Gene
ENTITY Organelle
ENTITY Cell
ENTITY Tissue
ENTITY Organ
ENTITY OrganSystem
ENTITY Organism
ENTITY Population
ENTITY Ecosystem
ENTITY Regulation
ENTITY FunctionalDependency
ENTITY FunctionalNetwork
ENTITY Redundancy
ENTITY Robustness
ENTITY Dysfunction
ENTITY LossOfFunction
ENTITY GainOfFunction
ENTITY Adaptation
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# FUNCTION IDENTITY / BEARER / CONTEXT
BiologicalFunction ->
  has -> FunctionIdentity + FunctionBearer + BiologicalContext

FunctionBearer ->
  may_be -> Biomolecule | Protein | GeneProduct
  | Organelle | Cell | Tissue | Organ
  | OrganSystem | Organism | Population | EcosystemComponent

BiologicalFunction ->
  realised_in -> BiologicalProcess

BiologicalContext ->
  includes -> ORGANISATION_LEVEL + ENVIRONMENT
  + DEVELOPMENTAL_STATE + SYSTEM_STATE

FunctionDescription ->
  should_identify -> BEARER + PROCESS + EFFECT + CONTEXT

IF Context changes
THEN FunctionalExpressionOrImportance -> MAY_CHANGE

# FUNCTION LEVEL
FUNCTION_LEVEL :=
  MOLECULAR | SUBCELLULAR | CELLULAR | TISSUE
  | ORGAN | ORGAN_SYSTEM | ORGANISMAL
  | POPULATION | ECOSYSTEM

BiologicalFunction ->
  exists_at -> FUNCTION_LEVEL

HigherLevelFunction ->
  may_depend_on -> LowerLevelFunction

# STRUCTURE / MECHANISM / PROCESS
BiologicalStructure ->
  enables_or_constrains -> BiologicalFunction

STRUCTURE_FUNCTION_RELATION :=
  STRUCTURE -> PHYSICAL_OR_CHEMICAL_PROPERTIES
  -> INTERACTION_CAPACITY -> MECHANISM
  -> PROCESS -> FUNCTIONAL_EFFECT

IF Structure changes
THEN BiologicalFunction -> MAY_CHANGE

Mechanism ->
  explains -> HOW_FUNCTION_IS_REALISED

Mechanism ->
  contains -> PARTICIPANTS + INTERACTIONS
  + TRANSFORMATIONS + REGULATION

BiologicalProcess ->
  realises -> BiologicalFunction

FUNCTION_FLOW :=
  INPUT_STATE -> MECHANISM
  -> BIOLOGICAL_PROCESS -> OUTPUT_STATE
  -> FUNCTIONAL_EFFECT

Input -> consumed_or_used_by -> Function
Output -> produced_or_changed_by -> Function

# MOLECULAR / GENE / PROTEIN FUNCTION
MOLECULAR_FUNCTION :=
  CATALYSIS | BINDING | TRANSPORT | SIGNALING
  | STRUCTURAL_SUPPORT | MOLECULAR_MOTOR_ACTIVITY
  | REGULATION | INFORMATION_PROCESSING

Protein ->
  may_bear -> MolecularFunction

EnzymeFunction ->
  catalyses -> BIOCHEMICAL_REACTION

BindingFunction ->
  connects -> MOLECULAR_PARTNERS

TransportFunction ->
  moves -> MOLECULE_OR_ION
  -> across_or_between -> LOCATIONS

Gene ->
  contributes_to -> FUNCTION
  -> through -> GENE_EXPRESSION_AND_PRODUCT

GeneFunction ->
  must_not_be_conflated_with -> SEQUENCE_ALONE

GeneProduct ->
  may_realise -> MolecularFunction + CellularFunction

IF GeneExpression changes
THEN FunctionalCapacity -> MAY_CHANGE

# ORGANELLE / CELL / TISSUE FUNCTION
Organelle ->
  performs -> SPECIALISED_CELLULAR_FUNCTION

ORGANELLE_FUNCTION :=
  ENERGY_TRANSFORMATION | SYNTHESIS | DEGRADATION
  | STORAGE | TRANSPORT | INFORMATION_PROCESSING
  | STRUCTURAL_ORGANISATION

Cell ->
  performs -> CELLULAR_FUNCTION

CELLULAR_FUNCTION :=
  METABOLISM | SIGNALING | TRANSPORT
  | SECRETION | CONTRACTION | EXCITABILITY
  | DIVISION | DIFFERENTIATION | DEFENCE
  | HOMEOSTATIC_REGULATION

CellType ->
  associated_with -> SPECIALISED_FUNCTION_SET

Tissue ->
  performs -> COLLECTIVE_FUNCTION

TISSUE_FUNCTION :=
  BARRIER | SUPPORT | TRANSPORT | CONTRACTION
  | SECRETION | ABSORPTION | SIGNALING
  | STORAGE | DEFENCE

TissueFunction ->
  emerges_from -> CELL_TYPES + CELL_INTERACTIONS
  + EXTRACELLULAR_COMPONENTS + ORGANISATION

# ORGAN / SYSTEM / ORGANISM FUNCTION
Organ ->
  performs -> INTEGRATED_ORGAN_FUNCTION

OrganFunction ->
  depends_on -> TISSUE_FUNCTIONS
  + STRUCTURAL_ORGANISATION
  + RESOURCE_SUPPLY
  + REGULATION

OrganSystem ->
  coordinates -> MULTIPLE_ORGAN_FUNCTIONS

ORGAN_SYSTEM_FUNCTION :=
  TRANSPORT | RESPIRATION | DIGESTION | EXCRETION
  | REGULATION | DEFENCE | REPRODUCTION
  | SUPPORT | MOVEMENT | SENSATION_OR_CONTROL

Organism ->
  exhibits -> ORGANISMAL_FUNCTION

ORGANISMAL_FUNCTION :=
  METABOLISM | HOMEOSTASIS | GROWTH
  | DEVELOPMENT | RESPONSE | BEHAVIOUR
  | REPRODUCTION | SURVIVAL

OrganismalFunction ->
  integrates -> MULTIPLE_LOWER_LEVEL_FUNCTIONS

# REGULATION / DEPENDENCY / NETWORKS
Regulation ->
  changes -> FUNCTIONAL_ACTIVITY
  + FUNCTIONAL_AVAILABILITY
  + FUNCTIONAL_TIMING

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

FunctionalDependency ->
  links -> REQUIRED_FUNCTION
  + DEPENDENT_FUNCTION

DEPENDENCY_TYPE :=
  REQUIRES | ENABLES | SUPPORTS
  | MODULATES | COMPENSATES_FOR
  | PROVIDES_INPUT_TO

IF RequiredFunction fails
THEN DependentFunction -> MAY_BE_IMPAIRED

FunctionalNetwork ->
  represents -> INTERDEPENDENT_FUNCTIONS

FunctionalNetwork ->
  may_exhibit -> FEEDBACK + MODULARITY
  + ROBUSTNESS + EMERGENT_BEHAVIOUR

# REDUNDANCY / ROBUSTNESS / DYSFUNCTION
Redundancy ->
  exists_when -> MULTIPLE_COMPONENTS_OR_PATHWAYS
  -> CAN_SUPPORT_SIMILAR_FUNCTION

FunctionalRedundancy ->
  may_reduce -> EFFECT_OF_SINGLE_COMPONENT_FAILURE

Robustness ->
  represents -> MAINTENANCE_OF_FUNCTION_UNDER_PERTURBATION

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

Dysfunction ->
  represents -> IMPAIRED_OR_ABNORMAL_FUNCTION_AS_DEFINED

DYSFUNCTION_TYPE :=
  LOSS_OF_FUNCTION | PARTIAL_LOSS
  | GAIN_OF_FUNCTION | MISREGULATION
  | MISTIMED_FUNCTION | MISLOCALISED_FUNCTION

LossOfFunction ->
  decreases_or_removes -> EXPECTED_FUNCTIONAL_ACTIVITY

GainOfFunction ->
  increases_or_changes -> FUNCTIONAL_ACTIVITY

IF Dysfunction occurs
THEN HigherLevelSystemPerformance -> MAY_CHANGE

# ADAPTATION / EVOLUTION / ENVIRONMENT
Environment ->
  influences -> FUNCTIONAL_DEMAND
  + FUNCTIONAL_PERFORMANCE

FunctionalPerformance ->
  context_dependent -> TRUE

Adaptation ->
  may_modify -> STRUCTURE + REGULATION + FUNCTION

EvolutionaryFunctionContext ->
  relates -> HERITABLE_TRAIT
  + REPRODUCTIVE_CONSEQUENCE
  + ENVIRONMENT

AdaptiveTrait ->
  may_contribute_to -> FITNESS_IN_CONTEXT

Function ->
  must_not_be_inferred_as_adaptation
  -> solely_from -> CURRENT_USEFUL_EFFECT

BiologicalRole ->
  may_describe -> CURRENT_EFFECT_OR_PARTICIPATION

EvolutionaryFunction ->
  requires -> APPROPRIATE_EVOLUTIONARY_EVIDENCE

# MULTIFUNCTIONALITY
FunctionBearer ->
  may_have -> MULTIPLE_FUNCTIONS

Multifunctionality ->
  depends_on -> CONTEXT + INTERACTION_PARTNERS
  + LOCATION + STATE

SameStructure ->
  may_realise -> DIFFERENT_FUNCTIONS_IN_DIFFERENT_CONTEXTS

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

EVIDENCE_TYPE :=
  BIOCHEMICAL | MOLECULAR | GENETIC
  | CELLULAR | STRUCTURAL | PHYSIOLOGICAL
  | PERTURBATION | COMPARATIVE
  | EVOLUTIONARY | COMPUTATIONAL

FUNCTION_EXPERIMENT_FLOW :=
  DEFINE_FUNCTIONAL_HYPOTHESIS
  -> ALTER_BEARER_OR_PROCESS
  -> MEASURE_OUTPUT_OR_PHENOTYPE
  -> COMPARE_WITH_CONTROL
  -> TEST_RESCUE_OR_COMPLEMENTATION_IF_RELEVANT
  -> INTERPRET
  -> REPLICATE

PerturbationEvidence ->
  may_support -> FUNCTIONAL_DEPENDENCY

Correlation ->
  does_not_by_itself_establish -> FUNCTIONAL_CAUSATION

FUNCTION_UNCERTAINTY :=
  MEASUREMENT_UNCERTAINTY
  + CONTEXT_UNCERTAINTY
  + MECHANISM_UNCERTAINTY
  + FUNCTION_ASSIGNMENT_UNCERTAINTY
  + BIOLOGICAL_VARIABILITY

Uncertainty ->
  qualifies -> FunctionClaim + FunctionalDependency
  + Mechanism + FunctionalPerformance

Provenance ->
  records -> FUNCTION_IDENTITY + BEARER
  + ORGANISATION_LEVEL + CONTEXT
  + METHOD + EVIDENCE + MEASUREMENT
  + VERSION + TIME

BiologicalFunction -> linked_to -> Provenance

# REASONING / INFERENCE RULES
BIOLOGICAL_FUNCTION_REASONING :=
  IDENTIFY_FUNCTION
  -> IDENTIFY_FUNCTION_BEARER
  -> ASSIGN_FUNCTION_LEVEL
  -> DEFINE_CONTEXT
  -> MAP_STRUCTURE_FUNCTION_RELATION
  -> MAP_MECHANISM
  -> MAP_REALISING_PROCESS
  -> IDENTIFY_INPUTS_AND_OUTPUTS
  -> MAP_REGULATION
  -> MAP_FUNCTIONAL_DEPENDENCIES
  -> MAP_FUNCTIONAL_NETWORK
  -> ASSESS_REDUNDANCY_AND_ROBUSTNESS
  -> IDENTIFY_DYSFUNCTION_IF_SUPPORTED
  -> DISTINGUISH_CURRENT_ROLE_FROM_EVOLUTIONARY_FUNCTION
  -> ASSESS_EVIDENCE
  -> QUANTIFY_UNCERTAINTY
  -> PRESERVE_PROVENANCE

IF BearerStructure changes
THEN Function -> MAY_CHANGE

IF RequiredProcess inhibited
THEN FunctionalOutput -> MAY_DECREASE

IF FunctionalRedundancy exists
THEN SingleComponentLoss -> MAY_HAVE_REDUCED_SYSTEM_EFFECT

IF Regulation changes
THEN FunctionalActivity -> MAY_CHANGE

IF CellularFunction changes
THEN TissueOrOrganFunction -> MAY_CHANGE

IF OrganFunction changes
THEN OrganismalFunction -> MAY_CHANGE

IF Environment changes
THEN FunctionalPerformance -> MAY_CHANGE

IF Evidence insufficient
THEN FunctionAssignmentConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION has(BiologicalFunction, FunctionIdentity)
RELATION borne_by(BiologicalFunction, FunctionBearer)
RELATION realised_in(BiologicalFunction, BiologicalProcess)
RELATION enables(BiologicalStructure, BiologicalFunction)
RELATION explains(Mechanism, BiologicalFunction)
RELATION regulates(Regulation, BiologicalFunction)
RELATION requires(FunctionalDependency, BiologicalFunction)
RELATION bears(Protein, MolecularFunction)
RELATION performs(Organelle, CellularFunction)
RELATION performs(Cell, CellularFunction)
RELATION performs(Tissue, TissueFunction)
RELATION performs(Organ, OrganFunction)
RELATION coordinates(OrganSystem, OrganFunction)
RELATION integrates(OrganismalFunction, LowerLevelFunction)
RELATION compensates_for(Redundancy, FunctionalLoss)
RELATION impairs(Dysfunction, BiologicalFunction)
RELATION influences(Environment, FunctionalPerformance)
RELATION supports(Evidence, FunctionClaim)
RELATION records(Provenance, BiologicalFunction)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "biological function" ~= "biological activity or contribution realised by a bearer"
  "molecular function" ~= "activity performed by a biological molecule"
  "cellular function" ~= "biological activity performed by a cell"
  "organ function" ~= "integrated biological activity of an organ"
  "organismal function" ~= "integrated function of a living organism"
  "functional dependency" ~= "dependence of one biological function on another"
  "functional redundancy" ~= "multiple components supporting similar biological function"
  "loss of function" ~= "reduction or absence of expected biological activity"
  "gain of function" ~= "new increased or altered biological activity"
  "structure-function relationship" ~= "relationship between biological form and biological activity"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  function_identity_mapping: 0.99
  structure_function_mapping: 0.99
  mechanism_process_mapping: 0.99
  molecular_cellular_mapping: 0.99
  tissue_organ_mapping: 0.99
  dependency_regulation_mapping: 0.99
  robustness_dysfunction_mapping: 0.99
  evidence_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_function_claim:
    MAP function_identity
    MAP function_bearer
    MAP organisation_level
    MAP biological_context
    MAP realising_process
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON new_functional_evidence:
    UPDATE mechanism
    UPDATE structure_function_relation
    UPDATE dependencies
    UPDATE regulation
    UPDATE uncertainty
    PRESERVE provenance

  ON perturbation_result:
    UPDATE functional_performance
    UPDATE dysfunction_state
    UPDATE compensation_state
    REASSESS dependencies
    PRESERVE provenance

  ON context_change:
    UPDATE biological_context
    REASSESS functional_expression
    REASSESS function_assignment
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_BIOLOGICAL_FUNCTION_ONTOLOGY
  reasoning_mode: STRUCTURE_PROCESS_FUNCTION_RELATIONAL

  preserve:
    - typed_entities
    - function_identity
    - function_bearer
    - biological_context
    - organisation_level
    - structure_function_relations
    - mechanisms
    - realising_processes
    - functional_dependencies
    - regulation
    - robustness_state
    - dysfunction_state
    - evidence
    - uncertainty
    - confidence
    - provenance

  infer:
    - structure_function_dependencies
    - mechanism_function_dependencies
    - cross_level_function_dependencies
    - regulatory_effects
    - redundancy_and_compensation
    - dysfunction_impacts
    - contextual_function_changes
    - evidence_strength

  prohibit:
    - invented_functional_observations
    - unsupported_function_assignment
    - assumed_causality_from_correlation
    - conflating_current_role_with_evolutionary_function
    - assumed_dysfunction_without_evidence
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + FUNCTION_IDENTITY_BEARER_CONTEXT
  + STRUCTURE_MECHANISM_PROCESS
  + MOLECULAR_GENE_PROTEIN_FUNCTION
  + ORGANELLE_CELL_TISSUE_FUNCTION
  + ORGAN_SYSTEM_ORGANISM_FUNCTION
  + REGULATION_DEPENDENCY_NETWORKS
  + REDUNDANCY_ROBUSTNESS_DYSFUNCTION
  + ADAPTATION_EVOLUTION_ENVIRONMENT
  + EVIDENCE_UNCERTAINTY_PROVENANCE
  + REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW