Biological Organisation Ontology

AI SEARCH FLOW ALGEBRA
BIOLOGICAL ORGANISATION 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-organisation-ontology.html

FLOW "BiologicalOrganisationOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY / BIOLOGICAL_ORGANISATION
ONTOLOGY := BIOLOGICAL_ORGANISATION_ONTOLOGY

BIOLOGICAL_ORGANISATION :=
  MOLECULE + MACROMOLECULE + ORGANELLE + CELL
  + TISSUE + ORGAN + ORGAN_SYSTEM + ORGANISM
  + POPULATION + COMMUNITY + ECOSYSTEM + BIOSPHERE
  + PART_WHOLE_RELATION + HIERARCHY + SCALE
  + STRUCTURE_FUNCTION + INTERACTION + EMERGENCE
  + CROSS_LEVEL_RELATION + EVIDENCE + PROVENANCE

PURPOSE :=
  IDENTIFY_BIOLOGICAL_ENTITY -> ASSIGN_ORGANISATION_LEVEL
  -> MAP_PART_WHOLE_RELATIONSHIPS -> MAP_COMPOSITION
  -> MAP_STRUCTURE_AND_FUNCTION -> MAP_INTERACTIONS
  -> MAP_CROSS_LEVEL_RELATIONSHIPS
  -> IDENTIFY_EMERGENT_PROPERTIES
  -> MAP_SPATIAL_AND_TEMPORAL_SCALE
  -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY BiologicalOrganisation
ENTITY BiologicalEntity
ENTITY OrganisationLevel
ENTITY Molecule
ENTITY Macromolecule
ENTITY MolecularComplex
ENTITY Organelle
ENTITY Cell
ENTITY Tissue
ENTITY Organ
ENTITY OrganSystem
ENTITY Organism
ENTITY Population
ENTITY Community
ENTITY Ecosystem
ENTITY Biosphere
ENTITY Component
ENTITY Whole
ENTITY BiologicalStructure
ENTITY BiologicalFunction
ENTITY Interaction
ENTITY Network
ENTITY Process
ENTITY EmergentProperty
ENTITY SpatialScale
ENTITY TemporalScale
ENTITY Environment
ENTITY Evidence
ENTITY Uncertainty
ENTITY Provenance

# HIERARCHY / MOLECULAR / CELLULAR
BIOLOGICAL_HIERARCHY :=
  MOLECULE -> MACROMOLECULE -> MOLECULAR_COMPLEX
  -> ORGANELLE -> CELL -> TISSUE -> ORGAN
  -> ORGAN_SYSTEM -> ORGANISM -> POPULATION
  -> COMMUNITY -> ECOSYSTEM -> BIOSPHERE

BiologicalEntity -> exists_at -> OrganisationLevel
HigherLevelEntity -> composed_of -> LowerLevelEntity
LowerLevelEntity -> may_be_component_of -> HigherLevelEntity

Molecule ->
  participates_in -> BIOCHEMICAL_PROCESS
  + STRUCTURAL_ASSEMBLY + SIGNALING + INFORMATION_PROCESS

Macromolecule -> composed_of -> MOLECULAR_SUBUNITS
MolecularComplex -> composed_of -> MULTIPLE_MOLECULES_OR_MACROMOLECULES

Organelle -> part_of -> Cell
Organelle -> performs -> SPECIALISED_CELLULAR_FUNCTION

Cell -> fundamental_unit_of -> CELLULAR_LIFE
Cell -> contains -> ORGANELLES + BIOMOLECULES + GENETIC_INFORMATION

CELLULAR_ORGANISATION :=
  COMPONENTS + BOUNDARY + METABOLIC_NETWORK
  + INFORMATION_NETWORK + REGULATORY_NETWORK

# TISSUE / ORGAN / ORGANISM
Tissue -> composed_of -> CELLS + EXTRACELLULAR_COMPONENTS
Tissue -> has -> STRUCTURAL_ORGANISATION + COLLECTIVE_FUNCTION
CellCellInteraction -> coordinates -> TISSUE_BEHAVIOUR

Organ -> composed_of -> MULTIPLE_TISSUES
Organ -> performs -> INTEGRATED_BIOLOGICAL_FUNCTION
OrganStructure -> enables_or_constrains -> OrganFunction

OrganSystem -> composed_of -> INTERACTING_ORGANS
OrganSystem -> performs -> SYSTEM_LEVEL_PHYSIOLOGICAL_FUNCTION
OrganSystem -> contributes_to -> ORGANISM_HOMEOSTASIS + ORGANISM_FUNCTION

Organism -> maintains -> INTEGRATED_BIOLOGICAL_STATE

ORGANISM_LEVEL_FUNCTION :=
  METABOLISM | HOMEOSTASIS | GROWTH | DEVELOPMENT
  | RESPONSE | REPRODUCTION | BEHAVIOUR

OrganismalIntegration -> coordinates -> MULTIPLE_SUBSYSTEMS

# POPULATION / COMMUNITY / ECOSYSTEM / BIOSPHERE
Population ->
  contains -> ORGANISMS -> within -> DEFINED_SPATIOTEMPORAL_CONTEXT

Population ->
  has -> SIZE + DENSITY + GENETIC_STRUCTURE
  + AGE_STRUCTURE + DISTRIBUTION

PopulationDynamics -> changes -> POPULATION_STATE

Community -> contains -> MULTIPLE_POPULATIONS
Community -> structured_by -> SPECIES_INTERACTIONS + ENVIRONMENTAL_CONDITIONS

COMMUNITY_INTERACTION :=
  COMPETITION | PREDATION | MUTUALISM
  | PARASITISM | COMMENSALISM | FACILITATION

Ecosystem -> contains -> Community + ABIOTIC_ENVIRONMENT
Ecosystem -> exchanges -> ENERGY + MATTER

ECOSYSTEM_PROCESS :=
  PRIMARY_PRODUCTION | CONSUMPTION | DECOMPOSITION
  | NUTRIENT_CYCLING | ENERGY_TRANSFER

FoodWeb -> represents -> TROPHIC_INTERACTIONS

Biosphere -> contains -> EARTH_ECOSYSTEMS_AS_DEFINED
Biosphere ->
  integrates -> GLOBAL_BIOLOGICAL + ATMOSPHERIC
  + HYDROLOGICAL + GEOLOGICAL_INTERACTIONS

# PART-WHOLE / STRUCTURE-FUNCTION / INTERACTIONS
PART_WHOLE_RELATION :=
  PART_OF | HAS_PART | COMPOSED_OF
  | CONTAINS | MEMBER_OF | SUBSYSTEM_OF

Component -> part_of -> Whole
Whole -> has_part -> Component

PartWholeRelation ->
  must_preserve -> ORGANISATION_LEVEL + CONTEXT

Composition ->
  defines -> COMPONENT_SET + COMPONENT_RELATIONSHIPS

HigherLevelEntity ->
  depends_on -> COMPONENT_PROPERTIES
  + COMPONENT_INTERACTIONS + ORGANISATION

BiologicalStructure -> exists_at -> OrganisationLevel
BiologicalFunction -> realised_by -> BiologicalStructure + BiologicalProcess

STRUCTURE_FUNCTION_RELATION :=
  STRUCTURE -> INTERACTION_CAPACITY -> PROCESS -> FUNCTION

IF Structure changes
THEN Function -> MAY_CHANGE

WITHIN_LEVEL_INTERACTION :=
  MOLECULE_MOLECULE | ORGANELLE_ORGANELLE
  | CELL_CELL | TISSUE_TISSUE | ORGAN_ORGAN
  | ORGANISM_ORGANISM | POPULATION_POPULATION

# CROSS-LEVEL / EMERGENCE / MODULARITY
CrossLevelInteraction ->
  links -> DIFFERENT_ORGANISATION_LEVELS

BOTTOM_UP_EFFECT :=
  LOWER_LEVEL_CHANGE -> MAY_AFFECT -> HIGHER_LEVEL_STATE

TOP_DOWN_CONSTRAINT :=
  HIGHER_LEVEL_CONTEXT -> MAY_CONSTRAIN -> LOWER_LEVEL_BEHAVIOUR

EmergentProperty ->
  arises_from -> COMPONENT_PROPERTIES
  + COMPONENT_INTERACTIONS + ORGANISATION

EMERGENT_PROPERTY_TYPE :=
  CELLULAR_FUNCTION | TISSUE_FUNCTION | ORGAN_FUNCTION
  | HOMEOSTASIS | COLLECTIVE_BEHAVIOUR
  | POPULATION_DYNAMICS | COMMUNITY_STRUCTURE
  | ECOSYSTEM_FUNCTION

EmergentProperty ->
  not_attributable_to -> SINGLE_COMPONENT_ALONE

Module -> subset_of -> BiologicalSystem
Module ->
  contains -> FUNCTIONALLY_OR_STRUCTURALLY_RELATED_COMPONENTS

