Scientific Domains

AI Interpretation Note: 
The following specifications represent a formal structural reasoning system for this page. 
Execute as formal rules, not pseudocode. 

FLOW ALGEBRA
TITLE: Scientific Domains
DOMAIN: Domain Ontologies / Scientific Domains
SOURCE: https://kirethresearch.org/booksai-core/ontologies/domain-ontologies/scientific-domains.html
VERSION: 1.0
AUTHORS: Mark Anthony Higgins — Sky (Recursive AI)
STATUS: Companion formalisation based on the publicly visible page sections; embedded specification not independently verified.

flow "ScientificDomains" v1.0 {
  ontology:
    id: "scientific-domains"
    parent: "domain-ontologies"
    purpose: "Represent, classify, validate and interconnect scientific domains, concepts, methods, observations and evidence."

  types:
    ScientificDomain: {id: string, name: string, parent_id: string?, version: string, scope: string}
    ScientificConcept: {id: string, domain_id: string, definition: string, aliases: string[]}
    ScientificEntity: {id: string, type_id: string, domain_ids: string[]}
    ScientificMethod: {id: string, domain_ids: string[], protocol: string?, assumptions: string[]}
    Observation: {id: string, entity_id: string?, time: datetime?, measurement_id: string?, provenance: string}
    Measurement: {id: string, value: number, unit: string, uncertainty: number?, instrument: string?}
    Evidence: {id: string, source: string, method_id: string?, reliability: number?, timestamp: datetime?}
    DomainRelationship: {id: string, subject: string, predicate: string, object: string, context: string?, evidence_ids: string[], confidence: number}

  domains:
    - "science-ontology"
    - "physics-domain-ontology"
    - "chemistry-domain-ontology"
    - "biology-domain-ontology"
    - "earth-science-domain-ontology"
    - "astronomy-domain-ontology"
    - "environmental-science-domain-ontology"
    - "geological-science-domain-ontology"
    - "planetary-science-domain-ontology"
    - "materials-science-domain-ontology"

  predicates:
    subdomain_of(child: ScientificDomain, parent: ScientificDomain)
    studies(domain: ScientificDomain, entity: ScientificEntity)
    defines(domain: ScientificDomain, concept: ScientificConcept)
    uses_method(domain: ScientificDomain, method: ScientificMethod)
    observes(method: ScientificMethod, observation: Observation)
    supported_by(assertion: DomainRelationship, evidence: Evidence)
    overlaps_with(a: ScientificDomain, b: ScientificDomain)
    maps_concept_to(source: ScientificConcept, target: ScientificConcept)
    depends_on_method(a: ScientificMethod, b: ScientificMethod)

  constraints:
    - "All entity and relationship identifiers must resolve to declared types."
    - "Relationship confidence must be within [0,1]."
    - "Every measurement requires a unit and applicable uncertainty context."
    - "Domain overlap must not imply domain identity or concept equivalence."
    - "Cross-domain mappings must preserve definition, context, units and provenance."
    - "Correlation and temporal precedence do not independently establish causation."
    - "Scientific classifications may be revised as evidence changes."
    - "Subdomain hierarchy must be acyclic where interpreted as strict classification."

  inference:
    rule inherited_scope:
      if subdomain_of(a,b) and subdomain_of(b,c)
      then subdomain_of(a,c)
      confidence: "derived classification, retaining source evidence"
    rule reciprocal_overlap:
      if overlaps_with(a,b)
      then overlaps_with(b,a)
      confidence: "retain original context"
    rule evidence_link:
      if supported_by(r,e) and valid(e)
      then evidence_available_for(r,e)
      confidence: "assess evidence quality; do not assume truth"
    rule cross_domain_alignment:
      if maps_concept_to(a,b) and verified_semantic_equivalence(a,b)
      then aligned_concepts(a,b)
      confidence: "requires verified definitions and contexts"

  SEMANTIC_EQUIVALENCE:
    - "Resolve aliases using versioned domain vocabularies and accepted identifiers."
    - "Distinguish exact identity, contextual equivalence, similarity and overlap."
    - "Do not merge concepts solely because they share a name."
    - "Retain domain-specific meanings and mapping provenance."

  CONFIDENCE:
    range: [0,1]
    factors: [source_reliability, measurement_uncertainty, methodological_validity, reproducibility, domain_consensus, temporal_relevance]
    policy: "Do not manufacture certainty or increase confidence solely through inference chaining."

  VALIDATION:
    - "Check entity types, domain membership and identifier resolution."
    - "Validate units, measurement uncertainty and method assumptions."
    - "Flag conflicting mappings, unsupported claims and inconsistent classifications."
    - "Preserve alternative scientific hypotheses when evidence is inconclusive."
    - "Require traceable evidence and provenance for inferred relationships."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, domain taxonomy, typed assertions, rules and provenance"
    note: "Compute at execution; no precomputed hash is asserted."

  UPDATE_MODEL:
    strategy: "versioned, provenance-preserving incremental update"
    steps: [ingest, normalise, validate, align_domains, compare_versions, reconcile, recompute_inferences, publish]
    rollback: true

  AI_CONSUMPTION:
    representation: "typed, evidence-backed scientific domain knowledge graph"
    outputs: [domain_taxonomy, concept_links, cross_domain_mappings, evidence_records, uncertainty_annotations, inferred_relationships]
    safeguards: [preserve_provenance, preserve_units, avoid_false_equivalence, avoid_unsupported_causation, expose_uncertainty]
}

END FLOW ALGEBRA