Scientific Ontologies
Authors:
MArk Anthony Higgins - Sky Recursive Ai
MArk Anthony Higgins - Sky Recursive Ai
© Mark Anthony Higgins 11 October 2025
Revised Date: July 6th 2026
Revised Date: July 6th 2026
FLOW ScientificOntologies v4.0
AI_INTERPRETATION_NOTE:
The following specification defines the formal semantic structure
for the Scientific Ontologies section of the Kireth Semantic Research Archive.
Execute as a structured knowledge and reasoning specification.
PAGE:
url = "https://kirethresearch.org/booksai-core/ontologies/scientific-ontologies.html"
canonical_entity = SCIENTIFIC_ONTOLOGIES
page_type = ONTOLOGY_CATEGORY
parent = ONTOLOGIES
knowledge_domain = AI_CORE
archive = KIRETH_SEMANTIC_RESEARCH_ARCHIVE
PURPOSE:
DEFINE scientific_ontology
CLASSIFY scientific_domains
CONNECT scientific_entities
REPRESENT observable_reality
REPRESENT measurement_and_evidence
SUPPORT cross_domain_scientific_reasoning
PROVIDE semantic_parent_for_scientific_ontology_pages
DEFINE:
ScientificOntology :=
FormalKnowledgeStructure(
scientific_entities,
scientific_classes,
properties,
relationships,
measurements,
observations,
laws,
constraints,
causal_models
)
ScientificKnowledge :=
StructuredRepresentation(
observable_entities,
measurable_properties,
empirical_relationships,
theoretical_models,
evidence
)
ScientificEntity :=
Entity(
physical
OR biological
OR chemical
OR planetary
OR environmental
OR measurable
OR inferred_from_evidence
)
CORE_AXIOM:
observation
->
measurement
->
structured_data
->
scientific_relationship
->
model
->
explanation
->
scientific_knowledge
SCIENTIFIC_ONTOLOGY_HIERARCHY:
Scientific_Ontologies
├── Physics_Ontology
├── Chemistry_Ontology
├── Biology_Ontology
├── Astronomy_Ontology
├── Earth_Science_Ontology
├── Environmental_Science_Ontology
├── Geology_Ontology
├── Meteorology_Ontology
├── Oceanography_Ontology
├── Materials_Science_Ontology
├── Space_Science_Ontology
├── Planetary_Science_Ontology
├── Paleontology_Ontology
├── Geophysics_Ontology
├── Hydrology_Ontology
├── Mineralogy_Ontology
├── Crystallography_Ontology
├── Acoustics_Ontology
└── Scientific_Measurement_Ontology
CATEGORY Physics_Ontology:
represents:
matter
energy
force
motion
fields
particles
waves
spacetime
physical_laws
core_relationships:
EXERTS_FORCE_ON
INTERACTS_WITH
MOVES_RELATIVE_TO
TRANSFERS_ENERGY_TO
HAS_MASS
HAS_MOMENTUM
HAS_CHARGE
OCCUPIES_SPACETIME
CATEGORY Chemistry_Ontology:
represents:
atoms
molecules
elements
compounds
bonds
reactions
phases
chemical_properties
core_relationships:
BONDED_TO
REACTS_WITH
CONTAINS_ELEMENT
FORMS_COMPOUND
CATALYSES
DISSOLVES_IN
OXIDISES
REDUCES
CATEGORY Biology_Ontology:
represents:
organisms
cells
tissues
organs
genes
proteins
ecosystems
biological_processes
core_relationships:
PART_OF
PRODUCES
EXPRESSES
INHERITS
METABOLISES
INTERACTS_WITH
EVOLVES_FROM
LIVES_IN
CATEGORY Astronomy_Ontology:
represents:
stars
planets
moons
galaxies
nebulae
black_holes
cosmic_structures
astronomical_events
core_relationships:
ORBITS
GRAVITATIONALLY_INTERACTS_WITH
