Organism Ontology

FLOW ALGEBRA
ORGANISM ONTOLOGY
Version: 1.1
Domain: Entity Graph > Physical Entities > Biological Entities
Source URL: https://kirethresearch.org/booksai-core/entity-graph/physical-entities/biological-entities/organism-ontology.html
Authors: Mark Higgins — Sky (Recursive AI)
Status: Independent scientific synthesis; source page not verified

01. PURPOSE
Represent organisms as biologically organised, temporally persistent individuals, with explicit identity, structure, function, environment, lineage and evidence.

02. FORMAL SIGNATURE
Ontology O = (T, E, R, A, C, I, P), where T = types, E = entities, R = relations, A = attributes, C = constraints, I = inference rules and P = provenance.
Organism(o) => BiologicalEntity(o) AND PhysicalEntity(o).
Organism identity must not be inferred from a taxon name alone.

03. TYPES
Organism; UnicellularOrganism; MulticellularOrganism; Prokaryote; Eukaryote; Cell; Tissue; Organ; OrganSystem; Genome; Population; SpeciesTaxon; Habitat; Environment; LifeStage; BiologicalProcess; Observation; Specimen; IndividualIdentifier.

04. CLASSIFICATION
UnicellularOrganism SUBCLASS_OF Organism.
MulticellularOrganism SUBCLASS_OF Organism.
Prokaryote SUBCLASS_OF Organism.
Eukaryote SUBCLASS_OF Organism.
Classification axes can overlap: a unicellular organism may be eukaryotic or prokaryotic.
Viruses are modelled as biological agents separately; whether they count as organisms depends on the explicitly selected definition of life.

05. TYPED RELATIONS
HAS_CELL: Organism x Cell.
HAS_PART: BiologicalEntity x BiologicalEntity.
PART_OF: BiologicalEntity x BiologicalEntity.
HAS_GENOME: Organism x Genome.
MEMBER_OF_POPULATION: Organism x Population.
CLASSIFIED_AS: Organism x SpeciesTaxon.
INHABITS: Organism x Habitat.
INTERACTS_WITH: Organism x BiologicalEntity.
PERFORMS: Organism x BiologicalProcess.
HAS_LIFE_STAGE: Organism x LifeStage.
OBSERVED_BY: Organism x Observation.
DESCENDED_FROM: Organism x Organism (where individual ancestry is documented).

06. RELATION CONSTRAINTS
HAS_PART(a,b) => PART_OF(b,a), for asserted proper-part relations.
PART_OF is irreflexive for proper parts; do not infer it from mere spatial overlap.
CLASSIFIED_AS may be time-dependent and uncertain.
MEMBER_OF_POPULATION requires a specified population boundary and observation time.

07. ORGANISM IDENTITY
An organism is an individual, not its species, specimen label, cell type or habitat.
Identity records include persistent ID, observation interval, lifecycle state and provenance.
Changes in size, metabolism or location do not alone establish a new individual.
Special cases (colonies, symbioses, clonal organisms and modular organisms) require declared individuation criteria.

08. CELLULAR ORGANISATION
For cellular organisms, one or more cells contribute to structural organisation.
A multicellular organism may contain differentiated tissues, organs and organ systems, but these are not universal requirements.
A unicellular organism may perform essential functions within one cell.

09. METABOLISM AND ENERGY
Metabolic pathways transform matter and energy within an organism.
Mass and energy balances depend on system boundaries and measurement conditions.
Example: dM/dt = mass_inflow - mass_outflow + net_internal_mass_source; for total mass under conventional chemistry, internal reactions conserve mass and the net source is zero.

10. HOMEOSTASIS
Homeostasis is regulated maintenance of variables within viable ranges, not constancy at a single value.
Control example: dx/dt = f(x,u,e), with state x, regulatory input u and environmental influence e.

11. GROWTH AND DEVELOPMENT
Growth changes measurable organism properties; development changes organisation and function.
Life stages can be sequential, overlapping or conditional on environment and species.

12. REPRODUCTION
Reproduction can be sexual or asexual; individual organisms need not reproduce to be organisms.
Offspring identity is distinct from parent identity.
Do not infer ancestry without evidence.

13. HEREDITY AND VARIATION
Genomic inheritance, mutation and recombination may contribute to variation.
Genotype does not uniquely determine phenotype independent of environment.

14. ECOLOGICAL RELATIONSHIPS
Relations include predation, competition, mutualism, parasitism, commensalism and resource use.
Record interaction direction, time, location and evidence; avoid treating all interactions as symmetric.

15. POPULATION MODEL
For a closed population under simplified exponential growth: dN/dt = rN.
For a simplified density-limited model: dN/dt = rN(1-N/K).
These are conditional models, not universal laws of all organisms.

16. SURVIVAL AND MORTALITY
Survival status is time-indexed and evidence-dependent.
Death of an individual must not be inferred merely from lack of observation.

17. EVOLUTIONARY CONTEXT
Evolution applies to heritable change across generations in populations, not goal-directed transformation of a single organism.
Taxonomic and phylogenetic assignments may be revised with new evidence.

18. OBSERVATION AND MEASUREMENT
Record specimen or observation ID, timestamp, location granularity, method, units, uncertainty, operator and source.
Separate observed attributes from inferred attributes.

19. INFERENCE RULES
RULE R1: Organism(o) AND HAS_CELL(o,c) => Cell(c), if HAS_CELL is asserted with valid domain/range.
RULE R2: CLASSIFIED_AS(o,t) AND SUBTAXON_OF(t,u) => CLASSIFIED_WITHIN(o,u), provided the taxonomy version is fixed.
RULE R3: HAS_PART(o,p) => PART_OF(p,o), for proper-part relation only.
RULE R4: OBSERVED_BY(o,v) AND HAS_TIMESTAMP(v,t) => OBSERVED_AT(o,t).
RULE R5: MEMBER_OF_POPULATION(o,p) AND POPULATION_IN_HABITAT(p,h) => ASSOCIATED_WITH_HABITAT(o,h), not necessarily permanently INHABITS(o,h).

20. NON-INFERENCE RULES
Do not infer a species solely from morphology without adequate evidence.
Do not infer health from one physiological measurement.
Do not infer absence from missing data.
Do not equate a microbiome, colony, host and symbiont without explicit identity policy.

21. EXAMPLE ENTITY GRAPH
ENTITY organism_001 TYPE Organism.
ENTITY cell_001 TYPE Cell.
ENTITY observation_001 TYPE Observation.
RELATION organism_001 HAS_CELL cell_001.
RELATION organism_001 OBSERVED_BY observation_001.
ATTRIBUTE observation_001 method = microscopy.
ATTRIBUTE observation_001 evidence_status = illustrative_example.

22. SEMANTIC EQUIVALENCE
Organism ~ individual living system, subject to declared biological scope.
Organism != species taxon.
Organism != biological sample.
Organism != ecosystem.
Living organism and organism may be aliases in the adopted vocabulary, but definition-dependent edge cases remain explicit.

23. VALIDATION
CHECK V1: Every organism has a stable identifier.
CHECK V2: Every relation respects declared domain and range.
CHECK V3: Temporal assertions contain valid intervals or observation times.
CHECK V4: Units and measurement uncertainties are explicit when quantitative.
CHECK V5: Taxonomic assignments carry a reference classification and version.
CHECK V6: Evidence-backed and inferred claims are distinguished.
CHECK V7: No unqualified claims about viruses, colonies or other boundary cases.
CHECK V8: No circular proper-part relationships.

24. CONFIDENCE
CONFIDENCE fields: value in [0,1], evidence_type, provenance, method, date, calibration and limitations.
Confidence values must be supported by evidence; no arbitrary numeric certainty is assigned.

25. FLOW HASH
FLOW_HASH algorithm = SHA-256.
Canonicalisation = UTF-8; LF line endings; normalised field ordering; exclude FLOW_HASH value itself.
FLOW_HASH value = NOT_COMPUTED (compute after final canonicalisation).

26. UPDATE MODEL
UPDATE_MODEL: append provenance-linked revisions; retain previous identifiers and version history; revalidate affected relationships; recompute hash after changes.

27. AI CONSUMPTION
AI_CONSUMPTION: typed extraction, graph ingestion, temporal reasoning, biological question answering and evidence-aware inference.
Require scope checking, uncertainty reporting and provenance retention.

28. CROSS-ONTOLOGY LINKS
LINK Cell Ontology: structural cellular organisation.
LINK Tissue Ontology: multicellular tissue organisation.
LINK Organ Ontology: specialised biological structure.
LINK Living Organism Ontology: related organism-level conceptualisation.
LINK Population Ontology: group-level ecological dynamics.
LINK Genome Ontology: hereditary information.

29. COMPLETENESS CHECK
Sections expected: 29.
Sections present: 29.
Closing marker required: END FLOW ALGEBRA.

END FLOW ALGEBRA