Biological Semantic Reasoning Ontology

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FLOW ALGEBRA — BIOLOGICAL SEMANTIC REASONING ONTOLOGY
Semantic Library
Version: 4.0
Canonical Page:
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/ai-biology/biological-semantic-reasoning-ontology.html

FLOW BIOLOGICAL_SEMANTIC_REASONING_ONTOLOGY {

  META {
    DOMAIN = "Biological Ontologies"
    SUBDOMAIN = "AI Biology"
    ONTOLOGY = "Biological Semantic Reasoning Ontology"
    PURPOSE = "Formalise semantic entities, relationships, inference rules and evidence structures enabling AI systems to reason consistently across biological knowledge."
    LOCALE = "en-GB"
  }

  ENTITY_TYPES {
    BIOLOGICAL_ENTITY
    SEMANTIC_ENTITY
    CONCEPT
    ONTOLOGY_TERM
    CLASS
    INSTANCE
    PROPERTY
    RELATION
    AXIOM
    RULE
    CONSTRAINT
    GENE
    DNA
    RNA
    PROTEIN
    MOLECULE
    METABOLITE
    CELL
    TISSUE
    ORGAN
    ORGANISM
    SPECIES
    PHENOTYPE
    TRAIT
    DISEASE
    PATHWAY
    BIOLOGICAL_PROCESS
    MOLECULAR_FUNCTION
    CELLULAR_COMPONENT
    INTERACTION
    EVENT
    STATE
    OBSERVATION
    EXPERIMENT
    DATASET
    KNOWLEDGE_GRAPH
    BIOLOGICAL_ONTOLOGY
    SEMANTIC_GRAPH
    CLAIM
    HYPOTHESIS
    INFERENCE
    EXPLANATION
    EVIDENCE
    SUPPORTING_EVIDENCE
    CONTRADICTORY_EVIDENCE
    CONFIDENCE_SCORE
    UNCERTAINTY
    PROVENANCE_RECORD
  }

  RELATIONSHIPS {
    IS_A
    INSTANCE_OF
    PART_OF
    HAS_PART
    LOCATED_IN
    CONTAINS
    ENCODES
    TRANSCRIBED_AS
    TRANSLATED_TO
    EXPRESSED_IN
    INTERACTS_WITH
    BINDS_TO
    REGULATES
    ACTIVATES
    INHIBITS
    PARTICIPATES_IN
    PRODUCES
    CONSUMES
    ASSOCIATED_WITH
    CAUSES
    CONTRIBUTES_TO
    PRECEDES
    FOLLOWS
    HAS_STATE
    HAS_PHENOTYPE
    HAS_FUNCTION
    HAS_PROPERTY
    HAS_EVIDENCE
    SUPPORTS
    CONTRADICTS
    DERIVED_FROM
    INFERRED_FROM
    EXPLAINED_BY
    HAS_CONFIDENCE
    HAS_UNCERTAINTY
    HAS_PROVENANCE
    MAPS_TO
    BROADER_THAN
    NARROWER_THAN
    RELATED_TO
    SEMANTICALLY_EQUIVALENT_TO
  }

  INPUTS {
    BIOLOGICAL_ENTITIES
    BIOLOGICAL_RELATIONSHIPS
    ONTOLOGY_TERMS
    TAXONOMIES
    KNOWLEDGE_GRAPHS
    GENOMIC_DATA
    MOLECULAR_DATA
    CELLULAR_DATA
    PHENOTYPE_DATA
    DISEASE_DATA
    PATHWAY_DATA
    EXPERIMENTAL_DATA
    SCIENTIFIC_LITERATURE
    EXISTING_CLAIMS
    EVIDENCE_RECORDS
    PROVENANCE_RECORDS
  }

  NORMALISE {
    STANDARDISE_IDENTIFIERS
    RESOLVE_ENTITY_IDENTITIES
    NORMALISE_TERMINOLOGY
    ALIGN_ONTOLOGY_CLASSES
    ALIGN_RELATION_TYPES
    RESOLVE_SYNONYMS
    RESOLVE_HOMONYMS
    MAP_HIERARCHICAL_RELATIONS
    NORMALISE_EVIDENCE_TYPES
    REMOVE_DUPLICATES
    VALIDATE_METADATA
    PRESERVE_PROVENANCE
  }

  PROCESS SEMANTIC_REASONING_PIPELINE {
    INPUT
      -> ENTITY_RECOGNITION
      -> ENTITY_RESOLUTION
      -> ONTOLOGY_ALIGNMENT
      -> RELATION_NORMALISATION
      -> KNOWLEDGE_GRAPH_CONSTRUCTION
      -> RULE_APPLICATION
      -> INFERENCE_GENERATION
      -> CONSISTENCY_CHECK
      -> EVIDENCE_INTEGRATION
      -> CONFIDENCE_ESTIMATION
      -> EXPLANATION_GENERATION
      -> OUTPUT
  }

  PROCESS TAXONOMIC_REASONING {
    INSTANCE + CLASS_HIERARCHY
      -> CLASS_MEMBERSHIP

    CLASS_MEMBERSHIP + IS_A_CHAIN
      -> INHERITED_PROPERTIES

    INHERITED_PROPERTIES
      -> CONSTRAINT_CHECK
      -> VALIDATED_INFERENCE
  }

  PROCESS PARTONOMIC_REASONING {
    ENTITY_A PART_OF ENTITY_B
    AND ENTITY_B PART_OF ENTITY_C
      -> TEST_TRANSITIVE_PART_RELATION

    IF RELATION_CONTEXT_ALLOWS_TRANSITIVITY
      -> ENTITY_A PART_OF ENTITY_C

    ELSE
      -> PRESERVE_DIRECT_RELATIONS_ONLY
  }

  PROCESS RELATIONAL_REASONING {
    ENTITY_A + RELATION + ENTITY_B
      -> DOMAIN_RANGE_VALIDATION

    DOMAIN_RANGE_VALIDATION
      -> RELATION_CHAIN_ANALYSIS
      -> INVERSE_RELATION_CHECK
      -> SYMMETRY_CHECK
      -> TRANSITIVITY_CHECK
      -> INFERRED_RELATIONS
  }

  PROCESS CAUSAL_REASONING {
    BIOLOGICAL_EVENT_A
      + TEMPORAL_ORDER
      + MECHANISTIC_EVIDENCE
      + OBSERVED_EFFECT_B
      -> CAUSAL_HYPOTHESIS

    CAUSAL_HYPOTHESIS
      -> CONFOUNDING_CHECK
      -> ALTERNATIVE_EXPLANATION_CHECK
      -> EVIDENCE_ASSESSMENT
      -> CAUSAL_CONFIDENCE
  }

  PROCESS SEMANTIC_EQUIVALENCE_REASONING {
    ENTITY_A + ENTITY_B
      -> IDENTIFIER_COMPARISON
      -> SYNONYM_COMPARISON
      -> ONTOLOGY_MAPPING
      -> CONTEXT_COMPARISON

    IF REFERENT_IDENTITY_CONFIRMED
      -> SEMANTICALLY_EQUIVALENT_TO

    ELSE
      -> PRESERVE_DISTINCT_ENTITIES
  }

  PROCESS EVIDENCE_REASONING {
    CLAIM
      + SUPPORTING_EVIDENCE
      + CONTRADICTORY_EVIDENCE
      -> EVIDENCE_GRAPH

    EVIDENCE_GRAPH
      -> SOURCE_QUALITY_ASSESSMENT
      -> DIRECTNESS_ASSESSMENT
      -> CONSISTENCY_ASSESSMENT
      -> REPLICATION_ASSESSMENT
      -> CONFIDENCE_SCORE
  }

  PROCESS KNOWLEDGE_GRAPH_REASONING {
    BIOLOGICAL_ENTITY
    + SEMANTIC_RELATION
    + EVIDENCE
      -> BIOLOGICAL_SEMANTIC_GRAPH

    BIOLOGICAL_SEMANTIC_GRAPH
      -> PATH_REASONING
      -> RELATION_INFERENCE
      -> CONTRADICTION_DETECTION
      -> EXPLANATION_PATH
  }

  AI_TASKS {
    BIOLOGICAL_ENTITY_RECOGNITION
    ENTITY_LINKING
    ONTOLOGY_ALIGNMENT
    SEMANTIC_NORMALISATION
    RELATION_EXTRACTION
    RELATION_INFERENCE
    CLASSIFICATION_REASONING
    TAXONOMIC_REASONING
    PARTONOMIC_REASONING
    CAUSAL_REASONING
    TEMPORAL_REASONING
    EVIDENCE_REASONING
    CONTRADICTION_DETECTION
    SEMANTIC_EQUIVALENCE_DETECTION
    KNOWLEDGE_GRAPH_COMPLETION
    HYPOTHESIS_GENERATION
    EXPLANATION_GENERATION
    BIOLOGICAL_QUESTION_ANSWERING
  }

  RULES {
    IF A IS_A B
    AND B IS_A C
    THEN INFER A IS_A C

    IF X INSTANCE_OF A
    AND A IS_A B
    THEN INFER X INSTANCE_OF B

    IF RELATION_HAS_INVERSE(R)
    AND A R B
    THEN INFER B INVERSE(R) A

    IF RELATION_IS_SYMMETRIC(R)
    AND A R B
    THEN INFER B R A

    IF RELATION_IS_TRANSITIVE(R)
    AND A R B
    AND B R C
    THEN INFER A R C

    IF CLAIM_IS_INFERRED
    THEN LINK {
      INFERENCE_RULE
      SUPPORTING_PREMISES
      EVIDENCE
      CONFIDENCE_SCORE
      PROVENANCE_RECORD
    }

    IF ASSOCIATION_EXISTS
    THEN DO_NOT_AUTOMATICALLY_INFER_CAUSATION

    IF CONTRADICTORY_EVIDENCE_EXISTS
    THEN PRESERVE_CONTRADICTION

    IF SEMANTIC_IDENTIFIERS_DIFFER
    AND BIOLOGICAL_REFERENT_IS_SAME
    THEN APPLY SEMANTIC_EQUIVALENCE
  }

  CONFIDENCE {
    CONFIDENCE_SCORE =
      WEIGHT(
        ENTITY_RESOLUTION_QUALITY,
        ONTOLOGY_ALIGNMENT_QUALITY,
        RULE_VALIDITY,
        EVIDENCE_QUALITY,
        EVIDENCE_DIRECTNESS,
        REPLICATION,
        CONSISTENCY,
        PROVENANCE_COMPLETENESS
      )

    LEVELS {
      HIGH
      MODERATE
      LOW
      INSUFFICIENT
    }

    IF INFERENCE_CHAIN_LENGTH_INCREASES
    THEN PROPAGATE_AND_REASSESS_UNCERTAINTY

    IF CONFLICTING_EVIDENCE
    THEN REDUCE CONFIDENCE_SCORE

    IF INDEPENDENT_SUPPORTING_EVIDENCE
    THEN INCREASE CONFIDENCE_SCORE
  }

  SEMANTIC_EQUIVALENCE {
    EQUIVALENCE_KEY =
      NORMALISE(
        ENTITY_TYPE,
        CANONICAL_IDENTIFIER,
        ONTOLOGY_CLASS,
        BIOLOGICAL_CONTEXT,
        TAXONOMIC_CONTEXT
      )

    IF EQUIVALENCE_KEY(A) == EQUIVALENCE_KEY(B)
    THEN A SEMANTICALLY_EQUIVALENT_TO B

    ELSE PRESERVE_DISTINCT_ENTITIES
  }

  REASONING_CONSTRAINTS {
    ASSOCIATION != CAUSATION
    SEMANTIC_SIMILARITY != IDENTITY
    RELATED_TO != EQUIVALENT_TO
    PART_OF_IS_NOT_UNIVERSALLY_TRANSITIVE
    MODEL_INFERENCE != DIRECT_OBSERVATION
    ABSENCE_OF_EVIDENCE != EVIDENCE_OF_ABSENCE
    TAXONOMIC_CONTEXT_MUST_BE_PRESERVED
    BIOLOGICAL_CONTEXT_MUST_BE_PRESERVED
    RELATION_DOMAIN_AND_RANGE_MUST_BE_VALID
    CONTRADICTORY_EVIDENCE_MUST_NOT_BE_DISCARDED
    PROVENANCE_MUST_BE_PRESERVED
    UNCERTAINTY_MUST_NOT_BE_DISCARDED
  }

  VALIDATION {
    CHECK_ENTITY_TYPES
    CHECK_CLASS_HIERARCHY
    CHECK_RELATION_DOMAINS_AND_RANGES
    CHECK_RELATION_PROPERTIES
    CHECK_IDENTIFIER_RESOLUTION
    CHECK_ONTOLOGY_ALIGNMENT
    CHECK_SEMANTIC_EQUIVALENCE
    CHECK_INFERENCE_RULES
    CHECK_CAUSAL_ASSERTIONS
    CHECK_CONTRADICTIONS
    CHECK_EVIDENCE_LINKS
    CHECK_PROVENANCE
    CHECK_CONFIDENCE
    CHECK_DUPLICATE_ENTITIES
  }

  OUTPUTS {
    NORMALISED_BIOLOGICAL_ENTITIES
    NORMALISED_SEMANTIC_RELATIONS
    ONTOLOGY_MAPPINGS
    CLASS_MEMBERSHIPS
    INFERRED_RELATIONSHIPS
    SEMANTIC_EQUIVALENCE_LINKS
    CAUSAL_HYPOTHESES
    CONTRADICTION_RECORDS
    KNOWLEDGE_GRAPH_EDGES
    CONFIDENCE_SCORES
    UNCERTAINTY_RECORDS
    EVIDENCE_LINKS
    PROVENANCE_RECORDS
    EXPLANATION_PATHS
  }

  UPDATE_MODEL {
    ON NEW_BIOLOGICAL_KNOWLEDGE {
      NORMALISE
      ENTITY_RESOLUTION
      ONTOLOGY_ALIGNMENT
      UPDATE_RELATIONSHIPS
      RECOMPUTE_DEPENDENT_INFERENCES
      UPDATE_CONFIDENCE
      PRESERVE_VERSION_HISTORY
    }

    ON NEW_EVIDENCE {
      LINK_EVIDENCE
      REASSESS_SUPPORT
      REASSESS_CONTRADICTIONS
      REASSESS_CAUSAL_CLAIMS
      UPDATE_CONFIDENCE
      RECORD_PROVENANCE
    }

    ON ONTOLOGY_REVISION {
      REMAP_TERMS
      CHECK_SEMANTIC_EQUIVALENCE
      IDENTIFY_DEPRECATED_TERMS
      MIGRATE_RELATIONSHIPS
      RECOMPUTE_AFFECTED_INFERENCES
      PRESERVE_PRIOR_VERSION_REFERENCES
    }
  }

  FLOW_HASH {
    HASH_INPUT =
      CANONICALISE(
        ENTITY_TYPES,
        RELATIONSHIPS,
        RULES,
        CONFIDENCE,
        SEMANTIC_EQUIVALENCE,
        REASONING_CONSTRAINTS,
        UPDATE_MODEL
      )

    FLOW_HASH = SHA256(HASH_INPUT)
  }

  AI_CONSUMPTION {
    INDEX {
      ONTOLOGY
      ENTITY_TYPES
      RELATIONSHIPS
      AI_TASKS
      RULES
      OUTPUTS
    }

    RETRIEVE {
      BY_ENTITY
      BY_CLASS
      BY_ONTOLOGY_TERM
      BY_RELATION
      BY_BIOLOGICAL_PROCESS
      BY_CLAIM
      BY_EVIDENCE
      BY_CONFIDENCE
      BY_PROVENANCE
    }

    REASON {
      APPLY_CLASS_HIERARCHIES
      APPLY_RELATION_PROPERTIES
      APPLY_INFERENCE_RULES
      CHECK_SEMANTIC_EQUIVALENCE
      INTEGRATE_EVIDENCE
      PRESERVE_UNCERTAINTY
      CHECK_CONTRADICTIONS
      TRACE_EVIDENCE
      TRACE_PROVENANCE
      GENERATE_EXPLANATION_PATH
    }

    RESPONSE_POLICY {
      DISTINGUISH_OBSERVED_FROM_INFERRED
      DISTINGUISH_ASSOCIATION_FROM_CAUSATION
      DISTINGUISH_SIMILARITY_FROM_EQUIVALENCE
      RETURN_CONFIDENCE_WHEN_AVAILABLE
      RETURN_PROVENANCE_WHEN_AVAILABLE
      EXPOSE_CONFLICTING_EVIDENCE
      PRESERVE_BIOLOGICAL_CONTEXT
      AVOID_UNSUPPORTED_SEMANTIC_INFERENCE
    }
  }

  TERMINAL {
    RESULT =
      VALIDATED(
        SEMANTICALLY_NORMALISED(
          EVIDENCE_LINKED(
            CONFIDENCE_AWARE(
              BIOLOGICAL_SEMANTIC_REASONING_KNOWLEDGE
            )
          )
        )
      )
  }
}

END FLOW