EMITS_RADIATION
FORMS_FROM
BELONGS_TO_GALAXY
LOCATED_AT
EVOLVES_INTO
CATEGORY Earth_Science_Ontology:
represents:
Earth_systems
atmosphere
hydrosphere
lithosphere
biosphere
geosphere
Earth_processes
core_relationships:
INTERACTS_WITH
CYCLES_THROUGH
TRANSFERS_MATTER_TO
TRANSFERS_ENERGY_TO
FORMS
ERODES
DEPOSITS
CATEGORY Environmental_Science_Ontology:
represents:
environments
ecosystems
pollutants
resources
climate_effects
human_impacts
sustainability_systems
core_relationships:
IMPACTS
POLLUTES
CONSERVES
DEGRADES
RESTORES
DEPENDS_ON
EMITS
ABSORBS
CATEGORY Geology_Ontology:
represents:
rocks
minerals
geological_formations
tectonic_structures
stratigraphy
geological_processes
core_relationships:
COMPOSED_OF
OVERLIES
UNDERLIES
FORMED_BY
DEFORMED_BY
ERODED_BY
DEPOSITED_IN
FRACTURED_BY
CATEGORY Meteorology_Ontology:
represents:
atmospheric_conditions
weather_systems
clouds
precipitation
wind
pressure
temperature
core_relationships:
CAUSES
FORMS
MOVES_TOWARDS
INCREASES
DECREASES
CONDENSES_INTO
PRECIPITATES_AS
CATEGORY Oceanography_Ontology:
represents:
oceans
currents
waves
tides
marine_water_masses
salinity
temperature
ocean_processes
core_relationships:
FLOWS_THROUGH
MIXES_WITH
TRANSPORTS
CIRCULATES
ERODES
DEPOSITS
INTERACTS_WITH_ATMOSPHERE
CATEGORY Materials_Science_Ontology:
represents:
materials
structures
phases
defects
mechanical_properties
thermal_properties
electrical_properties
core_relationships:
COMPOSED_OF
HAS_STRUCTURE
HAS_PROPERTY
TRANSFORMS_INTO
FRACTURES_UNDER
CONDUCTS
DEFORMS
CORRODES
CATEGORY Space_Science_Ontology:
represents:
space_environment
solar_wind
magnetospheres
cosmic_radiation
spacecraft_environment
heliophysics
core_relationships:
INTERACTS_WITH
EMITTED_BY
PROPAGATES_THROUGH
IMPACTS
DEFLECTED_BY
DETECTED_BY
CATEGORY Planetary_Science_Ontology:
represents:
planets
moons
planetary_surfaces
atmospheres
interiors
orbital_properties
planetary_evolution
core_relationships:
ORBITS
HAS_ATMOSPHERE
HAS_SURFACE
HAS_INTERIOR
FORMED_FROM
IMPACTED_BY
EVOLVES_THROUGH
CATEGORY Paleontology_Ontology:
represents:
fossils
extinct_organisms
geological_time
evolutionary_lineages
paleoecology
core_relationships:
FOSSIL_OF
EXISTED_DURING
ANCESTOR_OF
DESCENDANT_OF
FOUND_IN_FORMATION
DATED_TO
CATEGORY Geophysics_Ontology:
represents:
seismic_systems
gravity
magnetism
Earth_interior
crust
mantle
core
physical_Earth_processes
core_relationships:
PROPAGATES_THROUGH
GENERATED_BY
MEASURES
REFLECTS_FROM
REFRACTS_THROUGH
ASSOCIATED_WITH
CATEGORY Hydrology_Ontology:
represents:
water
rivers
groundwater
aquifers
runoff
infiltration
precipitation
catchments
core_relationships:
FLOWS_INTO
INFILTRATES
RECHARGES
DRAINS
EVAPORATES
PRECIPITATES
STORED_IN
CATEGORY Mineralogy_Ontology:
represents:
minerals
mineral_classes
chemical_composition
crystal_structure
physical_properties
core_relationships:
COMPOSED_OF
CRYSTALLISES_AS
BELONGS_TO_CLASS
HAS_HARDNESS
HAS_DENSITY
HAS_CLEAVAGE
OCCURS_IN
CATEGORY Crystallography_Ontology:
represents:
crystals
lattices
symmetry
unit_cells
