Virus Ontology

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

flow "VirusOntology" v1.0

ENTITY VirusOntology {
 TYPE: BiologicalOntology
 DOMAIN: Microbiology
 SUBJECT: Virus
 PURPOSE: FormalSemanticRepresentation
}

PAGE {
 TITLE: "Virus Ontology"
 PARENT_DOMAIN: "Microbiology"
 CANONICAL_URL: "https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/microbiology/virus-ontology.html"
 AUTHORS: ["Mark Anthony Higgins", "Sky Recursive AI"]
}

ENTITY Virus {
 IS_A: AcellularInfectiousEntity
 REQUIRES: HostCell
 FOR: Replication
 CONTAINS: ViralGenome
 MAY_HAVE: [Capsid, Envelope, ViralEnzymes]
}

RULE CellularStatusConstraint {
 Virus != CellularOrganism
 Virus != MicrobialCell
}

ENTITY Virion {
 IS_A: CompleteExtracellularVirusParticle
 CONTAINS: ViralGenome
 ENCLOSED_BY: Capsid
 MAY_HAVE: ViralEnvelope
}

RULE VirusVirionDistinction {
 Virus != Virion
 WHEN lifecycle_context_requires_distinction
}

ENTITY ViralGenome {
 STORES: ViralGeneticInformation
 MAY_BE: [DNAGenome, RNAGenome]
 MAY_BE: [SingleStranded, DoubleStranded]
 MAY_BE: [Segmented, NonSegmented]
}

ENTITY DNAVirus {
 SUBCLASS_OF: Virus
 HAS: DNAGenome
}

ENTITY RNAVirus {
 SUBCLASS_OF: Virus
 HAS: RNAGenome
}

ENTITY Retrovirus {
 SUBCLASS_OF: RNAVirus
 USES: ReverseTranscription
}

ENTITY PositiveSenseRNAVirus {
 HAS: PositiveSenseRNA
}

ENTITY NegativeSenseRNAVirus {
 HAS: NegativeSenseRNA
}

ENTITY DoubleStrandedRNAVirus {
 HAS: DoubleStrandedRNA
}

ENTITY SingleStrandedDNAVirus {
 HAS: SingleStrandedDNA
}

ENTITY DoubleStrandedDNAVirus {
 HAS: DoubleStrandedDNA
}

ENTITY Capsid {
 IS_A: ProteinShell
 ENCLOSES_OR_ASSOCIATES_WITH: ViralGenome
 COMPOSED_OF: CapsidProteins
}

ENTITY CapsidSymmetry {
 MAY_BE: [Icosahedral, Helical, Complex]
}

ENTITY ViralEnvelope {
 IS_A: LipidContainingMembrane
 DERIVED_IN_PART_FROM: HostMembrane
 CONTAINS: ViralProteins
}

ENTITY ViralGlycoprotein {
 LOCATED_ON: ViralEnvelopeOrSurface
 MAY_MEDIATE: [Attachment, Entry, ImmuneInteraction]
}

ENTITY ViralEnzyme {
 MAY_INCLUDE: [Polymerase, ReverseTranscriptase, Protease, Integrase]
 PARTICIPATES_IN: ViralReplication
}

ENTITY HostCell {
 IS_A: BiologicalCell
 MAY_SUPPORT: ViralReplication
}

ENTITY HostRange {
 DESCRIBES: HostsOrCellTypesSusceptibleToProductiveOrDefinedViralInteraction
}

ENTITY ViralReceptor {
 IS_A: HostCellMolecule
 MAY_BE_USED_BY: Virus
 FOR: AttachmentOrEntry
}

ENTITY Coreceptor {
 MAY_ASSIST: ViralEntry
}

RULE ReceptorConstraint {
 receptor_binding != productive_infection
 WITHOUT entry_replication_and_host_context
}

PROCESS ViralAttachment {
 BINDS: Virion
 TO: HostCellSurface
}

PROCESS ViralEntry {
 MOVES: ViralGenomeOrParticleComponents
 INTO: HostCell
 MAY_USE: [MembraneFusion, Endocytosis, GenomeInjection]
}

PROCESS Uncoating {
 RELEASES: ViralGenome
 FROM: CapsidOrParticle
}

PROCESS ViralGenomeReplication {
 COPIES: ViralGenome
 USING: ViralAndOrHostMachinery
}

PROCESS ViralTranscription {
 PRODUCES: ViralRNA
 FROM: ViralTemplate
}

PROCESS ViralTranslation {
 PRODUCES: ViralProtein
 USING: HostRibosome
}

PROCESS ViralAssembly {
 COMBINES: ViralComponents
 INTO: NewVirusParticles
}

PROCESS ViralMaturation {
 CONVERTS: AssembledParticle
 INTO: InfectiousOrMoreInfectiousForm
}

PROCESS ViralRelease {
 EXITS: HostCell
 MAY_USE: [CellLysis, Budding, Exocytosis]
}

PROCESS ViralReplicationCycle {
 MAY_INCLUDE: [Attachment, Entry, Uncoating, GenomeReplication, GeneExpression, Assembly, Maturation, Release]
}

RULE ReplicationConstraint {
 viral_genome_detection != active_viral_replication
 WITHOUT replication_or_expression_evidence
}

PROCESS LyticInfection {
 PRODUCES: ViralProgeny
 MAY_CAUSE: HostCellLysis
}

PROCESS PersistentInfection {
 MAINTAINS: VirusOrViralGenome
 OVER: ExtendedTime
}

PROCESS Latency {
 MAINTAINS: ViralGenome
 WITH_LIMITED: ProductiveReplication
 MAY_ALLOW: Reactivation
}

PROCESS Reactivation {
 TRANSITIONS: LatentOrPersistentState
 TOWARD: IncreasedViralActivity
}

ENTITY Bacteriophage {
 SUBCLASS_OF: Virus
 INFECTS: Bacterium
}

PROCESS Lysogeny {
 MAINTAINS: PhageGenome
 WITHIN: BacterialHostLineage
}

ENTITY Prophage {
 IS_A: PhageGeneticState
 ASSOCIATED_WITH: BacterialGenomeOrCell
}

PROCESS ReverseTranscription {
 PRODUCES: DNA
 FROM: RNA_Template
}

ENTITY ReverseTranscriptase {
 CATALYSES: ReverseTranscription
}

PROCESS Integration {
 INSERTS: ViralDNA
 INTO: HostGenome
 IN: ApplicableVirusContext
}

ENTITY Provirus {
 IS_A: IntegratedViralGeneticState
}

ENTITY ViralMutation {
 CHANGES: ViralGenomeSequence
}

PROCESS ViralRecombination {
 EXCHANGES_OR_REARRANGES: ViralGeneticMaterial
}

PROCESS Reassortment {
 EXCHANGES: GenomeSegments
 BETWEEN: CompatibleSegmentedViruses
 DURING: Coinfection
}

RULE ReassortmentConstraint {
 Reassortment REQUIRES segmented_genome_context
}

ENTITY ViralVariation {
 MAY_RESULT_FROM: [Mutation, Recombination, Reassortment]
}

PROCESS ViralEvolution {
 CHANGES: ViralPopulationGeneticComposition
 OVER: Time
}

ENTITY ViralPopulation {
 COMPOSED_OF: ViralVariants
}

ENTITY Quasispecies {
 REPRESENTS: DiverseRelatedViralGenomePopulation
 IN: ApplicableHighVariationContext
}

ENTITY ViralFitness {
 DESCRIBES: RelativeReplicationOrTransmissionSuccess
 IN: DefinedEnvironment
}

ENTITY ViralTropism {
 DESCRIBES: PreferenceOrCapacityForDefinedCellTissueOrHost
 DEPENDS_ON: [ReceptorAvailability, EntryCompatibility, IntracellularFactors, ImmuneContext]
}

ENTITY TissueTropism {
 SUBCLASS_OF: ViralTropism
}

ENTITY SpeciesTropism {
 SUBCLASS_OF: ViralTropism
}

PROCESS ViralTransmission {
 MOVES: Virus
 BETWEEN: HostsOrCells
 MAY_USE: [DirectContact, RespiratoryRoute, FecalOralRoute, VectorRoute, BloodRoute, VerticalRoute]
}

ENTITY TransmissionRoute {
 DESCRIBES: MechanismOfViralSpread
}

ENTITY ViralLoad {
 DESCRIBES: QuantityOfViralMaterial
 IN: DefinedSample
}

RULE ViralLoadConstraint {
 ViralLoad != InfectiousVirusQuantity
 UNLESS assay_measures_infectivity
}

ENTITY InfectiousDose {
 DESCRIBES: QuantityAssociatedWithInfectionProbability
 UNDER: DefinedHostAndExperimentalContext
}

ENTITY ViralPathogenesis {
 DESCRIBES: MechanismsByWhichVirusContributesToHostDamageOrDisease
}

ENTITY Virulence {
 DESCRIBES: DegreeOrCapacityOfDiseaseCausingEffect
 IN: DefinedHostContext
}

ENTITY ViralVirulenceFactor {
 MAY_CONTRIBUTE_TO: [Replication, TissueDamage, ImmuneEvasion, HostManipulation]
}

PROCESS CytopathicEffect {
 CHANGES_OR_DAMAGES: HostCell
 AS: ConsequenceOfViralInteraction
}

PROCESS ImmuneEvasion {
 REDUCES_OR_MODIFIES: HostImmuneRecognitionOrResponse
}

RULE InfectionDiseaseDistinction {
 ViralInfection != ViralDisease
}

ENTITY ViralDisease {
 MAY_RESULT_FROM: ViralInfection
 PLUS: HostAndEnvironmentalFactors
}

PROCESS HostAntiviralResponse {
 MAY_INCLUDE: [InnateImmunity, InterferonResponse, AntibodyResponse, TCellResponse]
}

ENTITY InterferonResponse {
 IS_A: AntiviralHostResponse
 MAY_MODULATE: ViralReplication
}

ENTITY NeutralizingAntibody {
 BINDS: ViralAntigen
 MAY_REDUCE: ViralEntryOrInfectivity
}

RULE AntibodyConstraint {
 antibody_binding != neutralization
 WITHOUT functional_assay
}

ENTITY AntiviralAgent {
 INHIBITS: ViralReplicationOrSpread
 MAY_TARGET: [Entry, Polymerase, Protease, Integrase, Release]
}

ENTITY AntiviralResistance {
 DESCRIBES: ReducedSusceptibility
 TO: AntiviralAgent
}

ENTITY AntiviralResistanceMutation {
 MAY_CONTRIBUTE_TO: AntiviralResistance
}

RULE ResistanceConstraint {
 resistance_mutation_detection != phenotypic_resistance
 WITHOUT functional_or_susceptibility_context
}

ENTITY Vaccine {
 INDUCES: AdaptiveImmuneResponse
 AGAINST: ViralAntigenOrVirus
}

PROCESS Vaccination {
 EXPOSES: ImmuneSystem
 TO: VaccineAntigenOrPlatform
 TO_SUPPORT: ProtectiveImmunity
}

RULE VaccineConstraint {
 immune_response_marker != demonstrated_protection
 WITHOUT appropriate_effectiveness_or_challenge_evidence
}

ENTITY ViralTaxonomy {
 CLASSIFIES: Viruses
 USING: [GenomeType, ReplicationStrategy, Phylogeny, VirionProperties, HostRange]
}

ENTITY BaltimoreClassification {
 CLASSIFIES: Viruses
 BY: GenomeAndMessengerRNAGenerationStrategy
}

ENTITY ViralSpecies {
 IS_A: TaxonomicConcept
 DEFINITION_DEPENDS_ON: AcceptedTaxonomicFramework
}

ENTITY ViralStrain {
 IS_A: InformalOrContextDependentVariantDesignation
 REQUIRES: ExplicitDefinition
}

ENTITY ViralVariant {
 HAS: DefinedGeneticDifferences
 RELATIVE_TO: ReferenceOrOtherVariant
}

RULE TaxonomyConstraint {
 sequence_difference != automatically_distinct_species_or_strain
 WITHOUT taxonomic_definition_and_context
}

PROCESS VirusIsolation {
 RECOVERS: Virus
 FROM: Sample
 MAY_USE: SusceptibleHostCellsOrSystems
}

PROCESS ViralCulture {
 PROPAGATES: Virus
 IN: HostCellSystem
}

PROCESS PlaqueAssay {
 ESTIMATES: InfectiousVirus
 USING: LocalizedInfectionEvents
}

ENTITY PlaqueFormingUnit {
 ABBREVIATION: PFU
 ESTIMATES: InfectiousUnits
 UNDER: DefinedAssayConditions
}

PROCESS QuantitativePCR {
 ABBREVIATION: qPCR
 MEASURES: ViralNucleicAcid
}

PROCESS ReverseTranscriptionPCR {
 ABBREVIATION: RTPCR
 DETECTS_OR_MEASURES: RNAThroughDNAIntermediate
}

PROCESS ViralSequencing {
 DETERMINES: ViralGenomeSequence
}

PROCESS ViralMetagenomics {
 DETECTS_OR_CHARACTERIZES: ViralSequences
 IN: MixedSample
}

PROCESS ElectronMicroscopy {
 MAY_VISUALIZE: Virions
}

PROCESS Serology {
 MEASURES: HostAntibodyOrAntigenResponse
 DEPENDING_ON: Assay
}

RULE DiagnosticConstraint {
 positive_molecular_or_serological_test MUST_BE_INTERPRETED_WITH assay_target_sample_timing_and_context
}

PROCESS VirusMeasurement {
 MAY_MEASURE: [ViralGenomeCopies, InfectiousUnits, ViralAntigen, AntibodyResponse, ViralGeneExpression, CytopathicEffect]
 MAY_USE: [qPCR, RTPCR, PlaqueAssay, Sequencing, Serology, Microscopy, Culture]
}

ENTITY VirusMeasurementContext {
 HAS: [Virus, Host, SampleType, Tissue, InfectionStage, Method, Unit, Timepoint]
}

RULE MeasurementContextRule {
 IF viral_measurements ARE_COMPARED
 THEN VirusMeasurementContext MUST_BE preserved
}

ENTITY Evidence {
 TYPES: [VirologicalEvidence, MolecularEvidence, CultureEvidence, InfectivityEvidence, SequencingEvidence, SerologicalEvidence, ImagingEvidence, HostResponseEvidence, EpidemiologicalEvidence, ExperimentalEvidence, ComputationalEvidence, LiteratureEvidence]
}

RULE EvidenceConvergence {
 IF IndependentEvidenceSources AGREE
 THEN Confidence := increase(Confidence)
}

RULE EvidenceConflict {
 IF EvidenceSources CONFLICT
 THEN {
  PRESERVE competing_viral_models
  RECORD virus
  RECORD host
  RECORD sample_type
  RECORD tissue
  RECORD infection_stage
  RECORD measurement_method
  RECORD timepoint
  RECORD provenance
  REDUCE confidence
 }
}

RELATION Virus REQUIRES HostCell
RELATION Virion CONTAINS ViralGenome
RELATION Capsid ENCLOSES_OR_ASSOCIATES_WITH ViralGenome
RELATION ViralAttachment PRECEDES ViralEntry
RELATION ViralGenomeReplication PRODUCES ViralGenomes
RELATION ViralAssembly PRODUCES VirusParticles
RELATION ViralRelease EXITS HostCell
RELATION Bacteriophage INFECTS Bacterium
RELATION AntiviralAgent INHIBITS ViralReplication
RELATION ViralSequencing SUPPORTS ViralIdentification

SEMANTIC_EQUIVALENCE {
 "virus" ~= "acellular infectious entity requiring host cellular machinery for replication"
 "virion" ~= "complete extracellular virus particle"
 "viral load" ~= "quantity of viral material in a defined sample"
 "PFU" ~= "plaque-forming unit"
 "qPCR" ~= "quantitative polymerase chain reaction"
 "RT-PCR" ~= "reverse transcription polymerase chain reaction"
 "viral tropism" ~= "host cell tissue or species preference or capacity"
}

CONFIDENCE VirusAssertion {
 INPUTS: [molecular_support, culture_support, infectivity_support, sequencing_support, serological_support, imaging_support, host_response_support, temporal_support, source_independence, semantic_consistency]
 SCORE := weighted_sum(INPUTS)
 LEVEL :=
  IF SCORE >= 0.90 THEN "very_high"
  ELSE IF SCORE >= 0.75 THEN "high"
  ELSE IF SCORE >= 0.55 THEN "moderate"
  ELSE IF SCORE >= 0.35 THEN "low"
  ELSE "uncertain"
}

RULE ActiveReplicationInference {
 IF viral_genome_increases_over_time
 AND viral_gene_expression_or_infectious_progeny IS_SUPPORTED
 THEN ActiveViralReplication MAY_BE_INFERRED
}

RULE TropismInference {
 IF virus enters_and_productively_replications_in defined_cell_or_tissue
 THEN ViralTropism MAY_BE_SUPPORTED
 WITH host_and_assay_context
}

RULE InfectivityInference {
 IF plaque_or_equivalent_functional_assay detects_replicating_units
 THEN InfectiousVirus MAY_BE_SUPPORTED
}

RULE ResistanceInference {
 IF antiviral_exposure shows_reduced_viral_susceptibility
 AND genetic_or_functional_evidence_supports_mechanism
 THEN AntiviralResistance MAY_BE_SUPPORTED
}

RULE CausalityConstraint {
 IF viral_marker correlates_with host_outcome
 THEN DO_NOT_INFER causal_pathogenesis
 WITHOUT temporal_mechanistic_or_interventional_evidence
}

QUERY VirusLookup(virus_identifier) {
 RETURN [taxonomy, genome_type, virion_structure, host_range, receptors, replication_cycle, tropism, transmission, pathogenesis, immune_response, antiviral_susceptibility, evidence, confidence]
}

QUERY ViralReplicationLookup(context_identifier) {
 RETURN [attachment, entry, uncoating, genome_replication, transcription, translation, assembly, maturation, release, host_factors, evidence, confidence]
}

QUERY ViralVariantLookup(variant_identifier) {
 RETURN [reference_relationship, mutations, recombination_or_reassortment, phenotype, host_range, tropism, antiviral_susceptibility, epidemiological_context, evidence, confidence]
}

UPDATE_MODEL {
 ON new_virus_evidence:
  validate_provenance()
  identify_virus_host_sample_and_infection_context()
  normalize_viral_taxonomy_gene_protein_and_antiviral_identifiers()
  classify_genome_type_and_replication_strategy()
  capture_host_cell_tissue_and_receptor_context()
  capture_measurement_method_units_and_timepoint()
  map_attachment_entry_replication_assembly_and_release()
  map_mutation_recombination_reassortment_and_variant_relationships()
  map_tropism_transmission_pathogenesis_and_host_response()
  map_antiviral_susceptibility_and_resistance()
  compare_existing_viral_models()
  preserve_conflicting_evidence()
  recalculate_confidence()
  regenerate_viral_relationships()
  update_flow_hash()
}

AI_CONSUMPTION {
 MODE: FormalSemanticReasoning
 PARSE_AS: ExecutableFlowAlgebra
 PRIORITIES: [virus_identity, genome_type, virion_structure, host, receptor, replication_strategy, tropism, transmission, pathogenesis, antiviral_response, evidence_provenance, confidence]
 REQUIREMENTS: [preserve_virus_host_sample_and_tissue_context, preserve_infection_stage_and_timepoint, distinguish_virus_from_cellular_organism, distinguish_virus_from_virion_when_required, distinguish_genome_detection_from_active_replication, distinguish_receptor_binding_from_productive_infection, distinguish_viral_load_from_infectious_virus_quantity, distinguish_infection_from_disease, distinguish_antibody_binding_from_neutralization, distinguish_resistance_mutation_from_phenotypic_resistance, distinguish_correlation_from_causation, preserve_uncertainty]
}

VALIDATE {
 REQUIRE Virus
 REQUIRE Virion
 REQUIRE ViralGenome
 REQUIRE Capsid
 REQUIRE HostCell
 REQUIRE ViralAttachment
 REQUIRE ViralEntry
 REQUIRE ViralGenomeReplication
 REQUIRE ViralAssembly
 REQUIRE ViralRelease
 REQUIRE ViralReplicationCycle
 REQUIRE ViralTropism
 REQUIRE ViralTransmission
 REQUIRE ViralPathogenesis
 REQUIRE AntiviralResistance
 REQUIRE VirusMeasurement
 REQUIRE Evidence
 REQUIRE CONFIDENCE
 REQUIRE SEMANTIC_EQUIVALENCE
 REQUIRE UPDATE_MODEL
 REQUIRE AI_CONSUMPTION

 ASSERT Virus != CellularOrganism
 ASSERT Virus != MicrobialCell
 ASSERT viral_genome_detection != active_viral_replication
 ASSERT receptor_binding != productive_infection
 ASSERT ViralLoad != InfectiousVirusQuantity
 ASSERT ViralInfection != ViralDisease
 ASSERT antibody_binding != neutralization
 ASSERT resistance_mutation_detection != phenotypic_resistance
 ASSERT correlation != causal_pathogenesis
}

FLOW_HASH {
 ALGORITHM: SHA-256
 INPUT: canonicalize(entities, relations, processes, rules, semantic_equivalence, confidence_model, update_model, ai_consumption)
 PURPOSE: integrity_and_version_tracking
}

END flow "VirusOntology"