Microorganism Ontology

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

01. PURPOSE
Represent microscopic biological entities, their classification, structure, metabolism, reproduction, environments, interactions, and evidence with typed, checkable rules.

02. SCOPE
Includes bacteria, archaea, microscopic fungi, protists, microscopic algae and other microscopic cellular organisms. Viruses and prions are represented as associated acellular infectious agents, not automatically classified as living cellular microorganisms. Microscopic is contextual rather than an absolute taxonomic boundary.

03. CORE TYPES
TYPE Entity
TYPE BiologicalEntity <: Entity
TYPE CellularOrganism <: BiologicalEntity
TYPE Microorganism <: CellularOrganism [contextual microscopic classification]
TYPE Bacterium <: Microorganism
TYPE Archaeon <: Microorganism
TYPE MicroscopicEukaryote <: Microorganism
TYPE MicroscopicFungus <: MicroscopicEukaryote
TYPE Protist <: MicroscopicEukaryote [informal grouping]
TYPE MicroscopicAlga <: MicroscopicEukaryote [where eukaryotic]
TYPE AcellularInfectiousAgent <: BiologicalEntity
TYPE Virus <: AcellularInfectiousAgent
TYPE Prion <: AcellularInfectiousAgent
TYPE Habitat; TYPE Population; TYPE Community; TYPE Host
TYPE MetabolicPathway; TYPE Nutrient; TYPE Gene; TYPE Genome
TYPE Observation; TYPE Assay; TYPE Evidence; TYPE Taxon

04. IDENTIFIERS
microbe_id: URI; taxon_id: authoritative taxonomy identifier where available; observation_id: URI; strain_id: URI or curated accession. Taxon identity, strain identity and individual-cell identity MUST NOT be conflated.

05. TYPED RELATIONSHIPS
INSTANCE_OF(Entity, Type)
CLASSIFIED_AS(Microorganism, Taxon)
HAS_GENOME(CellularOrganism, Genome)
HAS_GENE(Genome, Gene)
USES_PATHWAY(Microorganism, MetabolicPathway)
CONSUMES(Microorganism, Nutrient)
INHABITS(Microorganism, Habitat)
PART_OF_POPULATION(Microorganism, Population)
PART_OF_COMMUNITY(Population, Community)
INTERACTS_WITH(Entity, Entity)
COLONISES(Microorganism, Host)
CAUSES_DISEASE(Microorganism, Host) [requires evidence and context]
OBSERVED_BY(Entity, Observation)
SUPPORTED_BY(Assertion, Evidence)

06. TAXONOMY RULE
CLASSIFIED_AS(x,t) does not imply all members of taxon t are microscopic at every life stage. Record taxonomy authority and version.

07. CELLULARITY RULE
Microorganism(x) -> CellularOrganism(x) within this ontology's core definition. Virus(x) -> AcellularInfectiousAgent(x). Virus(x) does not entail CellularOrganism(x).

08. PROKARYOTIC ORGANISATION
Bacteria and archaea lack a membrane-bound nucleus; their cellular envelopes, membranes, genomes and metabolic pathways differ across lineages. Do not infer a universal cell wall composition.

09. EUKARYOTIC ORGANISATION
Microscopic eukaryotes may have nuclei and organelles; morphology and life cycles vary. Some protists are multicellular or macroscopic, so classification requires context.

10. METABOLISM
Represent energy source (light/chemical), electron donor (organic/inorganic), and carbon source (organic/inorganic) as separate dimensions. Aerobic, anaerobic and facultative labels require organism- and condition-specific evidence.

11. GROWTH
Population growth under idealised unrestricted conditions: dN/dt = r*N; N(t)=N0*exp(r*t). Applicability: constant per-capita growth rate, adequate resources and stable conditions.

12. LOGISTIC MODEL
For density-dependent growth: dN/dt = r*N*(1-N/K). K is environment-dependent carrying capacity, not an intrinsic universal species constant.

13. GENERATION TIME
For exponential binary fission under suitable conditions: g = ln(2)/r. Not universally applicable to all microbial reproductive modes.

14. REPRODUCTION
Represent binary fission, budding, sporulation and sexual/asexual eukaryotic reproduction as distinct processes. Sporulation does not necessarily imply reproduction; bacterial endospores primarily support survival.

15. GENETIC VARIATION
MUTATION, TRANSFORMATION, TRANSDUCTION and CONJUGATION are distinct processes; horizontal gene transfer is not equivalent to vertical inheritance.

16. ECOLOGICAL ROLES
Roles include decomposition, primary production, nutrient cycling, symbiosis, fermentation and pathogenesis. Roles are context-specific and not exclusive.

17. HOST RELATIONSHIPS
COLONISES(x,h) does not imply CAUSES_DISEASE(x,h). Distinguish commensalism, mutualism, opportunism and pathogenicity with explicit evidence.

18. BIOFILMS
Biofilm membership may involve extracellular matrix, adhesion and community-level interactions. Biofilm formation is not a universal microbial trait.

19. ENVIRONMENTAL VARIABLES
Record temperature [K or deg C], pH [dimensionless], salinity [specified units], oxygen availability, water activity and pressure [Pa]. Always record units and measurement method.

20. OBSERVATION METHODS
Microscopy, culture, sequencing, qPCR, flow cytometry and metabolomics provide different evidence. DNA detection alone does not establish viability or active infection.

21. ABUNDANCE
Cell concentration C = n/V [cells per volume]; distinguish measured cells, colony-forming units, gene copies and relative sequence abundance. These quantities are not interchangeable.

22. DIVERSITY
Community diversity measures depend on sampling, detection, sequencing pipeline and taxonomic resolution. Missing observations do not prove absence.

23. SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE('microbe','microorganism') = contextual alias only; do not assert unconditional identity. 'Bacteria' != 'prokaryotes'; archaea are also prokaryotic. 'Virus' != 'cellular organism'.

24. INFERENCE RULES
RULE R1: Bacterium(x) -> Microorganism(x).
RULE R2: Archaeon(x) -> Microorganism(x).
RULE R3: Microorganism(x) AND INHABITS(x,h) -> MicrobialOccurrence(x,h) [when supported by observation].
RULE R4: OBSERVED_BY(x,o) AND SUPPORTED_BY(o,e) -> EvidenceLinkedObservation(x,o,e).
RULE R5: COLONISES(x,h) -/-> CAUSES_DISEASE(x,h).
RULE R6: DNA_DETECTED(x,s) -/-> VIABLE(x,s).
RULE R7: CLASSIFIED_AS(x,t) -/-> PATHOGENIC(x).

25. CONSTRAINTS
ASSERT organism_id unique within dataset.
ASSERT each numeric measurement has unit, method, time and uncertainty where available.
ASSERT taxonomic assertion carries source/version.
ASSERT disease claims include host, condition and evidence.
ASSERT acellular agents are not inferred to possess cellular metabolism.

26. WORKED EXAMPLE A — GROWTH
N0=1000 cells; r=0.6931 per hour; t=3 h.
N(t)=1000*exp(0.6931*3) ~= 8000 cells.
Interpretation valid only under idealised exponential growth assumptions.

27. WORKED EXAMPLE B — CLASSIFICATION
Entity E1: Escherichia coli strain identifier S1.
INSTANCE_OF(E1,Bacterium); HAS_GENOME(E1,G1).
Do not infer that E1 is pathogenic without strain-specific evidence.

28. WORKED EXAMPLE C — DETECTION
Sequencing detects a microbial marker in sample A.
Inference permitted: marker detected subject to assay limits.
Inference prohibited: live organism proven; infection proven; abundance equals read count.

29. UNCERTAINTY
Confidence is attached to individual assertions, not entire taxa by default. Separate taxonomic confidence, measurement uncertainty and causal confidence.

30. CONFIDENCE MODEL
CONFIDENCE(assertion) = calibrated value in [0,1] when empirical calibration exists; otherwise use qualitative evidence labels. Never fabricate numeric probabilities.

31. PROVENANCE
Store source URI, authorship, observation time, instrument or assay, software version, dataset version, and transformations.

32. FLOW HASH
FLOW_HASH = SHA-256(canonical UTF-8 content excluding mutable hash field). This is a generation specification; no computed digest is claimed.

33. UPDATE MODEL
On taxonomy revisions, preserve prior identifiers, record mapping and version, invalidate dependent inferences where appropriate, and recompute affected hashes.

34. AI CONSUMPTION
Expose typed entities, relation signatures, domain/range checks, provenance, uncertainty, negation-safe inference and machine-readable unit annotations. Avoid converting correlation into causation.

35. VALIDATION TESTS
TEST T1: bacterium subtype recognised -> PASS expected.
TEST T2: virus automatically recognised as cellular -> FAIL expected.
TEST T3: DNA detection implies viability -> FAIL expected.
TEST T4: colony-forming units equal cell counts universally -> FAIL expected.
TEST T5: taxon name without authority/version -> FLAG.
TEST T6: growth calculation without model assumptions -> FLAG.

36. CROSS-ONTOLOGY LINKS
Related: Cell Ontology; Organism Ontology; Biological Entities; Genetics; Ecology; Microbiology; Environmental Metadata; Scientific Measurement; Disease Ontology.

37. LIMITATIONS
Biological taxonomy evolves; microbial boundaries are partly operational. Model assumptions must be tested against observations. This flow is a structured scientific synthesis rather than a validated copy of the linked webpage.

38. AUTHORSHIP AND LICENCE NOTE
Mark Higgins — Sky (Recursive AI)
Kireth Research | https://kirethresearch.org
No licence is asserted beyond the author's own publishing decisions.

39. COMPLETENESS CHECK
Sections expected: 01–39 inclusive.
Core entities: PRESENT.
Typed relationships: PRESENT.
Inference rules: PRESENT.
Validation: PRESENT.
Provenance and update model: PRESENT.
Closing marker: PRESENT.

END FLOW ALGEBRA — MICROORGANISM ONTOLOGY