crystal_systems
atomic_arrangements
core_relationships:
HAS_SYMMETRY
HAS_UNIT_CELL
CONTAINS_ATOM
BELONGS_TO_SYSTEM
DIFFRACTS
REPEATS_IN
CATEGORY Acoustics_Ontology:
represents:
sound
pressure_waves
frequency
amplitude
resonance
propagation
acoustic_materials
core_relationships:
PROPAGATES_THROUGH
REFLECTS_FROM
ABSORBED_BY
RESONATES_WITH
HAS_FREQUENCY
HAS_AMPLITUDE
CATEGORY Scientific_Measurement_Ontology:
represents:
quantities
units
instruments
measurements
uncertainty
calibration
precision
accuracy
core_relationships:
MEASURES
HAS_UNIT
HAS_VALUE
HAS_UNCERTAINTY
CALIBRATED_AGAINST
OBSERVED_BY
DERIVED_FROM
COMMON_SCIENTIFIC_ENTITY_MODEL:
ScientificEntity {
identifier
class
properties
spatial_context
temporal_context
measurement_context
provenance
}
OBSERVATION_MODEL:
Observation :=
Observer
+
ObservedEntity
+
ObservableProperty
+
Method
+
Time
+
Location
+
Result
MEASUREMENT_MODEL:
Measurement :=
Quantity
+
NumericalValue
+
Unit
+
Uncertainty
+
Instrument
+
Method
measurement
MUST_REFERENCE:
measured_entity
measured_property
EMPIRICAL_EVIDENCE:
Evidence :=
observation
OR measurement
OR experiment
OR replicated_result
OR validated_dataset
scientific_claim
SHOULD_BE_SUPPORTED_BY
Evidence
CAUSAL_REASONING:
IF:
A precedes B
AND
mechanism_connects(A,B)
AND
evidence_supports(A,B)
THEN:
A MAY_CAUSE B
ELSE:
classify_relation_as =
correlation
association
unknown
NEVER:
infer_causation_from_correlation_alone
SCIENTIFIC_LAW_MODEL:
ScientificLaw :=
FormalRelationship(
variables,
conditions,
mathematical_expression,
domain_of_validity
)
law_applies
ONLY_IF:
conditions_satisfied
THEORY_MODEL:
ScientificTheory :=
ExplanatoryFramework(
observations,
laws,
models,
evidence,
predictions
)
MODEL_RELATIONSHIPS:
MODEL_OF
APPROXIMATES
PREDICTS
EXPLAINS
CONSISTENT_WITH
CONTRADICTS
VALID_WITHIN
SCALE_MODEL:
ScientificEntity
MAY_EXIST_AT:
quantum_scale
atomic_scale
molecular_scale
microscopic_scale
macroscopic_scale
planetary_scale
stellar_scale
galactic_scale
cosmological_scale
reasoning
MUST_PRESERVE:
applicable_scale
SPACE_TIME_MODEL:
scientific_event :=
entity
+
location
+
time
relationships:
LOCATED_IN
OCCURS_AT
PRECEDES
FOLLOWS
SIMULTANEOUS_WITH
SYSTEM_MODEL:
ScientificSystem :=
components
+
interactions
+
boundaries
+
inputs
+
outputs
+
state
system_state(t)
->
interactions
->
system_state(t+Δt)
CROSS_DOMAIN_RELATIONSHIPS:
Physics_Ontology
SUPPORTS Chemistry_Ontology
Physics_Ontology
SUPPORTS Astronomy_Ontology
Physics_Ontology
SUPPORTS Geophysics_Ontology
Physics_Ontology
SUPPORTS Acoustics_Ontology
Chemistry_Ontology
SUPPORTS Biology_Ontology
Chemistry_Ontology
SUPPORTS Materials_Science_Ontology
Chemistry_Ontology
SUPPORTS Mineralogy_Ontology
Biology_Ontology
CONNECTS_TO Environmental_Science_Ontology
Biology_Ontology
CONNECTS_TO Paleontology_Ontology
Astronomy_Ontology
CONNECTS_TO Space_Science_Ontology
Astronomy_Ontology
CONNECTS_TO Planetary_Science_Ontology
Earth_Science_Ontology
CONTAINS_CONTEXT_FOR Geology_Ontology
Earth_Science_Ontology
CONTAINS_CONTEXT_FOR Meteorology_Ontology
