Biological Ontologies

AI SEARCH FLOW ALGEBRA
BIOLOGICAL ONTOLOGIES
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies.html

FLOW "BiologicalOntologies" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES
ONTOLOGY := BIOLOGICAL_ONTOLOGIES_PARENT

BIOLOGY :=
  MOLECULES + GENES + CELLS + TISSUES + ORGANS
  + ORGAN_SYSTEMS + ORGANISMS + POPULATIONS
  + COMMUNITIES + ECOSYSTEMS + METABOLISM
  + PHYSIOLOGY + DEVELOPMENT + REPRODUCTION
  + HEREDITY + EVOLUTION + TAXONOMY
  + ECOLOGY + BIOLOGICAL_INFORMATION + INTERACTIONS

PURPOSE :=
  IDENTIFY_BIOLOGICAL_ENTITY
  -> DETERMINE_LEVEL_OF_ORGANISATION
  -> MAP_STRUCTURE_AND_FUNCTION
  -> MAP_GENETIC_AND_MOLECULAR_INFORMATION
  -> MAP_PROCESSES_AND_INTERACTIONS
  -> MAP_DEVELOPMENT_AND_REPRODUCTION
  -> MAP_EVOLUTIONARY_RELATIONSHIPS
  -> MAP_ECOLOGICAL_CONTEXT
  -> PRESERVE_EVIDENCE_AND_PROVENANCE

# CORE ENTITIES
ENTITY BiologicalEntity
ENTITY Biomolecule
ENTITY DNA
ENTITY RNA
ENTITY Protein
ENTITY Gene
ENTITY Genome
ENTITY Chromosome
ENTITY Cell
ENTITY Organelle
ENTITY Tissue
ENTITY Organ
ENTITY OrganSystem
ENTITY Organism
ENTITY Species
ENTITY Population
ENTITY Community
ENTITY Ecosystem
ENTITY Trait
ENTITY Phenotype
ENTITY Genotype
ENTITY MetabolicProcess
ENTITY PhysiologicalProcess
ENTITY DevelopmentalProcess
ENTITY ReproductiveProcess
ENTITY EvolutionaryProcess
ENTITY EcologicalInteraction
ENTITY Environment
ENTITY Taxon
ENTITY Ancestor
ENTITY BiologicalFunction
ENTITY BiologicalStructure
ENTITY BiologicalInformation
ENTITY Evidence
ENTITY Provenance

# LEVELS OF ORGANISATION
BIOLOGICAL_ORGANISATION :=
  MOLECULAR -> SUBCELLULAR -> CELLULAR -> TISSUE
  -> ORGAN -> ORGAN_SYSTEM -> ORGANISM
  -> POPULATION -> COMMUNITY -> ECOSYSTEM -> BIOSPHERE

BiologicalEntity -> exists_at -> BIOLOGICAL_ORGANISATION_LEVEL
HigherLevelEntity -> composed_of -> LowerLevelEntity

# MOLECULAR BIOLOGY
BIOMOLECULE_TYPE :=
  NUCLEIC_ACID | PROTEIN | LIPID
  | CARBOHYDRATE | METABOLITE | SIGNALING_MOLECULE

DNA -> stores -> GENETIC_INFORMATION
RNA -> transfers_or_executes -> GENETIC_INFORMATION
Protein -> performs -> STRUCTURAL_OR_FUNCTIONAL_ROLE

MOLECULAR_INFORMATION_FLOW :=
  DNA -> RNA -> PROTEIN

# GENETICS
Gene -> located_on -> Chromosome
Genome -> contains -> Gene
Genotype -> represents -> GENETIC_COMPOSITION
Phenotype -> influenced_by -> Genotype + Environment

GENETIC_PROCESS :=
  REPLICATION | TRANSCRIPTION | TRANSLATION
  | RECOMBINATION | MUTATION | GENE_REGULATION

Mutation -> changes -> GENETIC_SEQUENCE
Mutation -> may_affect -> Trait

# CELL BIOLOGY / STRUCTURE / FUNCTION
Cell -> fundamental_unit_of -> LIFE
Cell -> contains -> Organelle

CELL_TYPE :=
  PROKARYOTIC | EUKARYOTIC | SOMATIC
  | GERMLINE | STEM_CELL | DIFFERENTIATED_CELL

CELLULAR_PROCESS :=
  CELL_DIVISION | CELL_DIFFERENTIATION | APOPTOSIS
  | TRANSPORT | SIGNAL_TRANSDUCTION
  | ENERGY_PRODUCTION | PROTEIN_SYNTHESIS | HOMEOSTASIS

Tissue -> composed_of -> CELLS + EXTRACELLULAR_COMPONENTS
Organ -> composed_of -> MULTIPLE_TISSUES
OrganSystem -> composed_of -> ORGANS

STRUCTURE_FUNCTION :=
  BiologicalStructure -> enables -> BiologicalFunction

IF Structure changes
THEN Function -> MAY_CHANGE

# ORGANISM / PHYSIOLOGY
Organism -> instance_of -> Species
Organism -> has -> Genotype + Phenotype
Organism -> interacts_with -> Environment

ORGANISM_PROCESS :=
  GROWTH | DEVELOPMENT | METABOLISM | HOMEOSTASIS
  | RESPONSE | REPRODUCTION | AGING

PHYSIOLOGICAL_FUNCTION :=
  CIRCULATION | RESPIRATION | DIGESTION | EXCRETION
  | NEURAL_CONTROL | ENDOCRINE_REGULATION
  | IMMUNE_RESPONSE | LOCOMOTION | THERMOREGULATION

Homeostasis -> maintains -> INTERNAL_CONDITIONS_WITHIN_RANGE

# METABOLISM / DEVELOPMENT / REPRODUCTION
MetabolicProcess -> transforms -> SUBSTRATE -> PRODUCT
METABOLISM := CATABOLISM + ANABOLISM
MetabolicPathway -> contains -> REACTION_SEQUENCE
Enzyme -> catalyses -> BiochemicalReaction

DEVELOPMENT :=
  FERTILISATION -> EMBRYOGENESIS
  -> GROWTH -> DIFFERENTIATION -> MATURATION

Development ->
  regulated_by -> GENES + SIGNALS + ENVIRONMENT

ReproductiveProcess -> produces -> OFFSPRING
REPRODUCTION_TYPE := SEXUAL | ASEXUAL
Inheritance -> transfers -> GENETIC_INFORMATION_TO_OFFSPRING

# EVOLUTION
EvolutionaryProcess ->
  changes -> POPULATION_TRAITS_OVER_GENERATIONS

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

NaturalSelection ->
  acts_on -> HERITABLE_PHENOTYPIC_VARIATION

Evolution -> occurs_at -> POPULATION_LEVEL

# PHYLOGENY / TAXONOMY
Ancestor -> related_to -> Descendant
Phylogeny -> represents -> EVOLUTIONARY_RELATIONSHIPS

TAXONOMIC_RANK :=
  DOMAIN | KINGDOM | PHYLUM | CLASS
  | ORDER | FAMILY | GENUS | SPECIES

Taxon -> classifies -> BiologicalEntity
Species -> member_of -> Genus
Genus -> member_of -> Family

# POPULATION / ECOLOGY / ENVIRONMENT
Population ->
  contains -> ORGANISMS_OF_RELATED_GROUP_IN_DEFINED_AREA

POPULATION_PROPERTY :=
  SIZE | DENSITY | AGE_STRUCTURE | SEX_RATIO
  | GENETIC_VARIATION | GROWTH_RATE

PopulationDynamics ->
  changes -> POPULATION_STATE_OVER_TIME

Community -> contains -> MULTIPLE_POPULATIONS
Ecosystem -> contains -> Community + ABIOTIC_ENVIRONMENT

ECOLOGICAL_INTERACTION :=
  COMPETITION | PREDATION | HERBIVORY
  | MUTUALISM | COMMENSALISM | PARASITISM

ECOLOGICAL_FLOW :=
  PRIMARY_PRODUCERS -> CONSUMERS -> DECOMPOSERS

FoodWeb -> represents -> TROPHIC_RELATIONSHIPS

Environment ->
  contains -> BIOTIC_FACTORS + ABIOTIC_FACTORS

ABIOTIC_FACTOR :=
  TEMPERATURE | WATER | LIGHT | PH | SALINITY
  | NUTRIENTS | PRESSURE | SUBSTRATE

EnvironmentalCondition ->
  influences -> Organism + Population + Ecosystem

Adaptation ->
  may_increase -> FITNESS_IN_DEFINED_ENVIRONMENT

Adaptation -> arises_through -> EVOLUTIONARY_PROCESS

# INFORMATION / SIGNALING / NETWORKS
BiologicalInformation ->
  encoded_in -> DNA | RNA | EPIGENETIC_STATE

INFORMATION_FLOW :=
  STORAGE -> TRANSMISSION -> EXPRESSION
  -> REGULATION -> PHENOTYPIC_EFFECT

GeneRegulation -> controls -> GENE_EXPRESSION

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

BIOLOGICAL_INTERACTION :=
  MOLECULAR_INTERACTION
  | CELL_CELL_INTERACTION
  | ORGANISM_ORGANISM_INTERACTION
  | ORGANISM_ENVIRONMENT_INTERACTION

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

Node -> represents -> BiologicalEntity
Edge -> represents -> BiologicalInteraction

SYSTEMS_BIOLOGY :=
  COMPONENTS + NETWORKS + DYNAMICS
  + FEEDBACK + EMERGENT_BEHAVIOUR

HOMEOSTATIC_LOOP :=
  VARIABLE -> SENSOR -> REGULATOR
  -> EFFECTOR -> RESPONSE -> VARIABLE

# EVIDENCE / VARIATION / UNCERTAINTY
BiologicalClaim -> supported_by -> Evidence

EVIDENCE_TYPE :=
  OBSERVATIONAL | EXPERIMENTAL | MOLECULAR
  | GENETIC | PHYLOGENETIC | ECOLOGICAL
  | COMPUTATIONAL

Evidence ->
  has -> SOURCE + METHOD + CONTEXT + UNCERTAINTY

Correlation -> does_not_imply -> CAUSATION

VARIATION_SOURCE :=
  GENETIC | DEVELOPMENTAL | ENVIRONMENTAL | STOCHASTIC

BiologicalVariation ->
  may_affect -> Phenotype + Fitness + Function

BIOLOGICAL_TIME_SCALE :=
  MOLECULAR_EVENT | CELLULAR_CYCLE
  | ORGANISM_LIFETIME | GENERATION
  | EVOLUTIONARY_TIME | ECOLOGICAL_TIME

BIOLOGICAL_UNCERTAINTY :=
  MEASUREMENT_UNCERTAINTY
  + SAMPLING_UNCERTAINTY
  + MODEL_UNCERTAINTY
  + BIOLOGICAL_VARIABILITY

Uncertainty ->
  qualifies -> BiologicalClaim + Measurement + Prediction

# PROVENANCE
Provenance ->
  records -> SOURCE + OBSERVATION_OR_EXPERIMENT
  + METHOD + TAXON_OR_ORGANISM + SAMPLE
  + TIME + LOCATION_IF_RELEVANT + VERSION

BiologicalEntity -> linked_to -> Provenance

# REASONING / INFERENCE
BIOLOGICAL_ONTOLOGY_REASONING :=
  IDENTIFY_ENTITY
  -> CLASSIFY_LEVEL_OF_ORGANISATION
  -> IDENTIFY_STRUCTURE
  -> IDENTIFY_FUNCTION
  -> MAP_MOLECULAR_AND_GENETIC_INFORMATION
  -> MAP_CELLULAR_PROCESSES
  -> MAP_PHYSIOLOGY
  -> MAP_DEVELOPMENT_AND_REPRODUCTION
  -> MAP_INHERITANCE
  -> MAP_EVOLUTIONARY_RELATIONSHIPS
  -> MAP_POPULATION_AND_ECOLOGICAL_CONTEXT
  -> MAP_INTERACTIONS
  -> ASSESS_EVIDENCE
  -> QUANTIFY_UNCERTAINTY
  -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF GeneSequence changes
THEN GeneProductOrRegulation -> MAY_CHANGE

IF ProteinStructure changes
THEN ProteinFunction -> MAY_CHANGE

IF CellState changes
THEN TissueFunction -> MAY_CHANGE

IF OrganFunction changes
THEN OrganSystemPerformance -> MAY_CHANGE

IF HeritableVariation affects_reproductive_success
THEN AlleleFrequency -> MAY_CHANGE_ACROSS_GENERATIONS

IF EnvironmentalCondition changes
THEN OrganismAndPopulationResponse -> MAY_CHANGE

IF PopulationInteractions change
THEN CommunityStructure -> MAY_CHANGE

IF Evidence insufficient
THEN BiologicalClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION contains(Genome, Gene)
RELATION located_on(Gene, Chromosome)
RELATION encodes(Gene, BiologicalInformation)
RELATION produces(GeneExpression, RNA)
RELATION translates(RNA, Protein)
RELATION contains(Cell, Organelle)
RELATION composes(Cell, Tissue)
RELATION composes(Tissue, Organ)
RELATION composes(Organ, OrganSystem)
RELATION instantiates(Organism, Species)
RELATION contains(Population, Organism)
RELATION contains(Community, Population)
RELATION contains(Ecosystem, Community)
RELATION influences(Environment, Phenotype)
RELATION acts_on(NaturalSelection, HeritableVariation)
RELATION represents(Phylogeny, EvolutionaryRelationship)
RELATION classifies(Taxon, BiologicalEntity)
RELATION supports(Evidence, BiologicalClaim)
RELATION records(Provenance, BiologicalEntity)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "biological ontology" ~= "ontology of biological entities and processes"
  "biological organisation" ~= "levels of biological organization"
  "genetic information" ~= "heritable sequence information"
  "gene expression" ~= "use of genetic information to produce functional products"
  "cell signaling" ~= "cellular signal transduction"
  "physiology" ~= "biological function of organisms and systems"
  "evolution" ~= "heritable population change across generations"
  "phylogeny" ~= "evolutionary relationship history"
  "ecological interaction" ~= "interaction among organisms or populations"
  "systems biology" ~= "network-level study of interacting biological components"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  molecular_genetic_mapping: 0.99
  cellular_mapping: 0.99
  tissue_organ_mapping: 0.99
  physiology_mapping: 0.99
  development_reproduction_mapping: 0.99
  evolution_taxonomy_mapping: 0.99
  population_ecology_mapping: 0.99
  biological_information_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_biological_entity:
    MAP entity_type
    MAP organisation_level
    MAP structure
    MAP function
    MAP taxonomy
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON new_genetic_evidence:
    UPDATE gene_or_genome_state
    UPDATE genotype_relationships
    REASSESS phenotype_links
    PRESERVE provenance

  ON new_evolutionary_evidence:
    UPDATE phylogenetic_relationships
    UPDATE taxonomic_support
    UPDATE confidence
    RECOMPUTE FLOW_HASH

  ON new_ecological_observation:
    UPDATE population_state
    UPDATE interaction_state
    UPDATE environmental_context
    PRESERVE provenance

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_BIOLOGICAL_ONTOLOGIES_PARENT
  reasoning_mode: MULTISCALE_BIOLOGICAL_RELATIONAL

  preserve:
    - typed_entities
    - organisation_levels
    - molecular_relationships
    - genetic_relationships
    - cellular_relationships
    - structural_functional_relationships
    - taxonomic_identity
    - evolutionary_relationships
    - ecological_context
    - evidence
    - uncertainty
    - confidence
    - provenance

  infer:
    - composition_hierarchy
    - structure_function_dependencies
    - genotype_phenotype_dependencies
    - biological_process_dependencies
    - evolutionary_relationships
    - ecological_interactions
    - evidence_strength
    - uncertainty_impacts

  prohibit:
    - invented_biological_observations
    - fabricated_genetic_relationships
    - assumed_causality_from_correlation
    - unsupported_taxonomic_assignment
    - unsupported_evolutionary_relationships
    - missing_evidence_presented_as_established_fact

# FLOW HASH
FLOW_HASH_INPUT :=
  DOMAIN + ONTOLOGY + CORE_ENTITIES
  + BIOLOGICAL_ORGANISATION
  + MOLECULAR_BIOLOGY + GENETICS
  + CELL_BIOLOGY + STRUCTURE_FUNCTION
  + ORGANISM_PHYSIOLOGY
  + METABOLISM + DEVELOPMENT + REPRODUCTION
  + EVOLUTION + PHYLOGENY + TAXONOMY
  + POPULATION_ECOLOGY_ENVIRONMENT
  + BIOLOGICAL_INFORMATION + SIGNALING + NETWORKS
  + EVIDENCE + VARIATION + UNCERTAINTY
  + PROVENANCE + REASONING + INFERENCE_RULES
  + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE
  + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION

FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW