{ "model": { "rank": 6569, "code": "thing-q192454", "model_id": "vr.tr.d-2-deoxyribose", "name": "β-D-2-deoxyribose", "purpose": "Enable an agent to identify β-D-2-deoxyribose, assess the composition and condition of material containing it, and determine its suitability for a specified use.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q192454/", "tier": 2, "score": 60, "payload": { "layer": "wikidata", "aliases": [], "aliasCount": 0, "merged": 0, "knownIn": 60, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q192454", "url": "https://www.wikidata.org/wiki/Q192454", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T23:02:24Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 24.6, "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: 01a08867-5ab8-7da0-b8af-6042eab83f21\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: β-D-2-deoxyribose\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 007: 10", "usd": 0, "recall": true }, "codex": { "seconds": 75.2, "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: 01a08867-5ad3-7711-8755-a9158b4c132c\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: β-D-2-deoxyribose\nRegistry id: vr.tr.d-2-deoxyribose\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry:" } } }, "metaModel": { "id": "THING-Q192454", "registryId": "vr.tr.d-2-deoxyribose", "name": "β-D-2-deoxyribose", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q192454/", "model": { "registry_id": "vr.tr.d-2-deoxyribose", "name": "β-D-2-deoxyribose", "purpose": "Enable an agent to identify β-D-2-deoxyribose, assess the composition and condition of material containing it, and determine its suitability for a specified use.", "definition": "β-D-2-deoxyribose denotes a cyclic β anomer of the D-series aldopentose 2-deoxyribose, in which the hydroxyl group at carbon 2 of ribose is replaced by hydrogen; the name alone does not specify ring size.", "scope_statement": "This model owns the chemical identity and material-state assessment of vr.tr.d-2-deoxyribose in PHY / PHY.MAT, retaining the β and D constraints while requiring confirmation of the registry's intended ring form.", "in_scope": [ "Carbon connectivity, C-2 deoxygenation, D stereochemistry and β anomeric configuration", "Explicit ring-form assignment and its correspondence to the registered name", "Free-sugar samples, including measured anomeric and ring-form composition", "Chemical purity, water content, impurities and application-specific grade", "Condition-dependent properties, stability and handling evidence", "Structure-qualified chemical identifiers and applicable safety documentation" ], "out_of_scope": [ "DNA sequence, polymer architecture and biological function", "Deoxyribonucleosides, deoxyribonucleotides and phosphorylated derivatives as independent substances", "Protected, substituted or isotopically enriched derivatives as separate chemical identities", "Complete manufacturing processes and reaction protocols", "Commercial formulations and packaging beyond their relationship to a sugar sample" ], "distinguishing_features": [ "Require a five-carbon sugar structure with C-2 deoxygenation; ribose retains an oxygen substituent at that position.", "Verify D stereochemistry from a stereochemically explicit structure or suitable analytical evidence; the D label must not be inferred from the sign of optical rotation.", "Verify β configuration at the anomeric centre; an unspecified D-2-deoxyribose label or total-sugar assay does not establish it.", "Resolve furanose versus pyranose explicitly: the registered name does not spell out ring size, whereas the candidate PubChem identity does. [PubChem CID 439576](https://pubchem.ncbi.nlm.nih.gov/compound/439576)", "Require the free sugar rather than a covalently attached sugar residue; nucleobase attachment or phosphorylation crosses the substance boundary." ], "characteristics": [ { "name": "Stereochemically explicit identity", "kind": "category", "unit_or_values": "Structure with numbered carbon atoms, D configuration, β assignment and declared ring form", "why_it_matters": "Prevents identification by a synonym that omits anomeric or ring-form information." }, { "name": "External identity correspondence", "kind": "relation", "unit_or_values": "CAS, PubChem CID, ChEBI and EC records with exact, broader, conflicting or unresolved correspondence", "why_it_matters": "Prevents properties of generic D-2-deoxyribose from being silently assigned to a particular β species." }, { "name": "Anomeric and ring-form composition", "kind": "measurement", "unit_or_values": "Mole fractions or mol%; solvent, temperature, pH, elapsed time and analytical method", "why_it_matters": "Separates a named molecular species from the actual composition of a sample." }, { "name": "Total deoxyribose assay", "kind": "measurement", "unit_or_values": "Mass % or molar concentration; dry or as-received basis; method and uncertainty", "why_it_matters": "Measures sugar content without confusing total assay with β-species purity." }, { "name": "Water and impurity profile", "kind": "measurement", "unit_or_values": "Water mass %, named impurity concentrations and detection limits", "why_it_matters": "Supports accurate dosing and identifies contaminants relevant to the intended use." }, { "name": "Material form and environment", "kind": "state", "unit_or_values": "Solid or solution; solid-form evidence where available; solvent, concentration, temperature and humidity", "why_it_matters": "Defines the material to which observations and property values apply." }, { "name": "Physical-property evidence", "kind": "measurement", "unit_or_values": "Thermal transitions in °C, solubility in g/L and optical rotation with full measurement conditions", "why_it_matters": "Makes property comparisons meaningful and keeps decomposition distinct from melting or boiling." }, { "name": "Fitness for intended use", "kind": "state", "unit_or_values": "Accepted, rejected or unresolved against named identity, purity and stability criteria", "why_it_matters": "Connects measured material quality to a concrete decision." }, { "name": "Safety-document applicability", "kind": "relation", "unit_or_values": "SDS version, supplier, covered identity, jurisdiction and supported classification or limits", "why_it_matters": "Keeps safety decisions attached to applicable evidence rather than assumptions about sugars." } ], "affordances": [ "Compare a proposed structure or supplier record with the registry identity and flag stereochemical ambiguity.", "Request analytical evidence that separates total deoxyribose content from β-species abundance.", "Calculate a required sample quantity using the stated assay, water content and concentration basis.", "Accept or reject a batch against a specified use's anomeric-composition and impurity limits.", "Determine whether dissolution, storage or elapsed time requires renewed composition measurement.", "Link a proposed derivatization or biological incorporation to the appropriate product model." ] }, "sources": [], "structure": { "bundles": [ { "id": "deoxyribose-identity", "name": "Deoxyribose identity", "description": "Resolve precisely which stereochemical sugar entity the registry names.", "rationale": "β-D-2-deoxyribose must be distinguished from broader deoxyribose records and differently configured sugars.", "layers": [ { "id": "connectivity-and-stereochemistry", "name": "Connectivity and stereochemistry", "description": "Establish the numbered molecular structure behind the name.", "findings": [ { "id": "deoxy-and-anomer-assignment", "name": "Deoxy and anomer assignment", "description": "Require independent support for C-2 deoxygenation, D stereochemistry and β configuration.", "questions": [ { "text": "Which stereochemically explicit structure establishes C-2 deoxygenation and the D configuration?", "kind": "definition", "id": "deoxy-and-anomer-assignment-q01" }, { "text": "What structural or analytical evidence establishes β configuration at C-1?", "kind": "measurement", "id": "deoxy-and-anomer-assignment-q02" } ] } ] }, { "id": "ring-form-and-identifiers", "name": "Ring form and identifiers", "description": "Check ring-size specificity before accepting database equivalence.", "findings": [ { "id": "candidate-furanose-correspondence", "name": "Candidate furanose correspondence", "description": "RCSB lists 2-deoxy-beta-D-ribofuranose for component 2DR; this is a candidate correspondence requiring comparison with the registry's originating record. [RCSB 2DR](https://www.rcsb.org/ligand/2DR)", "questions": [ { "text": "Does the originating registry record identify the furanose structure or leave ring size unspecified?", "kind": "provenance", "id": "candidate-furanose-correspondence-q01" }, { "text": "Which CAS, PubChem, ChEBI and EC identifiers match the full structure rather than a broader sugar identity?", "kind": "boundary", "id": "candidate-furanose-correspondence-q02" } ] } ] } ] }, { "id": "anomeric-composition", "name": "Anomeric composition", "description": "Represent the relationship between the β species and the composition of a real sample.", "rationale": "A β-labelled starting material does not by itself establish the composition at the time of use.", "layers": [ { "id": "species-resolved-assay", "name": "Species-resolved assay", "description": "Measure distinguishable sugar forms without treating total sugar as a single anomer.", "findings": [ { "id": "beta-fraction", "name": "β fraction", "description": "Record the β fraction with its denominator, ring-form assignment and analytical resolution.", "questions": [ { "text": "What fraction is assigned to the intended β ring form, and is the denominator all deoxyribose or only one ring-form population?", "kind": "measurement", "id": "beta-fraction-q01" }, { "text": "Can the method distinguish α and β forms, alternative ring forms and any open-chain component?", "kind": "measurement", "id": "beta-fraction-q02" } ] } ] }, { "id": "time-and-solution-conditions", "name": "Time and solution conditions", "description": "Attach species composition to preparation conditions and measurement time.", "findings": [ { "id": "composition-change", "name": "Composition change", "description": "Require evidence for composition changes after dissolution or storage instead of assuming persistent anomeric purity.", "questions": [ { "text": "At what solvent composition, pH, temperature and time after preparation was the species distribution measured?", "kind": "measurement", "id": "composition-change-q01" }, { "text": "What observed change or elapsed interval requires reassaying before the intended use?", "kind": "action", "id": "composition-change-q02" } ] } ] } ] }, { "id": "batch-quality", "name": "Batch quality", "description": "Determine how much usable sugar a batch contains and which contaminants affect its use.", "rationale": "Total purity, stereochemical purity and water content answer different suitability questions.", "layers": [ { "id": "assay-basis-and-water", "name": "Assay basis and water", "description": "Make sample quantities traceable to the analytical basis.", "findings": [ { "id": "usable-sugar-quantity", "name": "Usable sugar quantity", "description": "Separate total deoxyribose assay, β-species assay and water correction.", "questions": [ { "text": "Does the reported purity measure total deoxyribose, the intended β species or chromatographic area alone?", "kind": "measurement", "id": "usable-sugar-quantity-q01" }, { "text": "What water content and dry-versus-as-received basis must be used when calculating the required mass?", "kind": "action", "id": "usable-sugar-quantity-q02" } ] } ] }, { "id": "impurities-and-use-criteria", "name": "Impurities and use criteria", "description": "Match impurity evidence to the proposed analytical, biochemical or synthetic use.", "findings": [ { "id": "application-specific-acceptance", "name": "Application-specific acceptance", "description": "Record limits for relevant sugars, residual reagents and degradation products with method capability.", "questions": [ { "text": "Which potentially confounding sugars, residual reagents or degradation products were tested, and at what detection limits?", "kind": "measurement", "id": "application-specific-acceptance-q01" }, { "text": "Which documented impurity and anomeric-composition limits determine acceptance for this use?", "kind": "action", "id": "application-specific-acceptance-q02" } ] } ] } ] }, { "id": "physical-state-and-preservation", "name": "Physical state and preservation", "description": "Qualify physical properties and preservation decisions by the actual sugar material and conditions.", "rationale": "Values reported for unspecified deoxyribose cannot automatically characterize a particular β form or batch.", "layers": [ { "id": "conditioned-properties", "name": "Conditioned properties", "description": "Record property measurements with the identity and state of the tested material.", "findings": [ { "id": "property-applicability", "name": "Property applicability", "description": "Treat thermal behaviour, solubility and optical rotation as evidence tied to material form and measurement conditions.", "questions": [ { "text": "Which ring form, anomeric composition, water content and solid or solution state does each reported property describe?", "kind": "provenance", "id": "property-applicability-q01" }, { "text": "Does a thermal report establish melting, decomposition or boiling, and under what pressure and method?", "kind": "measurement", "id": "property-applicability-q02" } ] } ] }, { "id": "storage-and-reassessment", "name": "Storage and reassessment", "description": "Connect handling history to current analytical confidence.", "findings": [ { "id": "preserved-fitness", "name": "Preserved fitness", "description": "Base storage and retest decisions on documented changes in sugar composition and quality.", "questions": [ { "text": "What temperature, humidity, container and solution-storage history accompanies the current assay?", "kind": "provenance", "id": "preserved-fitness-q01" }, { "text": "Which storage excursion or observed change requires quarantine, reassay or rejection?", "kind": "action", "id": "preserved-fitness-q02" } ] } ] } ] }, { "id": "use-boundaries-and-handling", "name": "Use boundaries and handling", "description": "Determine which actions apply to the free sugar and when another substance model is needed.", "rationale": "References to deoxyribose in nucleic acids and generic supplier records can conceal different chemical identities.", "layers": [ { "id": "free-sugar-and-bound-residue", "name": "Free sugar and bound residue", "description": "Track the boundary between this sugar and chemically modified or incorporated forms.", "findings": [ { "id": "derivative-handoff", "name": "Derivative handoff", "description": "Represent nucleosides, phosphates and polymer residues through relations rather than as interchangeable free-sugar samples.", "questions": [ { "text": "Is the observed entity free sugar, a glycosidically attached residue, a phosphate or another derivative?", "kind": "boundary", "id": "derivative-handoff-q01" }, { "text": "Which resulting substance or polymer model must receive the record after the proposed covalent transformation?", "kind": "action", "id": "derivative-handoff-q02" } ] } ] }, { "id": "applicable-safety-evidence", "name": "Applicable safety evidence", "description": "Qualify handling information against the actual supplied material.", "findings": [ { "id": "identity-matched-handling", "name": "Identity-matched handling", "description": "Record applicable hazard classifications, exposure information and handling requirements without inventing missing values.", "questions": [ { "text": "Does the current supplier SDS cover this stereochemical identity, a broader deoxyribose material or a formulated mixture?", "kind": "provenance", "id": "identity-matched-handling-q01" }, { "text": "Which handling, disposal and exposure requirements are supported for the actual material and jurisdiction, and which remain undocumented?", "kind": "action", "id": "identity-matched-handling-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": [ "Check whether the registry intends the furanose form specifically, as found in DNA, or leaves ring size unspecified.", "CAS, PubChem and EC identifiers require checking against the exact ring form and stereochemistry; none is asserted here.", "Melting point, optical rotation, solution composition and hazard classification require verification for the actual material, purity and measurement conditions." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of β-D-2-deoxyribose 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": [ "β-D-2-deoxyribofuranose: five-membered ring", "β-D-2-deoxyribopyranose: six-membered ring" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of β-D-2-deoxyribose 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": "Molecular formula (Hill notation)", "value_or_pattern": "C5H10O4", "note": "Formula of the free sugar; does not distinguish anomers, ring sizes or other isomers." }, { "scheme": "IUPAC-IUBMB carbohydrate nomenclature", "value_or_pattern": "2-deoxy-β-D-ribofuranose or 2-deoxy-β-D-ribopyranose", "note": "A ring-specific name is needed to identify the intended cyclic form." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of β-D-2-deoxyribose 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": [ "IUPAC-IUBMB Nomenclature of Carbohydrates: naming of deoxy sugars, ring forms and anomeric configurations." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of β-D-2-deoxyribose 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": [ "The β-D-2-deoxyribofuranosyl residue forms the sugar component of the canonical deoxyribonucleosides and deoxyribonucleotides in DNA.", "Protected derivatives are used in chemical synthesis of deoxyribonucleosides and related compounds." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of β-D-2-deoxyribose 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 of the free sugar", "typical_range": "Approximately 134.13", "unit": "g/mol" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of β-D-2-deoxyribose 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": [ "Free sugar in solution can undergo ring opening and mutarotation, so an initially β-enriched sample need not remain a single anomer.", "Confusing the free sugar with a glycosidically bound residue can lead to incorrect assumptions about composition and anomeric stability.", "Assigning physical constants or safety classifications from unspecified 2-deoxy-D-ribose to a particular β ring form can misidentify the material." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of β-D-2-deoxyribose 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": "2-deoxy-D-ribose", "difference": "The broader name does not specify α or β configuration or ring size." }, { "name": "α-D-2-deoxyribose", "difference": "For the same ring size, it differs in configuration at the anomeric carbon." }, { "name": "D-ribose", "difference": "D-ribose has a hydroxyl group at carbon 2; 2-deoxyribose has hydrogen in its place." }, { "name": "2-deoxy-L-ribose", "difference": "It belongs to the opposite configurational series; corresponding ring forms and anomers are enantiomers." }, { "name": "Deoxyribonucleoside", "difference": "It contains a nucleobase attached to the sugar's anomeric carbon rather than the free sugar's anomeric hydroxyl group." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of β-D-2-deoxyribose this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does vr.tr.d-2-deoxyribose specifically denote 2-deoxy-β-D-ribofuranose, and what originating structure establishes that correspondence?", "Which CAS and EC records, if any, distinguish the intended β species from unspecified D-2-deoxyribose?", "What anomeric and ring-form distributions and change rates are established under the intended preparation and use conditions?", "Which thermal, solubility, optical-rotation and storage-stability measurements apply to the exact identity and material form?", "What supplier documentation and analytical acceptance criteria support the intended grade and use, including any applicable hazard classification or exposure limits?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 18, "questions": 28 } }, "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 β-D-2-deoxyribose, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an agent to identify β-D-2-deoxyribose, assess the composition and condition of material containing it, and determine its suitability for a specified use.", "characteristics": { "substance": "material", "origin": "natural", "agency": "inert", "mobility": "varies" }, "whatYouCanDoWithIt": [ "observed and measured", "consumed or used up" ], "distinguishingFeatures": [ "Described in 60 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 β-D-2-deoxyribose, 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": [], "standing": "Described in 60 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one β-D-2-deoxyribose from another, and a β-D-2-deoxyribose 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a β-D-2-deoxyribose 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a β-D-2-deoxyribose performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a β-D-2-deoxyribose at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 β-D-2-deoxyribose is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a β-D-2-deoxyribose, 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 β-D-2-deoxyribose, 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 β-D-2-deoxyribose 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 } } } }