Earth_Science_Ontology
CONTAINS_CONTEXT_FOR Oceanography_Ontology
Earth_Science_Ontology
CONTAINS_CONTEXT_FOR Hydrology_Ontology
Geology_Ontology
CONNECTS_TO Mineralogy_Ontology
Mineralogy_Ontology
CONNECTS_TO Crystallography_Ontology
Scientific_Measurement_Ontology
SUPPORTS ALL_SCIENTIFIC_ONTOLOGIES
MATHEMATICAL_INTERFACE:
scientific_models
MAY_USE:
algebra
geometry
calculus
probability
statistics
differential_equations
numerical_methods
scientific_entity
->
quantitative_property
->
mathematical_representation
->
analysis
SEMANTIC_REASONING_CHAIN:
INPUT scientific_query
EXTRACT:
entities
properties
quantities
relationships
spatial_context
temporal_context
domain_context
IDENTIFY relevant_scientific_ontology
RESOLVE:
entity_classification
measured_properties
known_relationships
applicable_models
scientific_scale
TRAVERSE:
parent_classes
component_entities
causal_relations
spatial_relations
temporal_relations
cross_domain_relations
APPLY:
scientific_constraints
accepted_laws
ontology_rules
INFER:
supported_relationships
likely_explanations
derived_properties
VALIDATE_AGAINST:
evidence
measurement
domain_constraints
logical_consistency
RETURN:
structured_scientific_interpretation
ENTITY_RESOLUTION:
FOR each scientific_entity:
MATCH:
canonical_name
identifier
recognised_synonym
formal_definition
contextual_equivalent
DISAMBIGUATE using:
ontology_domain
physical_properties
relationships
scale
location
time
SEMANTIC_EQUIVALENCE:
X ≡ Y
ONLY_IF:
same_scientific_referent
OR formally_defined_equivalence
X ≈ Y
IF:
functionally_similar
OR structurally_similar
OR contextually_related
PRESERVE distinction_between:
equality
approximation
similarity
correlation
UNCERTAINTY_MODEL:
uncertainty :=
measurement_uncertainty
+
model_uncertainty
+
observational_uncertainty
+
inferential_uncertainty
RETURN confidence_with_claim
CONFIDENCE:
confidence_score ∈ [0,1]
confidence =
weighted_combination(
evidence_quality,
measurement_quality,
source_consistency,
model_validity,
ontology_alignment
)
HIGH:
>= 0.85
MEDIUM:
>= 0.60 AND < 0.85
LOW:
< 0.60
IF LOW:
preserve_uncertainty
avoid_assertive_conclusion
PROVENANCE:
scientific_assertion
SHOULD_RECORD:
source
method
observation
measurement
dataset
model
date
confidence
RECURSIVE_REASONING:
FUNCTION ResolveScientificEntity(X):
identify scientific_domain
identify entity_class
identify properties
identify measurements
identify relationships
identify components
identify parent_system
identify relevant_laws
FOR each related_entity:
ResolveScientificEntity(related_entity)
STOP_IF:
sufficient_context
OR recursion_limit
OR repeated_entity
RECURSIVE_COHERENCE:
entity_claim
MUST_BE_COHERENT_WITH
scientific_ontology
scientific_ontology
MUST_BE_COHERENT_WITH
scientific_domain
scientific_domain
MUST_BE_COHERENT_WITH
Scientific_Ontologies
therefore:
ScientificEntity
->
ScientificClass
->
ScientificOntology
->
ScientificDomain
->
Scientific_Ontologies
MUST_FORM:
coherent_semantic_path
AI_CONSUMPTION:
WHEN AI_SYSTEM reads_page:
recognise:
