{ "model": { "rank": 6560, "code": "thing-virus", "model_id": "vr.tr.virus", "name": "virus", "purpose": "(virology) ultramicroscopic infectious agent that replicates itself only within cells of living hosts; many are pathogenic; a piece of nucleic acid (DNA or RNA) wrapped in a thin coat of protein", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.LIV", "industry": "", "version": "", "url": "/models/thing/virus/", "tier": 2, "score": 60, "payload": { "layer": "wordnet", "aliases": [ "arbovirus", "arborvirus", "adenovirus", "parainfluenza virus", "arenavirus", "lymphocytic choriomeningitis virus", "bunyavirus", "filovirus", "alphavirus", "flavivirus", "vesiculovirus", "poxvirus", "myxoma virus", "variola virus", "smallpox virus", "variola major", "variola major virus", "variola minor", "variola minor virus", "tobacco mosaic virus", "TMV", "viroid", "virusoid", "bacteriophage", "phage", "coliphage", "typhoid bacteriophage", "plant virus", "animal virus", "hepadnavirus", "retrovirus", "human T-cell leukemia virus-1", "HTLV-1", "human immunodeficiency virus", "HIV", "myxovirus", "orthomyxovirus", "paramyxovirus", "respiratory syncytial virus", "picornavirus" ], "aliasCount": 84, "merged": 60, "knownIn": 0, "facets": { "substance": "living", "origin": "natural", "agency": "inert", "mobility": "not-applicable", "scale": "not-applicable", "affordances": [ "observable" ] }, "markers": [], "lexicalClass": "noun.animal", "senseRank": 0, "alsoRegisteredAs": null, "source": { "dataset": "oewn:2024", "synset": "oewn-01331343-n", "ili": "i42336", "license": "CC BY 4.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T23:00:15Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 27, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a08865-91c3-7b22-b2b0-38ee03cc36b0\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: virus\nSense to describe: (virology) ultramicroscopic infectious agent that replicates itself only within cells of living hosts; many are pathogenic; a p", "usd": 0, "recall": true }, "codex": { "seconds": 63.2, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a08865-91ca-7051-9781-efe245ced3be\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: virus\nRegistry id: vr.tr.virus\nPlane / domain: PHY / PHY.LIV\nRegistry definition: (virology) ultramicroscopic infectious agent that replicates itself" } } }, "metaModel": { "id": "THING-VIRUS", "registryId": "vr.tr.virus", "name": "virus", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.LIV" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/virus/", "model": { "registry_id": "vr.tr.virus", "name": "virus", "purpose": "Enable an agent to recognise a virus, distinguish its biological identity from a particle or detection result, assess its evidenced state, and determine appropriate handling or referral.", "definition": "A virus is an acellular infectious entity with a DNA or RNA genome that replicates through host-cell machinery and typically produces genome-containing particles called virions, whose protein capsid may be surrounded by a lipid envelope.", "scope_statement": "This model owns the registered biological concept vr.tr.virus in PHY / PHY.LIV, including viral identity, genome and particle organisation, host dependence, infection states, persistence, and evidence needed for decisions about a particular viral entity.", "in_scope": [ "Distinction between viral taxon, lineage, isolate, population and individual virion", "Genome organisation and relationships between genome, capsid and any envelope", "Host range, cellular susceptibility and dependence on host replication machinery", "Infection, replication, persistence and extracellular particle states", "Evidence of viral presence, identity, infectivity and applicable handling constraints" ], "out_of_scope": [ "The host organism and its complete physiology", "The disease or syndrome associated with infection", "Viroids, prions and other neighbouring infectious entities as independent models", "Diagnostic instruments, assay products and laboratory procedures", "Vaccines, antiviral medicines and treatment decisions", "Computer viruses and other malicious software" ], "distinguishing_features": [ "Separate the biological virus from a computer virus by requiring a biological host and a nucleic-acid-based infection context.", "Distinguish a virus from a cellular microorganism by examining cellular organisation and whether replication depends on infection of host cells.", "Distinguish a virus from a prion by establishing a viral nucleic acid genome rather than protein-only propagation.", "Distinguish a virus from a viroid by examining genome identity and encoded viral functions, including any particle-forming proteins; absence of an observed capsid alone does not settle the boundary.", "Distinguish an infectious virus from an isolated genome fragment, antigen or virus-like particle by recording what evidence supports identity and what separately supports infectivity." ], "characteristics": [ { "name": "Entity level", "kind": "category", "unit_or_values": "taxon | lineage | isolate | population | virion | unresolved", "why_it_matters": "Prevents properties of a taxon from being assigned automatically to a particular particle or sample." }, { "name": "Taxonomic assignment", "kind": "relation", "unit_or_values": "taxon name and identifier, authority, release or date, assignment evidence and confidence", "why_it_matters": "Makes identity traceable when names and classifications change." }, { "name": "Genome organisation", "kind": "category", "unit_or_values": "DNA or RNA; strandedness; polarity where applicable; topology; segment count; unknown", "why_it_matters": "Supports identification and distinguishes genome organisation from the mechanism used to replicate it." }, { "name": "Genome length", "kind": "measurement", "unit_or_values": "nt for single-stranded sequence or bp for double-stranded genome; per-segment and total lengths with completeness", "why_it_matters": "Allows sequence comparisons without treating an incomplete assembly as a complete genome." }, { "name": "Particle organisation", "kind": "category", "unit_or_values": "capsid architecture, envelope status, particle form, absent where established, or unresolved", "why_it_matters": "Separates observed particle properties from assumptions based on the registry definition." }, { "name": "Supported host and tissue range", "kind": "relation", "unit_or_values": "host taxon, tissue or cell type, exposure or infection evidence, productive replication evidence, conditions", "why_it_matters": "Detection in a host does not by itself establish that the host supports replication." }, { "name": "Biological state", "kind": "state", "unit_or_values": "extracellular particle | intracellular replication | persistent infection | latent state where applicable | inactivated | unresolved", "why_it_matters": "Identifies which actions and interpretations are relevant to the entity being assessed." }, { "name": "Measured viral abundance", "kind": "measurement", "unit_or_values": "genome copies, particle counts or assay-specific infectious units per stated quantity of material", "why_it_matters": "Keeps molecular abundance, particle abundance and infectious titre distinct." }, { "name": "Infectivity assessment", "kind": "state", "unit_or_values": "demonstrated | not detected under stated conditions | not assessed | indeterminate", "why_it_matters": "Prevents a positive molecular result or a negative infectivity assay from supporting an unrestricted conclusion." } ], "affordances": [ "Resolve a viral name or sequence assignment against a dated taxonomic authority.", "Compare isolates using genome and particle evidence while preserving uncertainty.", "Assess whether observations support exposure, infection or productive replication in a host.", "Interpret detection and abundance results within the limits of their assays.", "Track persistence or inactivation evidence under documented conditions.", "Refer handling, transport or disposal decisions to applicable reviewed requirements." ] }, "sources": [], "structure": { "bundles": [ { "id": "viral-identity-and-boundaries", "name": "Viral identity and boundaries", "description": "Establish what viral entity is being represented and how its identity is supported.", "rationale": "The same viral name can refer to a taxon, an isolate or a particle, each supporting different assertions.", "layers": [ { "id": "entity-and-taxonomy", "name": "Entity and taxonomy", "description": "Separate the represented entity from its classification.", "findings": [ { "id": "dated-identity-assignment", "name": "Dated identity assignment", "description": "Record entity level, accepted assignment, aliases and the authority used without implying that every virus has a species-level identification.", "questions": [ { "text": "Does this record represent a taxon, lineage, isolate, population or individual virion?", "kind": "definition", "id": "dated-identity-assignment-q01" }, { "text": "Which authority, release and underlying evidence support the name and taxonomic assignment?", "kind": "provenance", "id": "dated-identity-assignment-q02" } ] } ] }, { "id": "neighbouring-biological-entities", "name": "Neighbouring biological entities", "description": "Resolve boundaries with other infectious agents and virus-derived material.", "findings": [ { "id": "virus-versus-associated-material", "name": "Virus versus associated material", "description": "Require an explicit basis for distinguishing a virus from a viroid, prion, cellular organism, endogenous viral sequence or noninfectious particle.", "questions": [ { "text": "What evidence places this entity within the viral concept rather than a neighbouring infectious-agent category?", "kind": "boundary", "id": "virus-versus-associated-material-q01" }, { "text": "Is the observed material a virus, a viral component or a host-associated sequence whose relationship to an active virus remains unresolved?", "kind": "boundary", "id": "virus-versus-associated-material-q02" } ] } ] } ] }, { "id": "genome-and-particle-organisation", "name": "Genome and particle organisation", "description": "Describe the viral genome and its relationship to any physical infectious particle.", "rationale": "Viral identity and state require distinctions between sequence, genome complement and particle architecture.", "layers": [ { "id": "genome-architecture", "name": "Genome architecture", "description": "Represent genome composition and completeness without substituting a sequence fragment for the entire genome.", "findings": [ { "id": "genome-complement", "name": "Genome complement", "description": "Capture nucleic acid type, strandedness, polarity where relevant, topology, segments and uncertainty about completeness.", "questions": [ { "text": "What genome type, topology and segment organisation are supported for this virus?", "kind": "definition", "id": "genome-complement-q01" }, { "text": "What