{ "model": { "rank": 4777, "code": "thing-q178425", "model_id": "vr.tr.cytosine", "name": "cytosine", "purpose": "Enable an agent to identify cytosine, assess the form and quality of a particular sample, and determine its suitability for a proposed analytical, biochemical or material-handling task.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q178425/", "tier": 2, "score": 72, "payload": { "layer": "wikidata", "aliases": [ "6-(¹⁵N)Amino(2,6-¹³C₂,¹⁵N₂)pyrimidin-2(1H)-one", "6-Amino(¹⁵N₂)pyrimidin-2(1H)-one", "Cytosine-5-t" ], "aliasCount": 3, "merged": 3, "knownIn": 72, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q178425", "url": "https://www.wikidata.org/wiki/Q178425", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T20:58:58Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 18.7, "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: 01a087f6-71e6-7ca0-8a98-875b5a8c472d\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: cytosine\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 005: 1001 regist", "usd": 0, "recall": true }, "codex": { "seconds": 68.8, "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: 01a087f6-71d6-7500-9159-4083bd6fa52c\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: cytosine\nRegistry id: vr.tr.cytosine\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\nContex" } } }, "metaModel": { "id": "THING-Q178425", "registryId": "vr.tr.cytosine", "name": "cytosine", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q178425/", "model": { "registry_id": "vr.tr.cytosine", "name": "cytosine", "purpose": "Enable an agent to identify cytosine, assess the form and quality of a particular sample, and determine its suitability for a proposed analytical, biochemical or material-handling task.", "definition": "Cytosine is a pyrimidine nucleobase with molecular formula C4H5N3O that occurs in DNA and RNA as part of nucleotide residues and forms canonical Watson-Crick base pairs with guanine.", "scope_statement": "This model owns cytosine as a chemical substance and the identity, composition, condition and documented handling constraints of its samples; it represents cytosine residues in nucleic acids through relations to their host molecules.", "in_scope": [ "Molecular identity of the unmodified cytosine nucleobase, including distinctions among tautomeric and protonation states", "Sample composition, purity, impurities, water content and isotopic composition", "Solid-state and solution behaviour under explicitly recorded conditions", "Transformations that alter cytosine identity or explain sample deterioration", "Relations to cytidine, deoxycytidine, cytosine nucleotides and nucleic-acid residues", "Evidence supporting identification, storage, handling and intended-use decisions" ], "out_of_scope": [ "Complete models of cytidine, deoxycytidine and their phosphorylated derivatives", "Complete models of modified bases such as 5-methylcytosine and 5-hydroxymethylcytosine", "DNA or RNA sequence, polymer architecture and whole-molecule function", "Cytosine biosynthesis pathways, enzyme systems and industrial manufacturing processes", "Finished formulations and mixtures containing cytosine", "Clinical interpretation of mutations, methylation patterns or drug responses" ], "distinguishing_features": [ "Require a pyrimidine ring bearing an amino group at position 4 and an oxo group at position 2 in the conventional amino-oxo representation; a formula match alone does not establish cytosine identity.", "Distinguish the free base from cytidine and deoxycytidine by the absence of a covalently attached sugar.", "Distinguish cytosine from uracil by the amino-versus-oxo substitution at ring position 4; deamination changes the base identity.", "Distinguish unmodified cytosine from 5-methylcytosine and other substituted analogues by explicitly checking ring substituents.", "Treat complementary pairing with guanine as behaviour requiring a molecular context, rather than sufficient proof that an isolated substance is cytosine." ], "characteristics": [ { "name": "Molecular identity", "kind": "category", "unit_or_values": "C4H5N3O; structure representation with ring numbering and declared tautomer", "why_it_matters": "Separates cytosine from related bases and prevents identification from relying on a name or molecular formula alone." }, { "name": "Chemical identifier mapping", "kind": "relation", "unit_or_values": "Verified CAS, PubChem and applicable jurisdictional identifiers, each linked to its source and represented chemical form", "why_it_matters": "Supports reliable matching of supplier records, analytical references and handling documentation." }, { "name": "Material presentation", "kind": "category", "unit_or_values": "Free-base solid, dissolved free base, or explicitly identified associated form", "why_it_matters": "Determines whether measurements and instructions apply to the actual material." }, { "name": "Assay and impurity profile", "kind": "measurement", "unit_or_values": "Mass fraction or molar fraction with method, uncertainty and reporting basis; chromatographic area percentage identified separately", "why_it_matters": "Controls dosing and suitability while preventing chromatographic purity from being mistaken for absolute content." }, { "name": "Water and residual solvent content", "kind": "measurement", "unit_or_values": "Mass fraction with analytical method and distinction between lattice-associated and adventitious water where established", "why_it_matters": "Affects weighed amounts, solid-state interpretation and comparison between lots." }, { "name": "Isotopic composition", "kind": "category", "unit_or_values": "Natural-abundance or labelled material; isotope, labelled position and enrichment when applicable", "why_it_matters": "Distinguishes ordinary reagent material from tracers and mass-spectrometric standards." }, { "name": "Solution concentration", "kind": "measurement", "unit_or_values": "mol/L or g/L with solvent composition, temperature, pH and preparation basis", "why_it_matters": "Makes solution preparation and assay exposure reproducible." }, { "name": "Protonation and tautomeric state", "kind": "state", "unit_or_values": "Assigned or unresolved state with medium, pH, temperature and supporting evidence", "why_it_matters": "Influences recognition, hydrogen bonding and interpretation of spectra or calculations." }, { "name": "Solubility and thermal behaviour", "kind": "measurement", "unit_or_values": "Solubility in g/L or mol/L; thermal events in °C with pressure, method and decomposition assessment", "why_it_matters": "Constrains preparation and processing without assuming that every reported thermal event is melting or boiling." }, { "name": "Nucleic-acid context", "kind": "relation", "unit_or_values": "Free base or cytosine moiety linked to a separately identified nucleoside, nucleotide or polymer", "why_it_matters": "Prevents properties of bound cytosine from being assigned automatically to the isolated reagent." }, { "name": "Handling evidence status", "kind": "state", "unit_or_values": "Current applicable documentation, conflicting documentation, or evidence missing", "why_it_matters": "Makes handling decisions depend on the supplied form and documented conditions." } ], "affordances": [ "Match a cytosine sample to a verified chemical identity and distinguish it from related bases or nucleosides.", "Compare cytosine lots against the purity, water content and impurity requirements of a stated assay.", "Calculate a solution preparation using the measured assay, material form and required concentration.", "Select identification or quantification methods capable of separating cytosine from relevant impurities.", "Investigate suspected conversion to uracil using analytical evidence and the sample's exposure history.", "Determine whether documented storage and handling conditions support a proposed use." ] }, "sources": [], "structure": { "bundles": [ { "id": "cytosine-identity", "name": "Cytosine identity", "description": "Establishes which molecular entity the name cytosine denotes and where its boundaries lie.", "rationale": "Free cytosine, its modified analogues and its sugar-linked derivatives must not share an undifferentiated identity.", "layers": [ { "id": "base-structure", "name": "Base structure", "description": "Records the structural features that establish the unmodified nucleobase.", "findings": [ { "id": "pyrimidine-substitution", "name": "Pyrimidine substitution", "description": "Identity assessment must resolve connectivity and substituent positions, including how tautomerism is represented.", "questions": [ { "text": "Does the verified structure establish the cytosine ring connectivity and amino-oxo substitution pattern?", "kind": "definition", "id": "pyrimidine-substitution-q01" }, { "text": "Which analytical or authoritative structural evidence supports the assigned identity and tautomer representation?", "kind": "provenance", "id": "pyrimidine-substitution-q02" } ] } ] }, { "id": "identity-boundaries", "name": "Identity boundaries", "description": "Separates cytosine from related entities and reconciles identifiers.", "findings": [ { "id": "base-versus-derivative", "name": "Base versus derivative", "description": "Identifier matching must preserve distinctions between the free base, associated forms, sugar-linked derivatives and modified bases.", "questions": [ { "text": "Does this record describe free cytosine, an associated chemical form, or a cytosine moiety within another molecule?", "kind": "boundary", "id": "base-versus-derivative-q01" }, { "text": "Which verified identifiers refer to the exact represented form, and which refer to a neighbouring substance?", "kind": "provenance", "id": "base-versus-derivative-q02" } ] } ] } ] }, { "id": "cytosine-sample-quality", "name": "Cytosine sample quality", "description": "Connects the nominal substance identity to the actual contents and analytical quality of a sample.", "rationale": "A cytosine label alone cannot establish the amount of usable base or suitability for sensitive biochemical measurements.", "layers": [ { "id": "assay-and-contaminants", "name": "Assay and contaminants", "description": "Resolves cytosine content and impurities relevant to the intended use.", "findings": [ { "id": "quantified-base-content", "name": "Quantified base content", "description": "Content must have a stated reporting basis, with relevant related bases and residual materials assessed separately.", "questions": [ { "text": "What is the cytosine assay, and is it reported on an as-received, dry or other explicitly defined basis?", "kind": "measurement", "id": "quantified-base-content-q01" }, { "text": "Can the method distinguish cytosine from uracil and other impurities relevant to this sample's origin or use?", "kind": "measurement", "id": "quantified-base-content-q02" } ] } ] }, { "id": "water-and-isotopes", "name": "Water and isotopes", "description": "Records composition differences that can alter amount calculations or analytical interpretation.", "findings": [ { "id": "mass-basis-and-labelling", "name": "Mass basis and labelling", "description": "Water, residual solvent and isotopic enrichment require explicit treatment when converting a weighed sample into an amount of cytosine.", "questions": [ { "text": "What water and residual solvent measurements are needed to calculate the amount of cytosine in the weighed material?", "kind": "measurement", "id": "mass-basis-and-labelling-q01" }, { "text": "Is the material isotopically labelled, and what evidence establishes label positions and enrichment?", "kind": "provenance", "id": "mass-basis-and-labelling-q02" } ] } ] } ] }, { "id": "cytosine-physical-state", "name": "Cytosine physical state", "description": "Describes cytosine as a solid or dissolved base under specified conditions.", "rationale": "Solution preparation and thermal processing depend on the actual form and conditions of the material.", "layers": [ { "id": "solid-and-thermal-behaviour", "name": "Solid and thermal behaviour", "description": "Connects solid-form evidence with observed thermal events.", "findings": [ { "id": "interpreted-thermal-events", "name": "Interpreted thermal events", "description": "Thermal records must distinguish phase transitions, water loss and decomposition rather than reduce them to an unqualified temperature.", "questions": [ { "text": "What evidence establishes the sample's solid form and any associated water?", "kind": "measurement", "id": "interpreted-thermal-events-q01" }, { "text": "Does a reported thermal event indicate melting, decomposition, water loss or an unresolved combination, and under what conditions?", "kind": "measurement", "id": "interpreted-thermal-events-q02" } ] } ] }, { "id": "dissolution-and-speciation", "name": "Dissolution and speciation", "description": "Relates achievable concentration to solvent conditions and molecular state.", "findings": [ { "id": "conditioned-solution-state", "name": "Conditioned solution state", "description": "Solubility, concentration and protonation assignments need compatible solvent, temperature and pH records.", "questions": [ { "text": "What cytosine concentration is demonstrably dissolved in the specified solvent at the stated temperature and pH?", "kind": "measurement", "id": "conditioned-solution-state-q01" }, { "text": "How do the chosen solution conditions affect the protonation or tautomeric assumptions used by the intended assay?", "kind": "action", "id": "conditioned-solution-state-q02" } ] } ] } ] }, { "id": "cytosine-molecular-relations", "name": "Cytosine molecular relations", "description": "Represents cytosine's biochemical context and transformations without taking ownership of entire biological systems.", "rationale": "Cytosine's recognition and transformation behaviour must be tied to whether it is free or incorporated into another molecule.", "layers": [ { "id": "bound-base-context", "name": "Bound-base context", "description": "Places cytosine within nucleosides, nucleotides and nucleic acids through explicit relations.", "findings": [ { "id": "contextual-base-recognition", "name": "Contextual base recognition", "description": "Pairing and recognition statements require a specified host molecule and molecular environment.", "questions": [ { "text": "Is the behaviour being described observed for free cytosine or for its moiety within a named nucleoside, nucleotide or polymer?", "kind": "boundary", "id": "contextual-base-recognition-q01" }, { "text": "What evidence and molecular context support a claimed interaction with guanine or another binding partner?", "kind": "provenance", "id": "contextual-base-recognition-q02" } ] } ] }, { "id": "identity-changing-reactions", "name": "Identity-changing reactions", "description": "Tracks transformations that consume cytosine or produce a separately identified base.", "findings": [ { "id": "deamination-and-modification", "name": "Deamination and modification", "description": "Conversion to uracil or a modified base must be recorded as a change of chemical identity, with conditions and evidence.", "questions": [ { "text": "What analytical evidence demonstrates conversion of cytosine to uracil or another identified product in this context?", "kind": "measurement", "id": "deamination-and-modification-q01" }, { "text": "Which exposure conditions or biological mechanisms are evidenced, and which remain hypotheses about the observed transformation?", "kind": "provenance", "id": "deamination-and-modification-q02" } ] } ] } ] }, { "id": "cytosine-use-and-handling", "name": "Cytosine use and handling", "description": "Connects sample evidence to decisions about preparation, storage and permitted use.", "rationale": "Biological occurrence does not establish reagent suitability or replace documentation for the actual supplied material.", "layers": [ { "id": "fitness-for-assay", "name": "Fitness for assay", "description": "Evaluates whether a specific cytosine lot meets a defined analytical or biochemical task.", "findings": [ { "id": "task-specific-acceptance", "name": "Task-specific acceptance", "description": "Acceptance depends on measured attributes and the intended method rather than an unexplained grade label.", "questions": [ { "text": "What limits on cytosine assay, uracil contamination, water content and other relevant impurities does the intended task require?", "kind": "action", "id": "task-specific-acceptance-q01" }, { "text": "Does this lot have sufficient evidence for those limits, including any requirements for use as a calibration standard?", "kind": "provenance", "id": "task-specific-acceptance-q02" } ] } ] }, { "id": "storage-and-documentation", "name": "Storage and documentation", "description": "Uses applicable supplier and jurisdictional evidence to govern handling of cytosine solids and solutions.", "findings": [ { "id": "documented-handling-conditions", "name": "Documented handling conditions", "description": "Storage, hazard and disposal decisions require records applicable to the chemical form, concentration and jurisdiction.", "questions": [ { "text": "Which current safety document supports hazard classification and exposure controls for this supplied cytosine material?", "kind": "provenance", "id": "documented-handling-conditions-q01" }, { "text": "What documented storage conditions and stability evidence justify retaining, retesting or discarding this solid or prepared solution?", "kind": "action", "id": "documented-handling-conditions-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": [ "This description is recalled knowledge; no sources were consulted.", "Verify thermal decomposition, solubility and other physical constants against the specified solid form, purity and measurement conditions.", "Check current supplier safety data and jurisdiction-specific records for hazard classification, regulatory identifiers and any applicable exposure limits." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of cytosine 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": "CAS Registry Number", "value_or_pattern": "71-30-7", "note": "Identifies cytosine as the free base." }, { "scheme": "PubChem CID", "value_or_pattern": "597", "note": "Compound identifier for cytosine." }, { "scheme": "Chemical nomenclature", "value_or_pattern": "4-aminopyrimidin-2(1H)-one", "note": "Names the conventional amino-oxo tautomer." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of cytosine 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": [ "Starting material for synthesis of nucleosides, nucleotides and related compounds.", "Reference material in analytical methods that distinguish nucleic-acid bases.", "Research on base pairing, tautomerism and nucleic-acid chemistry." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of cytosine 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": "Molar mass", "typical_range": "111.10", "unit": "g/mol" }, { "quantity": "Hydrogen bonds in a canonical cytosine-guanine base pair", "typical_range": "3", "unit": "hydrogen bonds per base pair" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of cytosine 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": [ "Hydrolytic deamination converts cytosine to uracil; in DNA, an unrepaired lesion can lead to a C:G-to-T:A transition mutation.", "Rare tautomeric or protonation states can alter base-pairing specificity.", "Water content and chemical impurities can affect weighed concentrations and analytical results." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of cytosine 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": "cytidine", "difference": "Cytidine is cytosine attached to ribose; cytosine alone has no sugar." }, { "name": "deoxycytidine", "difference": "Deoxycytidine is cytosine attached to 2-deoxyribose." }, { "name": "cytidine monophosphate", "difference": "This nucleotide contains cytosine, ribose and a phosphate group." }, { "name": "uracil", "difference": "Uracil has a carbonyl group at position 4 where cytosine has an amino group." }, { "name": "5-methylcytosine", "difference": "5-Methylcytosine carries an additional methyl group at ring position 5." }, { "name": "guanine", "difference": "Guanine is a purine with two fused rings and is cytosine's canonical pairing partner." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of cytosine this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Which authoritative sources establish the CAS number, PubChem CID and applicable EC identity for the exact cytosine form represented?", "Which reported solubility and acid-base constants are sufficiently conditioned by solvent, temperature and measurement method to support preparation decisions?", "Which solid forms are established, and do reported high-temperature values describe melting, decomposition or overlapping events rather than a usable boiling point?", "What current hazard classifications and substance-specific or general exposure limits apply in the intended jurisdiction and to the supplied material?", "What evidence supports storage lifetimes and acceptable uracil or other impurity limits for the intended cytosine reagent and solution uses?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 16, "questions": 26 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "chemical substance or material", "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. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "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 cytosine, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an agent to identify cytosine, assess the form and quality of a particular sample, and determine its suitability for a proposed analytical, biochemical or material-handling task.", "characteristics": { "substance": "material", "origin": "natural", "agency": "inert", "mobility": "varies" }, "whatYouCanDoWithIt": [ "observed and measured", "consumed or used up" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: 6-(¹⁵N)Amino(2,6-¹³C₂,¹⁵N₂)pyrimidin-2(1H)-one, 6-Amino(¹⁵N₂)pyrimidin-2(1H)-one, Cytosine-5-t.", "3 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 72 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "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 cytosine, and on what evidence are they told apart?" ], "whatItIsMadeOf": "matter you can touch", "physicalCharacter": [ "Mobility varies between examples.", "Does nothing on its own; everything it does, something else did to it.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state", "use it up, and then need more of it" ], "howItIsRecognised": [ "Not recognisable by sight in any reliable way. Appearance varies with grade, form and additives; identification is by label, by documentation, or by assay." ], "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": [ "6-(¹⁵N)Amino(2,6-¹³C₂,¹⁵N₂)pyrimidin-2(1H)-one", "6-Amino(¹⁵N₂)pyrimidin-2(1H)-one", "Cytosine-5-t" ] } ], "standing": "Described in 72 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 3 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 cytosine from another, and a cytosine 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 cytosine, 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 cytosine, 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 cytosine 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 cytosine, 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 cytosine, 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 cytosine 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 cytosine 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 cytosine, 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 cytosine, 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 cytosine 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 cytosine from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a cytosine, 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 cytosine, 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 cytosine 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 cytosine 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 cytosine, 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 cytosine, 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 cytosine 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": "Materials, parts and how they are put together.", "findings": [ { "id": "parts-and-materials", "name": "Parts and materials", "description": "What a cytosine is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a cytosine, 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 cytosine, 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 cytosine 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 cytosine is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a cytosine, 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 cytosine, 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 cytosine is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "place-and-movement", "name": "Place and movement", "description": "Where a cytosine is, how it got there and where it may go (varies).", "rationale": "A thing that can move needs its position recorded with a time, or every later claim about it is about a place it has left.", "layers": [ { "id": "location-and-placement", "name": "Location and placement", "description": "Position, containment and the reference frame the position is given in.", "findings": [ { "id": "position-and-frame", "name": "Position, container and reference frame", "description": "Where a cytosine is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a cytosine, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "position-and-frame-q02", "text": "Who or what asserted this about the location of a cytosine, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "position-and-frame-q03", "text": "What may an agent decide or do once the location of a cytosine is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "movement-and-transfer", "name": "Movement and transfer", "description": "How a cytosine is carried, installed or relocated.", "findings": [ { "id": "movement-events", "name": "Movement events and constraints", "description": "What counts as a movement, what records it and what limits it.", "questions": [ { "id": "movement-events-q01", "text": "What identifies and describes the movement of a cytosine, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "movement-events-q02", "text": "Who or what asserted this about the movement of a cytosine, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "movement-events-q03", "text": "What may an agent decide or do once the movement of a cytosine 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 cytosine 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 cytosine between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a cytosine, 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 cytosine, 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 cytosine 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 cytosine, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a cytosine 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 cytosine, 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 cytosine, 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 cytosine is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "use-and-operation", "name": "Use and operation", "description": "What can be done with a cytosine and what it takes to do it.", "rationale": "An agent that can recognise a thing but not act on it has only half a model.", "layers": [ { "id": "intended-use", "name": "Intended use and function", "description": "What a cytosine is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a cytosine performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a cytosine, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "function-and-purpose-q02", "text": "Who or what asserted this about the use of a cytosine, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "function-and-purpose-q03", "text": "What may an agent decide or do once the use of a cytosine is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "handling-and-procedure", "name": "Handling and procedure", "description": "The steps, skills and tools involved in using a cytosine.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a cytosine at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a cytosine, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "procedures-and-skills-q02", "text": "Who or what asserted this about handling a cytosine, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "procedures-and-skills-q03", "text": "What may an agent decide or do once handling a cytosine is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "supply-and-consumption", "name": "Supply and consumption", "description": "Quantities, rates and what running out means.", "findings": [ { "id": "consumption-and-stock", "name": "Consumption, stock and replenishment", "description": "How much of a cytosine there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a cytosine, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "consumption-and-stock-q02", "text": "Who or what asserted this about the supply of a cytosine, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "consumption-and-stock-q03", "text": "What may an agent decide or do once the supply of a cytosine is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "composition-and-identity", "name": "Composition, grade and chemical identity", "description": "What cytosine is made of and how pure the thing in hand is.", "rationale": "Grade decides what a substance may be used for, so a model that records only the name cannot support any decision about use.", "layers": [ { "id": "chemical-identity", "name": "Chemical identity", "description": "Formula, structure and the registry numbers that name it unambiguously.", "findings": [ { "id": "identity-record", "name": "Identity and registry numbers", "description": "What identifies this substance across suppliers and regulators.", "questions": [ { "id": "identity-record-q01", "text": "What formula, structure and registry identifiers name cytosine unambiguously?", "kind": "definition" }, { "id": "identity-record-q02", "text": "Which related substances share a name in common use but not an identifier?", "kind": "boundary" } ] } ] }, { "id": "grade-and-impurities", "name": "Grade, purity and impurities", "description": "The specification a batch meets and what else is in it.", "findings": [ { "id": "specification", "name": "Specification and assay", "description": "How purity is stated and measured, and which impurities matter.", "questions": [ { "id": "specification-q01", "text": "What grades of cytosine exist, how is purity assayed, and which impurities are limited?", "kind": "measurement" }, { "id": "specification-q02", "text": "Which use requires which grade, and what happens when a lower grade is substituted?", "kind": "action" } ] } ] } ] }, { "id": "properties-and-behaviour", "name": "Properties and behaviour", "description": "How cytosine behaves under conditions an agent can measure or change.", "rationale": "Physical constants are the part of a substance model that transfers between contexts, and each needs its unit and its conditions.", "layers": [ { "id": "physical-constants", "name": "Physical constants", "description": "Values that hold for the pure substance, with their conditions.", "findings": [ { "id": "constants-record", "name": "Constants and conditions", "description": "The quantities worth recording and the state they apply in.", "questions": [ { "id": "constants-record-q01", "text": "What are the defining physical constants of cytosine, in what units and under what conditions?", "kind": "measurement" }, { "id": "constants-record-q02", "text": "Which of these values change with grade or form rather than being fixed?", "kind": "boundary" } ] } ] }, { "id": "stability-and-reactivity", "name": "Stability and reactivity", "description": "What it reacts with, degrades into, and how it is stored.", "findings": [ { "id": "incompatibilities", "name": "Incompatibilities and degradation", "description": "What must not meet it, and what it becomes over time.", "questions": [ { "id": "incompatibilities-q01", "text": "What is cytosine incompatible with, and what does it degrade into under storage?", "kind": "definition" }, { "id": "incompatibilities-q02", "text": "What storage and handling does that require, and who is competent to do it?", "kind": "action" } ] } ] } ] }, { "id": "hazard-and-regulation", "name": "Hazard classification and regulation", "description": "How cytosine can harm, and what the law says about holding and moving it.", "rationale": "A substance model without its hazard class and its regulatory identity is unusable in exactly the situations that matter.", "layers": [ { "id": "hazard-class", "name": "Hazard classification", "description": "Classified hazards, exposure limits and protective measures.", "findings": [ { "id": "classified-hazards", "name": "Classified hazards and limits", "description": "The classification, the scheme it belongs to, and the limits set.", "questions": [ { "id": "classified-hazards-q01", "text": "How is cytosine classified for hazard, under which scheme, and what exposure limits apply?", "kind": "definition" }, { "id": "classified-hazards-q02", "text": "What protection does handling require, and what must an agent refuse to do without it?", "kind": "action" } ] } ] }, { "id": "regulatory-identity", "name": "Regulatory identity and control", "description": "Registration, restriction and transport rules by jurisdiction.", "findings": [ { "id": "controls", "name": "Controls and jurisdiction", "description": "Where it is restricted and what the restriction attaches to.", "questions": [ { "id": "controls-q01", "text": "Which registrations, restrictions or transport rules cover cytosine, and where?", "kind": "provenance" }, { "id": "controls-q02", "text": "Does the control attach to the substance, its concentration, or its intended use?", "kind": "boundary" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a cytosine 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 cytosine and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a cytosine, 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 cytosine, 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 cytosine 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 cytosine is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a cytosine, 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 cytosine, 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 cytosine is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 9, "layers": 20, "findings": 22, "questions": 60 } } } }