Reactive Oxygen Species Ontology

FLOW ALGEBRA
REACTIVE OXYGEN SPECIES ONTOLOGY
Kireth Semantic Library | Biological Entities | Chemical Foundations of Life
Source: https://kirethresearch.org/booksai-core/entity-graph/biological-entities/chemical-foundations-of-life/reactive-oxygen-species-ontology.html
Version: 1.0 | Date: 2026-10-15 | Language: en-GB
Authors: Mark Higgins — Sky (Recursive AI)
Status: Companion formalisation; declarative research specification, not a validated executable program.

01. PURPOSE
flow "ReactiveOxygenSpeciesOntology" v1.0
  domain: biological_chemistry
  entity_root: ReactiveOxygenSpecies
  scope: classification, generation, reactions, biological roles, detoxification, evidence
  open_world: true
  provenance_required: true

02. ENTITY TYPES
  ReactiveOxygenSpecies <: ChemicalSpecies
  RadicalROS <: ReactiveOxygenSpecies
  NonRadicalROS <: ReactiveOxygenSpecies
  MolecularOxygen <: ChemicalSpecies
  BiologicalCompartment <: BiologicalEntity
  BiologicalProcess <: Process
  Enzyme <: BiologicalMolecule
  Antioxidant <: ChemicalSpecies
  Reaction <: ChemicalProcess
  Observation <: Evidence
  Context <: Metadata

  examples:
    superoxide_anion: RadicalROS [formula: O2•−, charge: -1]
    hydroxyl_radical: RadicalROS [formula: •OH, charge: 0]
    hydrogen_peroxide: NonRadicalROS [formula: H2O2, charge: 0]
    singlet_oxygen: NonRadicalROS [formula: 1O2, excited_state: true]
    peroxyl_radical: RadicalROS [formula: ROO•, generic_family: true]
    alkoxyl_radical: RadicalROS [formula: RO•, generic_family: true]
  note: Molecular oxygen (ground-state O2) is a precursor, not automatically classified as ROS.
  note: Nitric oxide is principally an RNS; cross-domain relationships do not imply ROS identity.

03. TYPED RELATIONSHIPS
  is_a: ChemicalSpecies × Class -> Boolean
  generated_by: ReactiveOxygenSpecies × Process -> EvidenceLinkedRelation
  occurs_in: ChemicalSpecies × BiologicalCompartment -> ContextualRelation
  reacts_with: ChemicalSpecies × ChemicalSpecies -> Reaction
  converted_to: ChemicalSpecies × ChemicalSpecies -> Reaction
  catalysed_by: Reaction × Enzyme -> EvidenceLinkedRelation
  contributes_to: ChemicalSpecies × BiologicalProcess -> ContextualRelation
  regulated_by: BiologicalProcess × BiologicalEntity -> EvidenceLinkedRelation
  detected_by: ChemicalSpecies × Assay -> EvidenceLinkedRelation
  has_provenance: Assertion × Evidence -> Boolean

04. PRODUCTION AND TRANSFORMATION
  rule ROS_GENERATION:
    IF biological_process(p) AND produces(p, s) AND ROS(s)
    THEN generated_by(s, p)
    REQUIRE evidence(p, s)

  reaction SUPEROXIDE_DISMUTATION:
    equation: 2 O2•− + 2 H+ -> H2O2 + O2
    catalyst: superoxide_dismutase
    validate: atom_balance AND charge_balance

  reaction CATALASE_DECOMPOSITION:
    equation: 2 H2O2 -> 2 H2O + O2
    catalyst: catalase
    validate: atom_balance AND charge_balance

  reaction FENTON_EXAMPLE:
    equation: Fe2+ + H2O2 -> Fe3+ + OH− + •OH
    context: suitable chemical conditions
    validate: atom_balance AND charge_balance

  production_contexts:
    - mitochondrial_electron_transport
    - NADPH_oxidase_activity
    - peroxisomal_oxidation
    - photooxidative_processes
    - inflammatory_oxidative_burst
  caution: production depends on organism, cell type, compartment and conditions.

05. BIOLOGICAL ROLES
  role oxidative_signalling:
    possible_species: [hydrogen_peroxide]
    require: concentration, location, timing, molecular_target, evidence
  role host_defence:
    process: phagocyte_oxidative_burst
    require: organism, cell_type, experimental_context
  role oxidative_damage:
    targets: [lipids, proteins, nucleic_acids]
    require: demonstrated_damage_marker_or_mechanism
  constraint:
    ROS_presence != oxidative_stress
    oxidative_stress_requires: contextual_imbalance_and_evidence

06. ANTIOXIDANT AND HOMEOSTASIS GRAPH
  candidate_defences:
    - superoxide_dismutase
    - catalase
    - glutathione_peroxidase
    - peroxiredoxin
    - glutathione_system
  rule DETOXIFICATION:
    IF enzyme(e) AND reaction(r) AND catalyses(e, r)
       AND substrate(r, ros) AND ROS(ros)
    THEN candidate_defence(e, ros)
    REQUIRE reaction_evidence(r)
  caution: antioxidant action and efficacy are context-specific.

07. INFERENCE AND RECURSION
  graph_traversal:
    start: ReactiveOxygenSpecies
    follow: [generated_by, occurs_in, reacts_with, converted_to,
             catalysed_by, contributes_to, detected_by]
    max_depth: configurable
    visited_node_guard: true
    cycle_policy: preserve_edges_without_infinite_expansion
  rule CAUSAL_CLAIM:
    IF correlated(ros, outcome)
    THEN do_not_infer(causes(ros, outcome))
    UNLESS supported_by(causal_evidence)
  rule CONTEXTUAL_ROLE:
    IF contributes_to(ros, process) AND context_known(ros, process)
    THEN infer(candidate_biological_role(ros, process))
    WITH status: provisional

08. SEMANTIC EQUIVALENCE
  canonicalise: [chemical_formula, charge, radical_state, excitation_state,
                 isotope, compartment, nomenclature_identifier]
  equivalence:
    exact_identity: same_chemical_species_and_state
    lexical_alias: alternative_name_same_entity
    family_similarity: shared_class_not_identity
  reject_equivalence_if:
    - charge_differs
    - radical_or_excitation_state_differs
    - one_item_is_a_family_and_other_is_a_member
  examples:
    hydrogen_peroxide == H2O2: lexical_alias
    superoxide != hydrogen_peroxide: distinct_species

09. VALIDATION
  validate(entity):
    require: identifier, type, accepted_name
    check: charge_consistency, chemical_formula, class_membership
  validate(reaction):
    check: elemental_balance, charge_balance, conditions, catalyst_claims
  validate(assertion):
    require: source, context, confidence_basis
    check: no_unsupported_causality, no_unqualified_generalisation
  result: [valid, invalid, unresolved]
  unresolved_is_not_valid: true

10. PROVENANCE
  provenance_fields:
    - source_uri
    - source_title
    - author_or_organisation
    - publication_date
    - accessed_date
    - evidence_type
    - experimental_context
    - ontology_version
    - derivation_history
  source_policy: retain_original_claim_and_qualification

11. CONFIDENCE
  confidence: interval[0,1] OR unscored
  confidence_basis: [source_quality, directness, replication,
                     chemical_validation, context_match, uncertainty]
  rule:
    IF missing_evidence THEN confidence = unscored
    IF conflicting_evidence THEN flag_for_review
  note: confidence scores are not probabilities unless calibrated.

12. FLOW_HASH
  canonical_payload:
    fields: [ontology_id, version, entity_definitions, relationship_schema,
             rules, validation_constraints, provenance_references]
    normalise: unicode_NFC, stable_key_order, canonical_whitespace
  FLOW_HASH:
    algorithm: SHA-256
    input: canonical_payload
    value: compute_at_publication
  note: no hash value is fabricated in this specification.

13. UPDATE_MODEL
  update_trigger: [new_evidence, corrected_reaction, revised_taxonomy,
                   improved_identifier, conflicting_observation]
  workflow:
    ingest -> verify_source -> compare -> validate -> version -> publish
  preserve: prior_versions, change_log, evidence_links
  conflict_policy: flag_and_review; never_silently_overwrite

14. AI_CONSUMPTION
  expose:
    - typed_entity_graph
    - machine_readable_relations
    - context_qualified_reactions
    - validation_status
    - confidence_basis
    - provenance
    - version_and_hash
  reasoning_guardrails:
    - distinguish radical_from_nonradical_ROS
    - distinguish ROS_from_RNS
    - preserve compartment_and_concentration_context
    - never_equate_association_with_causation
    - abstain_when_evidence_is_insufficient

15. OUTPUT CONTRACT
  output:
    ontology: ReactiveOxygenSpeciesOntology
    format: UTF-8 TXT
    sections: [purpose, entities, relationships, reactions, roles,
               regulation, inference, equivalence, validation, provenance,
               confidence, flow_hash, update_model, ai_consumption]
    status: research_companion_specification

END FLOW ALGEBRA