Plant Ontology

FLOW ALGEBRA
PLANT ONTOLOGY — BIOLOGICAL ENTITIES
Version: 1.1
Source URL: https://kirethresearch.org/booksai-core/entity-graph/physical-entities/biological-entities/plant-ontology-2.html
Authors: Mark Higgins — Sky (Recursive AI)
Publisher: Kireth Research | https://kirethresearch.org
Status: Independent scientific synthesis; source page not independently verified.

01. PURPOSE
Represent plants as typed biological entities with testable properties, relations, processes, observations and inference rules.

02. DOMAIN
Biology > Biological Entities > Plant. Scope includes extant embryophytes and broader botanical contexts when explicitly labelled.

03. ENTITY TYPES
Plant <: LivingOrganism
PlantCell <: Cell
PlantTissue <: Tissue
PlantOrgan <: Organ
Root, Stem, Leaf, Flower, Fruit, Seed <: PlantOrgan (where applicable)
Chloroplast <: Organelle
Xylem, Phloem <: VascularTissue
Species <: Taxon
Habitat <: Environment
Observation <: EvidenceRecord

04. TYPED ATTRIBUTES
Plant.id: Identifier
Plant.taxon: Taxon?
Plant.life_cycle: {annual,biennial,perennial,unknown}
Plant.growth_form: {tree,shrub,herb,grass,vine,other,unknown}
Plant.photosynthetic_pathway: {C3,C4,CAM,other,unknown}
Plant.vascular: Boolean?
Plant.flowering: Boolean?
Plant.location: GeospatialReference?
Plant.observed_at: Timestamp?
Plant.evidence: Set[EvidenceRecord]

05. RELATIONSHIPS
HAS_PART(Plant,PlantOrgan)
CONTAINS(PlantOrgan,PlantTissue)
CONTAINS(PlantTissue,PlantCell)
HAS_ORGANELLE(PlantCell,Chloroplast)
BELONGS_TO_TAXON(Plant,Taxon)
GROWS_IN(Plant,Habitat)
ABSORBS(Root,Water)
TRANSPORTS(Xylem,Water)
TRANSPORTS(Phloem,Photosynthate)
PERFORMS(Plant,PhysiologicalProcess)
INTERACTS_WITH(Plant,Organism)
DERIVED_FROM(Assertion,EvidenceRecord)

06. TYPE CONSTRAINTS
HAS_PART requires a physical part and a physical whole.
BELONGS_TO_TAXON targets a taxonomic concept, not an individual organism.
An unknown organ is not evidence of its absence.
Not every plant possesses flowers, seeds, xylem or phloem.
Not all plant cells contain chloroplasts.

07. IDENTITY AND GRANULARITY
Separate individual plant, population, species and specimen identifiers.
Different observations of one plant need not represent different plants.
Species assignment may be revised without changing individual identity.

08. CLASSIFICATION
Embryophytes include bryophyte lineages and vascular plants.
Vascular plants include lycophytes, ferns and seed plants.
Seed plants include gymnosperms and angiosperms.
Taxonomic boundaries and names are versioned claims.

09. CELLULAR STRUCTURE
Typical plant cells have a cellulose-rich wall, plasma membrane and vacuole.
Photosynthetic cells may contain chloroplasts.
Mitochondria support cellular respiration.
Cell wall composition varies by cell type and lineage.

10. ORGANISATION
Cells -> tissues -> organs -> whole plant, where applicable.
Meristems support continuing growth.
Roots commonly anchor and absorb; leaves commonly exchange gases and intercept light.
These are typical roles, not universal identity conditions.

11. PHOTOSYNTHESIS
Idealised oxygenic reaction:
6 CO2 + 6 H2O + light -> C6H12O6 + 6 O2
This is a net schematic, not a complete mechanistic pathway.
Net carbon assimilation depends on illumination, CO2, temperature, water and physiology.

12. RESPIRATION
Schematic aerobic respiration:
C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + usable energy
Plants respire in illuminated and dark conditions.

13. WATER TRANSPORT
Water uptake and transport respond to water-potential gradients.
Water potential: Psi_w = Psi_s + Psi_p + Psi_g + Psi_m (when relevant terms apply).
Transpiration depends on stomatal conductance and vapour-pressure difference.

14. NUTRIENT UPTAKE
Macronutrients include N, P, K, Ca, Mg and S.
Micronutrient requirements depend on species and growth conditions.
Nutrient availability is not identical to total soil nutrient content.

15. GROWTH
Growth rate may be measured as dM/dt for biomass M.
Relative growth rate: RGR = (1/M)(dM/dt), for M > 0.
Development includes differentiation and phase transitions.

16. REPRODUCTION
Sexual and asexual reproduction are distinguished.
Alternation of generations occurs across land plants.
Pollination and seed production apply only to relevant taxa.
Vegetative propagation may generate genetically similar offspring.

17. GENETICS
Plant genotype, phenotype and environment are distinct entities.
Phenotype = f(genotype, environment, developmental state, interactions).
Gene expression changes across tissue, time and conditions.

18. ECOLOGY
Plants participate in primary production, food webs and nutrient cycling.
Interactions include competition, herbivory, mutualism and parasitism.
A measured association does not by itself establish causation.

19. STRESS RESPONSES
Represent drought, salinity, heat, cold, pathogens and nutrient deficiency separately.
Response depends on intensity, duration, genotype and developmental stage.
Avoid assuming a single stress marker proves a diagnosis.

20. PHYSIOLOGICAL MEASURES
Leaf area: m^2
Biomass: kg or g dry mass
Assimilation rate: umol CO2 m^-2 s^-1
Stomatal conductance: mol m^-2 s^-1
Water potential: MPa
Measurements require method, units, timestamp and uncertainty.

21. INFERENCE RULES
RULE P01: Plant(x) AND HAS_PART(x,y) -> BiologicalPart(y), if part typing validated.
RULE P02: Angiosperm(x) -> SeedPlant(x).
RULE P03: SeedPlant(x) -> VascularPlant(x).
RULE P04: ObservedFlower(x) -> FloweringStructureObserved(x); species identity not inferred.
RULE P05: ChloroplastPresent(c) -> OrganellePresent(c,Chloroplast).
RULE P06: VerifiedTaxon(x,t) AND Subtaxon(t,u) -> MemberOfBroaderTaxon(x,u).
RULE P07: DroughtObservation(x) does NOT imply DroughtCausedSymptom(x) without causal evidence.

22. NEGATIVE AND OPEN-WORLD REASONING
No record of a flower does not mean non-flowering.
Unknown vascular status remains unknown.
Contradictory classifications trigger review rather than silent overwrite.

23. SEMANTIC EQUIVALENCE
"plant organism" ~ Plant only in biological contexts.
"flora" refers to a collection of plants, not necessarily an individual.
"crop" denotes a cultivation role, not a taxonomic class.
"tree" denotes growth form, not a single evolutionary lineage.

24. SEMANTIC DIFFERENCE
Plant != PlantCell
Plant != Species
Plant != Habitat
Photosynthesis != Respiration
Pollination != Fertilisation
WaterUptake != Transpiration

25. EXAMPLE A — OAK TREE
entity oak_001: Plant
BELONGS_TO_TAXON(oak_001,Quercus_robur) [provisional identification]
HAS_PART(oak_001,leaf_001)
GROWS_IN(oak_001,site_001)
Observation: leaf area measured on 2026-10-12, with method and units.
Do not infer age, health or growth rate from taxonomy alone.

26. EXAMPLE B — CARBON ASSIMILATION
Given leaf area A = 0.020 m^2 and assimilation rate a = 10 umol m^-2 s^-1,
instantaneous leaf assimilation = a*A = 0.20 umol CO2 s^-1.
Assumes rate uniform over the specified leaf area and measurement interval.

27. VALIDATION RULES
V01: All entity IDs unique within graph scope.
V02: Every relationship satisfies its domain and range.
V03: Quantities carry compatible units.
V04: Taxonomic claims record reference and version where available.
V05: Inferred statements retain their supporting evidence and rules.
V06: Unknown, absent and not-applicable are distinct values.
V07: Observations and model predictions are distinguished.
V08: Closing marker must be present.

28. CONFIDENCE
Confidence is assigned per claim, not globally to the ontology.
Store evidence quality, method, uncertainty, provenance and review status.
Do not invent numeric confidence scores without calibration.

29. PROVENANCE
Each claim may include source URI, observation ID, contributor, timestamp,
method, instrument, data licence and revision identifier.

30. FLOW HASH
Canonicalise UTF-8 content, normalise line endings, and hash using SHA-256.
FLOW_HASH.value = COMPUTE_ON_FINAL_FILE
FLOW_HASH.algorithm = SHA-256
A placeholder is not a computed hash.

31. UPDATE MODEL
Trigger updates on taxonomy revision, new measurements, corrected evidence,
relationship schema changes, or improved physiological models.
Maintain version history and reproducible derivations.

32. AI CONSUMPTION
Expose typed triples, explicit units, evidence links and validation outcomes.
AI agents must distinguish observed, inferred, modelled and hypothetical facts.
Use abstention for unsupported species identifications and causal claims.

33. INTEROPERABILITY
Map cautiously to recognised biological and taxonomic vocabularies.
Preserve original identifiers and source semantics.
Mappings are asserted with provenance; do not claim standards compliance untested.

34. LIMITATIONS
A generic ontology does not replace taxon-specific botanical descriptions.
Biological exceptions and evolving taxonomy require contextual validation.
This synthesis is not a verified transcription of the source webpage.

35. COMPLETENESS CHECK
Sections expected: 01-35
Sections present: 01-35
Required metadata: FLOW ALGEBRA, version, source, authors, provenance,
confidence, semantic equivalence, flow hash, update model, AI consumption.
Status: COMPLETE STRUCTURAL DRAFT

END FLOW ALGEBRA — PLANT ONTOLOGY