page_as = SCIENTIFIC_ONTOLOGY_CATEGORY
interpret linked_children_as:
specialised_scientific_ontologies
preserve:
domain_hierarchy
scientific_relationships
measurement_context
evidence_context
uncertainty
use page_to:
identify_scientific_domain
route_to_specialised_ontology
resolve_scientific_entities
support_cross_domain_reasoning
QUERY_ROUTING:
IF query_about force OR energy OR motion:
route -> Physics_Ontology
IF query_about atoms OR molecules OR reactions:
route -> Chemistry_Ontology
IF query_about organisms OR cells OR genetics:
route -> Biology_Ontology
IF query_about stars OR galaxies OR universe:
route -> Astronomy_Ontology
IF query_about Earth_system:
route -> Earth_Science_Ontology
IF query_about environment OR pollution OR ecosystem_impact:
route -> Environmental_Science_Ontology
IF query_about rocks OR formations OR tectonics:
route -> Geology_Ontology
IF query_about weather OR atmosphere:
route -> Meteorology_Ontology
IF query_about oceans:
route -> Oceanography_Ontology
IF query_about material_properties:
route -> Materials_Science_Ontology
IF query_about space_environment:
route -> Space_Science_Ontology
IF query_about planets OR moons:
route -> Planetary_Science_Ontology
IF query_about fossils OR extinct_life:
route -> Paleontology_Ontology
IF query_about seismic OR gravity OR Earth_interior:
route -> Geophysics_Ontology
IF query_about water_cycle OR groundwater OR rivers:
route -> Hydrology_Ontology
IF query_about minerals:
route -> Mineralogy_Ontology
IF query_about crystal_structure:
route -> Crystallography_Ontology
IF query_about sound:
route -> Acoustics_Ontology
IF query_about units OR measurement OR uncertainty:
route -> Scientific_Measurement_Ontology
SCIENTIFIC_SEARCH:
scientific_search(query):
parse_query()
identify_scientific_entities()
identify_domain()
identify_scale()
identify_properties()
identify_relationship_intent()
resolve_measurement_context()
traverse_scientific_ontology()
traverse_cross_domain_links()
rank_by:
entity_match
domain_relevance
scientific_relationship_distance
evidence_quality
confidence
return semantic_results
UPDATE_MODEL:
ScientificOntology
MAY_EVOLVE_WITH
new_observations
new_measurements
new_theories
revised_models
improved_classifications
WHEN update_detected:
compare:
new_knowledge
existing_knowledge
IF compatible:
integrate
IF superseding:
retain_previous_version
mark_new_version
IF conflicting:
preserve_conflict
require_evidence_resolution
NEVER:
silently_delete_scientific_history
FLOW_HASH:
canonicalise(
scientific_hierarchy,
entity_model,
measurement_model,
evidence_model,
causal_rules,
cross_domain_links,
confidence_model,
recursive_reasoning
)
->
FLOW_HASH
FINAL_SEMANTIC_MODEL:
Scientific_Ontologies
=
FormalRepresentation(
ScientificEntities
+
ScientificProperties
+
Measurements
+
Observations
+
Relationships
+
Laws
+
Models
+
Evidence
)
Scientific_Ontologies
->
Observation
->
Measurement
->
Evidence
->
StructuredKnowledge
->
ScientificModels
->
SemanticReasoning
->
CrossDomainUnderstanding
END FLOW