lengths were measured, in which units, and does the evidence establish a complete genome complement?", "kind": "measurement", "id": "genome-complement-q02" } ] } ] }, { "id": "particle-architecture", "name": "Particle architecture", "description": "Connect structural observations to the particles actually examined.", "findings": [ { "id": "observed-virion-structure", "name": "Observed virion structure", "description": "Record capsid, envelope, morphology and genome packaging as evidenced properties, allowing exceptional or unresolved cases.", "questions": [ { "text": "Which capsid, envelope and particle-form observations are directly supported, and by what methods?", "kind": "provenance", "id": "observed-virion-structure-q01" }, { "text": "Does a particle contain the complete required genome complement, only part of it, or no demonstrated viral genome?", "kind": "boundary", "id": "observed-virion-structure-q02" } ] } ] } ] }, { "id": "host-dependence-and-infection", "name": "Host dependence and infection", "description": "Represent the relationship between a virus, susceptible hosts and intracellular infection states.", "rationale": "Host association, cell entry and successful replication are distinct claims that must not be collapsed.", "layers": [ { "id": "host-range-and-tropism", "name": "Host range and tropism", "description": "Qualify host and tissue associations by the kind of evidence available.", "findings": [ { "id": "supported-host-relationship", "name": "Supported host relationship", "description": "Distinguish exposure or detection from entry, infection and production of infectious progeny.", "questions": [ { "text": "Which host taxa and cell or tissue types support infection, and which are merely associated with detection?", "kind": "boundary", "id": "supported-host-relationship-q01" }, { "text": "What evidence supports these relationships in natural hosts versus experimental systems?", "kind": "provenance", "id": "supported-host-relationship-q02" } ] } ] }, { "id": "replication-and-persistence-states", "name": "Replication and persistence states", "description": "Represent supported infection states and dependencies without assuming one universal viral life cycle.", "findings": [ { "id": "state-and-required-dependencies", "name": "State and required dependencies", "description": "Identify the evidenced infection state and any established host, helper-virus or integration dependencies.", "questions": [ { "text": "What observations distinguish productive replication, abortive infection, persistence or latency in this case?", "kind": "measurement", "id": "state-and-required-dependencies-q01" }, { "text": "Which host functions or helper entities are required, and is integration part of this virus's supported biology?", "kind": "definition", "id": "state-and-required-dependencies-q02" } ] } ] } ] }, { "id": "transmission-and-environmental-fate", "name": "Transmission and environmental fate", "description": "Connect movement between hosts and environmental conditions to evidence of retained infectivity.", "rationale": "Viral material can persist or move without establishing an infectious transmission route.", "layers": [ { "id": "transmission-relationships", "name": "Transmission relationships", "description": "Distinguish supported transmission pathways from incidental carriage or environmental detection.", "findings": [ { "id": "evidenced-transmission-route", "name": "Evidenced transmission route", "description": "Record source host, recipient host, route and any reservoir or vector role with separate supporting evidence.", "questions": [ { "text": "Which routes have evidence of transmission to a susceptible host rather than movement of viral material alone?", "kind": "provenance", "id": "evidenced-transmission-route-q01" }, { "text": "What establishes an associated organism as a reservoir or vector rather than an incidental carrier?", "kind": "boundary", "id": "evidenced-transmission-route-q02" } ] } ] }, { "id": "persistence-and-inactivation", "name": "Persistence and inactivation", "description": "Qualify survival and inactivation observations by material, conditions, duration and endpoint.", "findings": [ { "id": "condition-specific-infectivity", "name": "Condition-specific infectivity", "description": "Separate retained molecular detectability from retained infectivity under documented conditions.", "questions": [ { "text": "Under what matrix, environmental conditions and elapsed time was residual infectivity assessed?", "kind": "measurement", "id": "condition-specific-infectivity-q01" }, { "text": "Which reviewed evidence supports an inactivation decision for the relevant material and intended use?", "kind": "action", "id": "condition-specific-infectivity-q02" } ] } ] } ] }, { "id": "detection-evidence-and-decisions", "name": "Detection evidence and decisions", "description": "Define what measurements justify and which decisions require further evidence or specialist review.", "rationale": "Sequence detection, infectious titre and disease association answer different questions and support different actions.", "layers": [ { "id": "assay-interpretation", "name": "Assay interpretation", "description": "Bind each result to its target, sample context, method and limitations.", "findings": [ { "id": "presence-abundance-and-infectivity", "name": "Presence, abundance and infectivity", "description": "Keep genome copies, antigens, particle counts and infectious units distinct and preserve assay-specific uncertainty.", "questions": [ { "text": "What did the assay measure, in which sample and units, and with what detection limits and controls?", "kind": "measurement", "id": "presence-abundance-and-infectivity-q01" }, { "text": "Does the result support viral presence, identity, infectivity or disease causation, and where does that inference stop?", "kind": "boundary", "id": "presence-abundance-and-infectivity-q02" } ] } ] }, { "id": "handling-and-referral", "name": "Handling and referral", "description": "Link decisions to identified material, intended activity and applicable requirements.", "findings": [ { "id": "evidence-bounded-action", "name": "Evidence-bounded action", "description": "Record the basis for handling, transport, disposal or referral decisions without inferring requirements from the word virus alone.", "questions": [ { "text": "Which current institutional or jurisdictional requirements apply to this identified material and proposed activity?", "kind": "provenance", "id": "evidence-bounded-action-q01" }, { "text": "What unresolved identity, infectivity or host-risk evidence requires specialist review before the proposed action?", "kind": "action", "id": "evidence-bounded-action-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Virus is a broad category, not a species: no single binomial, geographic range or conservation assessment applies, and its placement among living things is conceptually contested.", "The six kinds summarize genome and replication distinctions; the Baltimore classification separates reverse-transcribing viruses into two groups, giving seven groups overall.", "This is recalled knowledge, not source-verified research; verify current ICTV names and virus-specific measurements or regulatory requirements before publication." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Double-stranded DNA viruses", "Single-stranded DNA viruses", "Double-stranded RNA viruses", "Positive-sense single-stranded RNA viruses", "Negative-sense single-stranded RNA viruses", "Reverse-transcribing viruses, including RNA-genome and DNA-genome groups" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "NCBI Taxonomy", "value_or_pattern": "10239", "note": "The broad Viruses node; individual viral taxa have their own taxonomy identifiers." }, { "scheme": "ICTV taxon names", "value_or_pattern": "Species names are binomials consisting of a genus name and a species epithet.", "note": "Species names identify taxa, not individual virions, isolates or strains; common virus names are distinct from formal species names." }, { "scheme": "INSDC sequence accession", "value_or_pattern": "Accession identifier with an optional sequence-version suffix", "note": "Identifies a deposited nucleotide sequence through GenBank, ENA or DDBJ, rather than a virus species." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "International Code of Virus Classification and Nomenclature, issued by the International Committee on Taxonomy of Viruses (ICTV)." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Viral vectors deliver genetic material in research and gene therapy.", "Bacteriophages are used in bacterial research and selected antibacterial applications.", "Modified or inactivated viruses serve as vaccine components.", "Oncolytic viruses are used in selected cancer treatments.", "Viruses provide experimental systems for studying replication, evolution and host defence." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Virion diameter", "typical_range": "Approximately 20-300 for many viruses; giant and filamentous forms fall outside this range.", "unit": "nm" }, { "quantity": "Infectious titre", "typical_range": "Depends on the virus, sample, host cells and assay; no universal typical range.", "unit": "plaque-forming units per mL" }, { "quantity": "Genome concentration", "typical_range": "Sample-dependent; genome counts do not directly establish infectivity.", "unit": "genome copies per mL" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Some viruses cause disease in humans, other animals, plants or microorganisms; infection does not necessarily cause disease.", "Host switching and transmission can produce outbreaks when suitable biological and ecological conditions coincide.", "Mutation, recombination or reassortment can alter viral properties; reassortment requires compatible segmented genomes.", "Persistent or latent infections can evade clearance, and some can reactivate.", "Certain viruses contribute to cancer through persistent infection or disruption of cellular regulation." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Distribution and transmission vary with host and vector ranges, climate, population immunity and contact patterns.", "Biosafety, transport and reporting requirements vary by jurisdiction and by the particular virus." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of virus this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "virion", "difference": "A virion is a virus particle; virus also refers to the biological entity across its intracellular replication cycle." }, { "name": "bacterium", "difference": "A bacterium is a cell with ribosomes and cellular organisation; a virus lacks its own ribosomes and depends on host-cell translation." }, { "name": "viroid", "difference": "A viroid is a small infectious RNA that does not encode proteins or form a virus-like protein capsid." }, { "name": "prion", "difference": "A prion propagates an infectious protein conformation without a nucleic-acid genome." }, { "name": "viral disease", "difference": "A viral disease is a pathological consequence of infection, not the infectious entity itself." }, { "name": "virus species", "difference": "A virus species is a taxonomic category encompassing related viruses, not an individual particle or infection." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of virus this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "How should the registry definition accommodate recognised viruses without a conventional extracellular protein-coated particle?", "Where should the model draw researched boundaries around satellite viruses, defective viral entities and endogenous viral elements?", "Which taxonomic authority and release should anchor classification, and how should unclassified sequence-based candidates be represented?", "What evidence thresholds should distinguish host association, productive infection, reservoir status and demonstrated transmission across different host groups?", "Which assay-specific and context-specific evidence is sufficient for an infectivity or inactivation decision without overstating a negative result?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 19, "questions": 29 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "organism", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched.", "facetsInferred": false, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a virus, record what state it is in, and decide what may be done with it.", "whatItIs": "(virology) ultramicroscopic infectious agent that replicates itself only within cells of living hosts; many are pathogenic; a piece of nucleic acid (DNA or RNA) wrapped in a thin coat of protein", "characteristics": { "substance": "living", "origin": "natural", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: arbovirus, arborvirus, adenovirus, parainfluenza virus, arenavirus, lymphocytic choriomeningitis virus, bunyavirus, filovirus, alphavirus, flavivirus, vesiculovirus, poxvirus.", "60 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a virus, and on what evidence are they told apart?" ], "whatItIsMadeOf": "a living thing", "physicalCharacter": [ "Does nothing on its own; everything it does, something else did to it." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state" ], "howItIsRecognised": [ "Recognised by diagnostic characters, and those differ by life stage - the young of many kinds are mistaken for other kinds entirely. A sighting is settled by characters, a photograph and a place, not by a name alone." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "arbovirus", "arborvirus", "adenovirus", "parainfluenza virus", "arenavirus", "lymphocytic choriomeningitis virus", "bunyavirus", "filovirus", "alphavirus", "flavivirus", "vesiculovirus", "poxvirus" ] } ], "standing": "60 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one virus from another, and a virus from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a virus sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a virus from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "form-and-composition", "name": "Form, composition and condition", "description": "What a virus is made of, what shape and size it takes, and what state it is in.", "rationale": "A physical thing can be measured, and a model that cannot record its measurements cannot support any decision that depends on them.", "layers": [ { "id": "form-and-dimensions", "name": "Form and dimensions", "description": "Shape, size, mass and the ranges these take across examples.", "findings": [ { "id": "measurable-dimensions", "name": "Measurable dimensions and their units", "description": "The quantities worth recording and the units they are recorded in.", "questions": [ { "id": "measurable-dimensions-q01", "text": "What identifies and describes the dimensions of a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "measurable-dimensions-q02", "text": "Who or what asserted this about the dimensions of a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "measurable-dimensions-q03", "text": "What may an agent decide or do once the dimensions of a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "material-and-composition", "name": "Material and composition", "description": "Anatomy, parts and life stage.", "findings": [ { "id": "parts-and-materials", "name": "Parts and life stages", "description": "The parts of a virus and the stages it passes through.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "parts-and-materials-q02", "text": "Who or what asserted this about the composition of a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "parts-and-materials-q03", "text": "What may an agent decide or do once the composition of a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "condition-and-integrity", "name": "Condition and integrity", "description": "Wear, damage, health and the difference between working and broken.", "findings": [ { "id": "condition-assessment", "name": "Condition, damage and health", "description": "How the condition of a virus is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "condition-assessment-q02", "text": "Who or what asserted this about the condition of a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "condition-assessment-q03", "text": "What may an agent decide or do once the condition of a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a virus passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a virus between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a virus, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a virus is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "taxonomic-placement", "name": "Taxonomic placement and identification", "description": "What virus is called scientifically, by whose authority, and how a specimen is recognised.", "rationale": "Names change with revisions while the organism does not, so a name without its authority and date cannot be reconciled later.", "layers": [ { "id": "accepted-name", "name": "Accepted name and synonymy", "description": "The current binomial, its author and date, and the names it replaced.", "findings": [ { "id": "name-and-authority", "name": "Accepted name, authority and synonyms", "description": "What to record so a later revision can be applied without losing the old data.", "questions": [ { "id": "name-and-authority-q01", "text": "What is the accepted scientific name of virus, with its author and year, and which synonyms does it absorb?", "kind": "definition" }, { "id": "name-and-authority-q02", "text": "Which taxonomic authority is being followed, and what would a competing authority say?", "kind": "provenance" } ] } ] }, { "id": "field-identification", "name": "Field identification", "description": "The characters that separate virus from what it is confused with.", "findings": [ { "id": "diagnostic-characters", "name": "Diagnostic characters and confusable kinds", "description": "Features that settle an identification, and those that only suggest it.", "questions": [ { "id": "diagnostic-characters-q01", "text": "Which observable characters distinguish virus from its closest look-alikes, and at which life stage are they visible?", "kind": "boundary" }, { "id": "diagnostic-characters-q02", "text": "What evidence is enough to record an identification as confirmed rather than provisional?", "kind": "provenance" } ] } ] } ] }, { "id": "life-cycle-and-condition", "name": "Life stages, condition and behaviour", "description": "What virus does over its life and how its state is judged.", "rationale": "Stage and condition change what may be done - handled, treated, harvested, left alone - and both are observations with a time.", "layers": [ { "id": "stages-and-reproduction", "name": "Stages and reproduction", "description": "Development from origin to death, including forms that look like different animals.", "findings": [ { "id": "life-stages", "name": "Life stages and their marks", "description": "The stages worth recording and what tells them apart.", "questions": [ { "id": "life-stages-q01", "text": "What stages does virus pass through, and what observable change marks each transition?", "kind": "definition" }, { "id": "life-stages-q02", "text": "Which stages are so unlike the adult that they are mistaken for another kind?", "kind": "boundary" } ] } ] }, { "id": "health-and-condition", "name": "Health and condition", "description": "How condition is assessed and by whom.", "findings": [ { "id": "condition-assessment", "name": "Condition assessment", "description": "Signs of health, injury and stress, and who is competent to judge them.", "questions": [ { "id": "condition-assessment-q01", "text": "How is the condition of virus judged, on what scale, and by whom?", "kind": "measurement" }, { "id": "condition-assessment-q02", "text": "What condition obliges an agent to act, and what act is permitted to whom?", "kind": "action" } ] } ] } ] }, { "id": "range-and-status", "name": "Habitat, range and conservation status", "description": "Where virus lives and how threatened it is.", "rationale": "Range and status govern what is lawful, and both are assessments with an assessor and a year rather than facts of nature.", "layers": [ { "id": "habitat-and-range", "name": "Habitat and range", "description": "Native range, introductions and the habitat it needs.", "findings": [ { "id": "range-record", "name": "Range, introductions and habitat", "description": "What to record about where it is found and how it got there.", "questions": [ { "id": "range-record-q01", "text": "What is the native range of virus, where has it been introduced, and what habitat does it require?", "kind": "definition" }, { "id": "range-record-q02", "text": "What distinguishes a native record from an introduced or vagrant one?", "kind": "boundary" } ] } ] }, { "id": "protection-status", "name": "Protection and legal status", "description": "Conservation assessments and the rules that follow from them.", "findings": [ { "id": "status-and-rules", "name": "Conservation status and legal consequence", "description": "The assessment, its date, and what it forbids or requires where.", "questions": [ { "id": "status-and-rules-q01", "text": "What conservation status does virus hold, under which assessment and year?", "kind": "provenance" }, { "id": "status-and-rules-q02", "text": "What does that status forbid or require of an agent, and in which jurisdiction?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a virus came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a virus and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a virus is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a virus, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a virus, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a virus is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 7, "layers": 15, "findings": 17, "questions": 45 } } } }