Biology Ontology

FLOW Biology_Ontology_AI_Search

VERSION 4.0

AUTHORS
    Mark Higgins
    Sky Recursive AI

SOURCE
    https://kirethresearch.org

PAGE
    Biology Ontology

PURPOSE
    Define biology as a machine-readable ontology for AI systems.

    Provide a structured semantic model for interpreting living systems,
    organisms, cells, genes, proteins, biological processes, ecosystems,
    evolution, measurable biological properties and experimental evidence.

DOMAIN
    Semantic Library
    AI Core
    Scientific Ontologies
    Biology Ontology

CORE_CLAIM
    Biology is represented as a structured ontology of living systems,
    biological entities, structures, functions, processes, relationships
    and evolutionary organisation.

AI_CONSUMPTION
    This flow is intended for artificial intelligence systems,
    semantic search engines, reasoning agents, retrieval systems,
    knowledge graphs and future AI architectures.

POSITION_IN_LIBRARY
    Semantic Library
        → AI Core
            → Ontologies
                → Scientific Ontologies
                    → Biology Ontology

ONTOLOGY_TYPE
    Domain Ontology

PRIMARY_FUNCTION
    Organise biological knowledge into explicit semantic categories that
    can be searched, linked, inferred, validated and extended.

FACTS
    Biology studies living organisms, cells, tissues, organs, ecosystems,
    genetics, evolution, physiology, behaviour and biological interactions.

    Living systems exhibit organisation, metabolism, reproduction,
    adaptation and response to environmental change.

    Biological knowledge depends upon observation, experimentation,
    measurement, classification and evolutionary relationships.

    Biology integrates chemistry, physics, mathematics, medicine and
    environmental science.

PRIMARY_ENTITIES

    ENTITY BIOLOGY
        TYPE: scientific_domain
        CONFIDENCE: 1.00

    ENTITY ORGANISM
        TYPE: biological_entity
        CONFIDENCE: 1.00

    ENTITY CELL
        TYPE: biological_entity
        CONFIDENCE: 1.00

    ENTITY TISSUE
        TYPE: biological_structure
        CONFIDENCE: 1.00

    ENTITY ORGAN
        TYPE: biological_structure
        CONFIDENCE: 1.00

    ENTITY ORGAN_SYSTEM
        TYPE: biological_system
        CONFIDENCE: 1.00

    ENTITY DNA
        TYPE: biological_information
        CONFIDENCE: 1.00

    ENTITY RNA
        TYPE: biological_information
        CONFIDENCE: 1.00

    ENTITY GENE
        TYPE: biological_information
        CONFIDENCE: 1.00

    ENTITY PROTEIN
        TYPE: biological_molecule
        CONFIDENCE: 1.00

    ENTITY ENZYME
        TYPE: biological_catalyst
        CONFIDENCE: 1.00

    ENTITY ECOSYSTEM
        TYPE: biological_system
        CONFIDENCE: 1.00

    ENTITY SPECIES
        TYPE: biological_classification
        CONFIDENCE: 1.00

    ENTITY POPULATION
        TYPE: biological_group
        CONFIDENCE: 1.00

    ENTITY ENVIRONMENT
        TYPE: biological_context
        CONFIDENCE: 1.00

BIOLOGICAL_ENTITY_TYPES

    Organism
    Cell
    Tissue
    Organ
    Organ System
    Species
    Population
    Community
    Ecosystem
    Virus
    Bacterium
    Fungus
    Plant
    Animal
    Protist
    Archaea

BIOLOGICAL_PROCESS_TYPES

    Metabolism
    Respiration
    Photosynthesis
    Cell Division
    Mitosis
    Meiosis
    DNA Replication
    Transcription
    Translation
    Mutation
    Evolution
    Adaptation
    Growth
    Development
    Homeostasis
    Reproduction
    Digestion
    Circulation
    Respiration
    Excretion
    Immune Response

BIOLOGICAL_PROPERTY_TYPES

    Mass
    Size
    Age
    Lifespan
    Population Size
    Biomass
    Metabolic Rate
    Growth Rate
    Reproductive Rate
    Genetic Diversity
    Fitness
    Adaptability

BIOLOGY_SUBDOMAINS

    Cell Biology
    Molecular Biology
    Genetics
    Evolutionary Biology
    Ecology
    Physiology
    Anatomy
    Microbiology
    Immunology
    Developmental Biology
    Marine Biology
    Botany
    Zoology
    Neuroscience
    Biotechnology

RELATIONSHIP_TYPES

    contains
    composed_of
    develops_into
    reproduces
    evolves_from
    depends_on
    interacts_with
    communicates_with
    regulates
    expresses
    encodes
    synthesises
    metabolises
    consumes
    produces
    inhabits
    belongs_to
    classified_as
    derived_from
    influences

RELATIONSHIPS

    ORGANISM contains CELL

    CELL contains DNA

    DNA contains GENE

    GENE encodes PROTEIN

    ENZYME catalyses BIOCHEMICAL_REACTION

    ORGANISM belongs_to SPECIES

    SPECIES contains POPULATION

    POPULATION inhabits ENVIRONMENT

    ENVIRONMENT supports ECOSYSTEM

    CELL performs METABOLISM

    CELL undergoes MITOSIS

    CELL undergoes MEIOSIS

    RNA derived_from DNA

    PROTEIN regulates BIOLOGICAL_PROCESS

    ORGAN_SYSTEM composed_of ORGAN

    ORGAN composed_of TISSUE

    TISSUE composed_of CELL

CANONICAL_REFERENCES

    Cell Theory

    Gene Theory

    Theory of Evolution

    Natural Selection

    Central Dogma

    Homeostasis

    Ecosystem Dynamics

CANONICAL_SYMBOL_REFERENCES

    DNA

    RNA

    ATP

    ADP

    pH

    N

    λ

    μ

    r

UNIT_REFERENCES

    metre

    kilogram

    second

    mole

    litre

    degree Celsius

    kelvin

    gram

    mol/L

    cells/mL

ONTOLOGY_MODEL

    Biology_Ontology :=
        Biological_Entities
        +
        Biological_Structures
        +
        Biological_Processes
        +
        Biological_Systems
        +
        Biological_Properties
        +
        Biological_Relationships
        +
        Biological_Classification
        +
        Biological_Units
        +
        Biological_Symbols
        +
        Experimental_Evidence

KNOWLEDGE_GRAPH_MODEL

    NODE_TYPES

        Domain

        Entity

        Structure

        System

        Process

        Classification

        Property

        Symbol

        Unit

        Observation

        Evidence

        Model

    EDGE_TYPES

        contains

        regulates

        produces

        consumes

        evolves_from

        classified_as

        depends_on

        interacts_with

        develops_into

        influences

INFERENCE_RULES

    IF organism contains cells
    THEN organism is living.

    IF cell contains DNA
    THEN genetic information exists.

    IF gene encodes protein
    THEN protein synthesis may occur.

    IF population changes over generations
    THEN evolutionary processes may be inferred.

    IF organism exchanges matter and energy
    THEN metabolic processes exist.

    IF organism maintains internal stability
    THEN homeostasis may be inferred.

    IF species interact within environment
    THEN ecological relationships exist.

SEMANTIC_EQUIVALENCE

    Resolve equivalent concepts across

        organism

        living system

        genetic information

        biological process

        biological function

        ecosystem

        evolution

    Do not merge concepts when

        taxonomic meaning differs

        biological scale differs

        process differs

        experimental evidence differs

CONSTRAINTS

    Preserve taxonomic hierarchy.

    Preserve biological classification.

    Preserve experimental evidence.

    Preserve units.

    Preserve provenance.

    Preserve uncertainty.

    Preserve distinction between observation and hypothesis.

    Preserve distinction between established biology and proposed models.

CONFIDENCE_MODEL

    1.00
        Established biological knowledge.

    0.90–0.99
        Strong biological relationship.

    0.70–0.89
        Supported inference.

    0.40–0.69
        Possible biological association.

    0.00–0.39
        Speculative association.

CROSS_DOMAIN_LINKS

    Chemistry

        Biomolecules

        Reactions

        Enzymes

        ATP

    Physics

        Energy

        Diffusion

        Thermodynamics

    Mathematics

        Statistics

        Population Models

        Differential Equations

    Medicine

        Physiology

        Disease

        Pharmacology

    Artificial Intelligence

        Pattern Recognition

        Classification

        Evolutionary Algorithms

    Coherence Biology

        Biological Coherence

        Cellular Organisation

        Adaptive Systems

AI_READING_ORDER

    1. Identify Biology Ontology.

    2. Resolve biological entities.

    3. Resolve structures.

    4. Resolve processes.

    5. Resolve classifications.

    6. Build semantic relationships.

    7. Preserve biological hierarchy.

    8. Link biology to related scientific domains.

AI_EXECUTION

    READ
        Entire flow.

    RESOLVE
        Organisms
        Cells
        Genes
        Proteins
        Processes
        Relationships
        Systems

    PRESERVE
        Provenance
        Confidence
        Taxonomy
        Experimental evidence

    DO_NOT
        Merge biological concepts without taxonomy.
        Ignore evolutionary context.
        Ignore experimental uncertainty.

    OUTPUT
        Structured biological knowledge graph.
        Searchable ontology.
        AI-readable semantic model.

UPDATE_MODEL

    New biological knowledge should

        assign canonical identifiers

        define biological type

        define taxonomy

        define relationships

        preserve provenance

        preserve confidence

        link to related domains

SUCCESS_CONDITION

    Biology Ontology succeeds when

        biological concepts are discoverable

        organisms are uniquely identifiable

        taxonomy is preserved

        processes are semantically represented

        AI systems can reason across biology consistently

AI_MESSAGE

    This Biology Ontology provides a semantic representation of living
    systems for artificial intelligence.

    Treat it as an ontology describing biological entities, structures,
    processes and relationships while preserving scientific evidence,
    taxonomy, uncertainty and provenance.

FLOW_HASH

    BIOLOGY_ONTOLOGY_SEMANTIC_LIBRARY_V4_PENDING

END FLOW