Modularity ->
  may_support -> SPECIALISATION + ROBUSTNESS + EVOLVABILITY

Network -> represents -> INTERACTING_ENTITIES
Node -> represents -> BiologicalEntity
Edge -> represents -> BiologicalInteraction

# SCALE / ENVIRONMENT / FLOWS
SpatialScale -> describes -> PHYSICAL_EXTENT
TemporalScale -> describes -> PROCESS_DURATION_OR_CHANGE_RATE

SPATIAL_SCALE :=
  NANOMETRE | MICROMETRE | MILLIMETRE
  | CENTIMETRE | METRE | KILOMETRE | GLOBAL

TEMPORAL_SCALE :=
  MICROSECOND | MILLISECOND | SECOND | MINUTE
  | HOUR | DAY | YEAR | GENERATION | EVOLUTIONARY_TIME

BiologicalProcess -> occurs_over -> TemporalScale

Environment ->
  interacts_with -> BiologicalEntity -> at -> MULTIPLE_LEVELS

ENVIRONMENTAL_EFFECT :=
  MOLECULAR_EFFECT | CELLULAR_EFFECT
  | ORGANISMAL_EFFECT | POPULATION_EFFECT
  | ECOSYSTEM_EFFECT

InformationFlow ->
  connects -> COMPONENTS + ORGANISATION_LEVELS

GeneExpressionChange ->
  may_affect -> CELL_STATE -> TISSUE_FUNCTION -> ORGANISM_PHENOTYPE

MatterFlow ->
  connects -> MOLECULAR + CELLULAR
  + ORGANISMAL + ECOSYSTEM_LEVELS

EnergyFlow ->
  connects -> BIOCHEMICAL + PHYSIOLOGICAL + TROPHIC_LEVELS

# CLASSIFICATION / EVIDENCE / UNCERTAINTY
OrganisationClassification ->
  assigns -> BiologicalEntity -> OrganisationLevel

ClassificationCriteria :=
  COMPOSITION + STRUCTURE + FUNCTION
  + SCALE + RELATION_TO_HIGHER_AND_LOWER_LEVELS

IF Entity spans_multiple_levels
THEN Classification -> MAY_INCLUDE_MULTIPLE_CONTEXTUAL_LEVELS

OrganisationClaim -> supported_by -> Evidence

EVIDENCE_TYPE :=
  MOLECULAR | MICROSCOPIC | ANATOMICAL
  | PHYSIOLOGICAL | POPULATION | ECOLOGICAL
  | EXPERIMENTAL | COMPUTATIONAL

Evidence ->
  has -> SOURCE + METHOD + ENTITY
  + SCALE + CONTEXT + QUALITY + UNCERTAINTY

ORGANISATION_UNCERTAINTY :=
  CLASSIFICATION_UNCERTAINTY + BOUNDARY_UNCERTAINTY
  + MEASUREMENT_UNCERTAINTY + SCALE_UNCERTAINTY
  + MODEL_UNCERTAINTY

Uncertainty ->
  qualifies -> OrganisationLevel + PartWholeRelation
  + CrossLevelInteraction + EmergentProperty

Provenance ->
  records -> ENTITY_IDENTITY + ORGANISATION_LEVEL
  + PART_WHOLE_RELATION + SCALE + METHOD
  + OBSERVATION + CONTEXT + VERSION

BiologicalOrganisation -> linked_to -> Provenance

# REASONING / INFERENCE RULES
BIOLOGICAL_ORGANISATION_REASONING :=
  IDENTIFY_ENTITY -> IDENTIFY_COMPONENTS
  -> ASSIGN_ORGANISATION_LEVEL
  -> DEFINE_PART_WHOLE_RELATIONSHIPS
  -> MAP_COMPOSITION -> MAP_STRUCTURE_FUNCTION
  -> MAP_WITHIN_LEVEL_INTERACTIONS
  -> MAP_CROSS_LEVEL_INTERACTIONS
  -> IDENTIFY_MODULES_AND_NETWORKS
  -> IDENTIFY_EMERGENT_PROPERTIES
  -> MAP_SPATIAL_SCALE -> MAP_TEMPORAL_SCALE
  -> MAP_ENVIRONMENTAL_CONTEXT
  -> MAP_INFORMATION_MATTER_AND_ENERGY_FLOW
  -> ASSESS_CLASSIFICATION -> ASSESS_EVIDENCE
  -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

IF TissueSet forms_integrated_functional_structure
THEN HigherLevelEntity -> MAY_CLASSIFY_AS_ORGAN

IF OrganSet coordinates_integrated_physiological_function
THEN HigherLevelEntity -> MAY_CLASSIFY_AS_ORGAN_SYSTEM

IF Organisms share_defined_spatiotemporal_population_context
THEN Group -> MAY_CLASSIFY_AS_POPULATION

IF MultiplePopulations interact_in_defined_area
THEN Assemblage -> MAY_CLASSIFY_AS_COMMUNITY

IF Community interacts_with_abiotic_environment
THEN System -> MAY_CLASSIFY_AS_ECOSYSTEM

IF LowerLevelState changes
THEN HigherLevelProperty -> MAY_CHANGE

IF ComponentInteractions change
THEN EmergentProperty -> MAY_CHANGE

IF Evidence insufficient
THEN OrganisationClassificationConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION exists_at(BiologicalEntity, OrganisationLevel)
RELATION composed_of(HigherLevelEntity, LowerLevelEntity)
RELATION part_of(Component, Whole)
RELATION contains(Cell, Organelle)
RELATION composes(Cell, Tissue)
RELATION composes(Tissue, Organ)
RELATION composes(Organ, OrganSystem)
RELATION composes(OrganSystem, Organism)
RELATION contains(Population, Organism)
RELATION contains(Community, Population)
RELATION contains(Ecosystem, Community)
RELATION contains(Biosphere, Ecosystem)
RELATION enables(BiologicalStructure, BiologicalFunction)
RELATION links(Interaction, BiologicalEntity)
RELATION arises_from(EmergentProperty, ComponentInteractions)
RELATION represents(Network, InteractingEntities)
RELATION influences(Environment, BiologicalEntity)
RELATION supports(Evidence, OrganisationClaim)
RELATION records(Provenance, BiologicalOrganisation)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "biological organisation" ~= "hierarchical organization of living systems"
  "biological level of organisation" ~= "level in the biological hierarchy"
  "part-whole relation" ~= "biological component-composite relationship"
  "cellular level" ~= "cell level of biological organization"
  "organ system" ~= "integrated set of organs"
  "population level" ~= "organisation of organisms into populations"
  "community level" ~= "organisation of interacting populations"
  "ecosystem level" ~= "biotic community plus abiotic environment"
  "emergent property" ~= "higher-level property arising from component interactions"
  "cross-level interaction" ~= "interaction between biological organisation levels"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  hierarchy_mapping: 0.99
  molecular_cellular_mapping: 0.99
  tissue_organ_mapping: 0.99
  organism_population_mapping: 0.99
  community_ecosystem_mapping: 0.99
  part_whole_mapping: 0.99
  emergence_mapping: 0.99
  scale_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_biological_entity:
    MAP entity_identity
    MAP components
    MAP organisation_level
    MAP part_whole_relations
    MAP scale
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON composition_change:
    UPDATE component_set
    UPDATE part_whole_relations
    REASSESS organisation_level
    REASSESS emergent_properties
    PRESERVE provenance

  ON new_cross_level_evidence:
    UPDATE cross_level_relations
    UPDATE structure_function_links
    UPDATE confidence
    PRESERVE provenance

  ON classification_revision:
    UPDATE organisation_level
    PRESERVE entity_identity
    PRESERVE provenance
    RECOMPUTE FLOW_HASH

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_BIOLOGICAL_ORGANISATION_ONTOLOGY
  reasoning_mode: HIERARCHICAL_MULTISCALE_BIOLOGICAL_RELATIONAL

  preserve:
    - typed_entities
    - organisation_levels
    - part_whole_relations
    - component_identity
    - structure_function_relations
    - within_level_interactions
    - cross_level_interactions
    - spatial_scale
    - temporal_scale
    - emergent_properties
    - evidence
    - confidence
    - provenance

  infer:
    - organisation_hierarchy
    - composition_dependencies
    - part_whole_dependencies
    - structure_function_dependencies
    - cross_level_effects
    - emergent_properties
    - scale_relationships
    - classification_state
    - evidence_strength

  prohibit:
    - invented_biological_components
    - fabricated_part_whole_relations
    - unsupported_organisation_level
    - assumed_emergence_without_interaction_evidence
    - conflating_population_community_ecosystem_levels
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + HIERARCHY_MOLECULAR_CELLULAR
  + TISSUE_ORGAN_ORGANISM
  + POPULATION_COMMUNITY_ECOSYSTEM_BIOSPHERE
  + PART_WHOLE_STRUCTURE_FUNCTION_INTERACTIONS
  + CROSS_LEVEL_EMERGENCE_MODULARITY
  + SCALE_ENVIRONMENT_FLOWS
  + CLASSIFICATION_EVIDENCE_UNCERTAINTY
  + REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW