Living Organism Ontology

FLOW ALGEBRA
LIVING ORGANISM ONTOLOGY
Version: 1.1
Library: Kireth Semantic Library
Source URL: https://kirethresearch.org/booksai-core/entity-graph/physical-entities/biological-entities/living-organism-ontology-2.html
Authors: Mark Higgins — Sky (Recursive AI)
Status: Independent scientific synthesis; source webpage not independently verified

01. PURPOSE
Model living organisms as biological individuals with organised structures, regulated processes, life histories, evolutionary lineages and environmental interactions.

02. SCOPE
Covers cellular organisms, unicellular and multicellular life, metabolism, homeostasis, reproduction, development, adaptation and death. Viruses and other acellular replicators require explicit boundary classifications; do not automatically classify them as cellular organisms.

03. TYPE SYSTEM
TYPE Entity
TYPE PhysicalEntity <: Entity
TYPE BiologicalEntity <: PhysicalEntity
TYPE Organism <: BiologicalEntity
TYPE Cell <: BiologicalEntity
TYPE Tissue <: BiologicalEntity
TYPE Organ <: BiologicalEntity
TYPE OrganSystem <: BiologicalEntity
TYPE Population <: BiologicalEntity
TYPE Species <: BiologicalEntity
TYPE Environment <: Entity
TYPE BiologicalProcess <: Entity
TYPE LifeStage <: Entity
TYPE Trait <: Entity
TYPE Genome <: BiologicalEntity
TYPE Observation <: Entity
TYPE Measurement <: Observation
TYPE Taxon <: Entity
TYPE TimeInterval <: Entity
TYPE Evidence <: Entity

04. CORE PREDICATES
organism(x): x is an organism
cellular(x): x has cellular organisation
has_part(x,y): y is part of x
has_cell(x,c): c is a cell belonging to x
member_of(x,p): x belongs to population p
assigned_taxon(x,t): x is assigned to taxon t under a specified taxonomy
participates_in(x,p): x participates in biological process p
inhabits(x,e): x occupies environment e
has_trait(x,t): x exhibits trait t
has_genome(x,g): genome g is associated with x
at_stage(x,s,t): x is in life stage s at time t
observed_at(x,t): observation of x at time t
supported_by(claim,e): evidence e supports claim

05. IDENTITY AND PERSISTENCE
An organism is an individual persisting across changes in composition, size, physiology and life stage. Identity is not reducible to a single genome sequence or a fixed collection of atoms.
Identity assertions require contextual evidence, especially for clonal organisms, colonial organisms, symbioses and metamorphosis.

06. CELLULAR ORGANISATION
RULE organism(x) AND cellular(x) -> EXISTS c: Cell(c) AND has_cell(x,c)
Do not infer multicellularity from cellularity. Unicellular organisms have one cell at a time in ordinary life stages; multicellular organisms have organised multiple cells.

07. LEVELS OF ORGANISATION
cell -> tissue -> organ -> organ_system -> organism is a useful hierarchy for many multicellular organisms, not a universal requirement. Bacteria and many protists lack tissues and organs.

08. METABOLISM
Metabolism comprises coupled biochemical transformations that support maintenance, growth and reproduction. Distinguish autotrophy/heterotrophy and aerobic/anaerobic pathways; do not infer that every organism uses oxygen.
Energy balance model: dE/dt = P_in - P_maintenance - P_growth - P_export, with all terms defined for a particular model boundary.

09. HOMEOSTASIS
Homeostasis denotes regulation of internal variables within viable ranges. It is not perfect constancy.
Feedback: error(t) = setpoint(t) - measured_value(t)
Regulatory response may be negative or positive feedback depending on mechanism.

10. GROWTH AND DEVELOPMENT
Growth is change in biomass, cell number or size; development is change in form or functional organisation. Some mature organisms do not continuously grow.
Simple illustrative growth: dB/dt = r B (1 - B/K), where r and K are context-dependent and not universal biological laws.

11. REPRODUCTION
Distinguish sexual, asexual and mixed reproductive modes. Reproduction is a property of lineages and biological systems, not a mandatory observed event for every individual organism.
RULE reproduces(x,y) -> offspring_of(y,x), only when parentage evidence establishes the relation.

12. HEREDITY
Genomes encode heritable information in cellular organisms; inheritance also includes epigenetic and cytoplasmic mechanisms. Genotype does not uniquely determine phenotype without environmental and developmental context.

13. EVOLUTIONARY CONTEXT
Organisms belong to populations and evolutionary lineages. Evolution concerns heritable change in populations across generations, not purposeful change by an individual organism.

14. ECOLOGICAL RELATIONSHIPS
RELATION consumes(organism, resource)
RELATION competes_with(organism, organism)
RELATION mutualistic_with(organism, organism)
RELATION parasitises(organism, host)
RELATION pollinates(organism, plant)
RELATION decomposes(organism, material)
Relationships must be evidenced and may vary by life stage or environment.

15. ENVIRONMENTAL DEPENDENCE
Organisms exchange matter, energy and information with environments. Environmental limits include temperature, water availability, nutrients, pH, salinity and radiation as appropriate to the taxon.

16. LIFE CYCLE
Life stages may include embryo, juvenile, adult, reproductive and senescent phases, but not all stages apply to all taxa. Use a taxon-specific state-transition model.
TRANSITION stage_a -> stage_b WHEN developmental_conditions_met

17. DEATH AND VIABILITY
Distinguish living, dormant, nonviable and dead states using domain-appropriate criteria. Dormancy is not equivalent to death. Clinical death criteria for animals do not automatically generalise to plants or microorganisms.

18. TAXONOMIC CLASSIFICATION
Taxonomic assignment is versioned and evidence-dependent. Species concepts differ across groups. A taxon name is not an immutable biological identity.

19. SYMBIOSIS AND HOLOBIONTS
Hosts and symbionts may form tightly integrated biological systems without becoming a single organism under every identity convention. Represent component organisms and their associations explicitly.

20. COLONIAL AND MODULAR ORGANISMS
Corals, fungi and clonal plants can challenge simple individual boundaries. Represent ramets, genets, colonies and modules separately when relevant.

21. MEASUREMENT MODEL
Measurement = (subject, property, value, unit, method, time, uncertainty, provenance)
Examples: biomass [kg], length [m], temperature [K], metabolic rate [W], population count [dimensionless].
Do not assign universal units to dimensionless biological scores without a defined scale.

22. DYNAMIC MODEL
STATE x(t) = [biomass, nutrient_reserves, hydration, physiological_variables, life_stage]
EVOLUTION dx/dt = f(x, environment, interactions, parameters)
The state vector and dynamics must be specified for each application; no single f describes all life.

23. POPULATION LINK
Population abundance N(t) may change through births, deaths, immigration and emigration:
dN/dt = B - D + I - E
The equation is a bookkeeping identity when quantities share a time basis.

24. INFERENCE RULES
RULE has_cell(x,c) AND Cell(c) -> cellular_structure_evidence(x)
RULE member_of(x,p) AND Population(p) -> population_member(x)
RULE at_stage(x,s,t1) AND at_stage(x,s2,t2) AND t2>t1 -> stage_history(x,s,s2)
RULE has_trait(x,t) AND supported_by(has_trait(x,t),e) -> evidence_backed_trait(x,t)
NONRULE organism(x) -> reproduces(x)
NONRULE organism(x) -> aerobic(x)
NONRULE has_genome(x,g) -> uniquely_identified_by(x,g)

25. CONSTRAINTS
C1: Every entity has a stable identifier within the dataset.
C2: Relations have declared domain and range.
C3: Temporal observations include timestamps or bounded intervals.
C4: Taxonomic assertions include source/version when available.
C5: Measurement values have units and uncertainty where applicable.
C6: Inferred claims preserve provenance and confidence.
C7: Conflicting observations are retained and reconciled, not silently overwritten.

26. EXAMPLE A — BACTERIUM
entity: Bacillus_subtilis_cell_001
class: Organism
cellularity: unicellular
assigned_taxon: Bacillus subtilis
process: cellular_respiration (under appropriate conditions)
validation: do not infer obligate aerobic metabolism from taxon membership alone.

27. EXAMPLE B — TREE
entity: oak_001
class: Organism
cellularity: multicellular
has_part: leaf_001, root_001
processes: photosynthesis, respiration, transpiration
validation: organ relations must refer to the same individual and observation period.

28. EXAMPLE C — FUNGAL NETWORK
entity: mycelium_001
class: BiologicalEntity
identity_scope: unresolved without sampling and genetic evidence
validation: distinguish a connected mycelial network from a genetically defined individual.

29. SEMANTIC EQUIVALENCE
living_organism ~ biological_individual [context-dependent]
organism != species
organism != population
organism != ecosystem
organism != cell (except where the individual is unicellular)
Equivalent terms require matching identity, taxonomic and temporal scope.

30. SEMANTIC DIFFERENCE
Living organism: individual biological system.
Population: collection of organisms in a specified context.
Species: taxonomic/evolutionary grouping under a defined species concept.
Ecosystem: organisms plus abiotic environment and interactions.

31. CONFIDENCE
CONFIDENCE in [0,1]
Evidence-supported confidence is claim-specific, not an intrinsic certainty of the ontology.
Do not fabricate numerical confidence. Use null/unassessed where no calibrated evidence model exists.

32. PROVENANCE
Capture source URI, observer, observation date, method, instrument, taxonomy version and transformation history where available.
SOURCE_PAGE_VERIFICATION: NOT_VERIFIED

33. FLOW HASH
FLOW_HASH.algorithm: SHA-256
FLOW_HASH.scope: canonical UTF-8 file bytes excluding any embedded hash field
FLOW_HASH.value: computed by external ingestion pipeline
Never claim a hash was computed unless the canonicalisation and digest were actually executed.

34. UPDATE MODEL
UPDATE_MODEL.version: 1.1
UPDATE_MODEL.strategy: append evidence, version assertions, revalidate dependent inferences
UPDATE_MODEL.conflict_policy: retain contradictory claims with provenance until adjudicated
UPDATE_MODEL.retraction: explicit tombstone/retraction event

35. AI CONSUMPTION
AI_CONSUMPTION.format: typed text flow algebra
AI_CONSUMPTION.tasks: entity linking, knowledge graph construction, biological reasoning, educational retrieval, evidence auditing
AI_CONSUMPTION.requirements: preserve uncertainty; distinguish observations from hypotheses; reject invalid cross-level inferences

36. VALIDATION TESTS
TEST organism_not_species: PASS if class distinction retained
TEST unicellular_not_multicellular: PASS if one-cell example is not assigned tissues
TEST dormant_not_dead: PASS if dormancy does not imply death
TEST taxonomy_version: PASS if taxonomic source can be recorded
TEST provenance: PASS if observations and inferences are traceable
TEST evidence_conflict: PASS if conflicting records are not silently deleted

37. LIMITATIONS
This ontology is a formal conceptual model, not a universal operational test for life. The status of viruses, prions and synthetic protocells depends on the scientific definition and context. Model predictions require independently validated empirical parameters.

38. COMPLETENESS CHECK
Required sections: 01-38
Section sequence: complete
Closing marker: present
Source verification: not independently verified

END FLOW ALGEBRA — LIVING ORGANISM ONTOLOGY