{ "model": { "rank": 14194, "code": "thing-q422529", "model_id": "vr.tr.nuclease", "name": "nuclease", "purpose": "Let an agent explain nucleases, relay classes, biological roles and laboratory and gene-editing uses from biochemistry sources with ethical debates attributed, describe the named enzymes, and distinguish nucleases from polymerases, ligases, proteases and helicases.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q422529/", "tier": 2, "score": 36, "payload": { "layer": "wikidata", "aliases": [ "ribonuclease", "deoxyribonuclease", "Pathogenesis-related protein-4", "RRNA endonuclease", "Ribonuclease T", "Ribonuclease V1", "VapC family", "Ribonuclease/ribotoxin", "Protein of unknown function DUF86", "Ribonuclease E/G", "Ribonuclease II/ribonuclease R", "Ribonuclease E", "Ribonuclease R", "Toxin endonuclease, YhaV", "Ribonuclease P/MRP protein subunit", "endoribonuclease", "exoribonuclease", "Ribonuclease P/MRP, subunit p29 superfamily", "Colicin D, C-terminal domain superfamily", "ribonuclease T1", "Colicin E5 ribonuclease domain, protein family", "NYN domain, limkain-b1-type, protein family", "Colicin D C-terminal domain, protein family", "KEN domain, protein family", "Ribonuclease P/MRP, subunit p29, protein family", "Ribonuclease II/R family", "exonuclease", "endonuclease", "DNA repair endonuclease XPF", "Head completion nuclease", "Endonuclease I", "Guanine-specific ribonuclease N1/T1/U2", "Fanconi-associated nuclease 1-like", "Nuclease SbcCD subunit D", "Bacteriophage P2, GpM", "Pyocin S killer protein", "Ribonuclease kappa", "UV-endonuclease UvdE", "CRISPR-associated protein Cas1", "Ribonuclease Nob1, eukaryote" ], "aliasCount": 131, "merged": 131, "knownIn": 36, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q422529", "url": "https://www.wikidata.org/wiki/Q422529", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-14T00:54:02Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 4, "engine": "claude" }, "metaModel": { "id": "THING-Q422529", "registryId": "vr.tr.nuclease", "name": "nuclease", "version": "0.2.0-wave.4", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q422529/", "model": { "registry_id": "vr.tr.nuclease", "name": "nuclease", "purpose": "Let an agent explain nucleases, relay classes, biological roles and laboratory and gene-editing uses from biochemistry sources with ethical debates attributed, describe the named enzymes, and distinguish nucleases from polymerases, ligases, proteases and helicases.", "definition": "An enzyme that cleaves the phosphodiester bonds between nucleotides in nucleic acids, classified as deoxyribonucleases acting on DNA and ribonucleases acting on RNA, and as endonucleases cutting within strands or exonucleases removing nucleotides from ends, with examples the registry aliases name such as ribonuclease T, ribonuclease V1, used to probe double-stranded RNA structure, rRNA endonucleases such as ricin-like toxins and pathogenesis-related protein 4 in plants; nucleases function in DNA repair, replication, RNA processing, immune defence and apoptosis, and engineered nucleases such as restriction enzymes, zinc-finger nucleases, TALENs and CRISPR-Cas9 are central tools in molecular biology and gene editing, whose applications raise ethical debates, attributed.", "what_it_is_for": "Cutting nucleic acids in cells and laboratories.", "affordances": [ "explain classes", "relay biological roles", "describe named enzymes", "relay tools and ethical debates" ], "distinguishing_features": [ "Phosphodiester bond cleavage", "DNA or RNA specificity", "Endo or exo activity", "Engineered tools" ], "appearance": "Not visible; proteins used as purified reagents.", "visual_identification": [ "Enzyme cleaving nucleic acids", "Ribonuclease, deoxyribonuclease, pathogenesis-related protein-4, rRNA endonuclease, ribonuclease T, ribonuclease V1", "Polymerases build nucleic acids; ligases join strands; proteases cut proteins; helicases unwind without cutting" ], "physical_properties": [ { "quantity": "EC class", "typical_range": "3.1", "unit": "EC", "note": "esterases acting on ester bonds" }, { "quantity": "restriction enzymes Nobel Prize", "typical_range": "1978", "unit": "year", "note": "Arber, Nathans, Smith" }, { "quantity": "CRISPR-Cas9 Nobel Prize in Chemistry", "typical_range": "2020", "unit": "year", "note": "Charpentier and Doudna" } ], "families_and_kinds": [ "deoxyribonucleases", "ribonucleases", "restriction endonucleases", "exonucleases", "programmable nucleases" ], "related_models": [ { "relation": "is a kind of", "target": "hydrolase", "why": "in registry terms" }, { "relation": "includes", "target": "restriction enzyme", "why": "" }, { "relation": "includes", "target": "Cas9", "why": "" }, { "relation": "is contrasted with", "target": "DNA ligase", "why": "" } ], "identifiers": [], "standards_and_regulation": [ "EC enzyme nomenclature", "Gene therapy and genome editing regulations", "Biosafety rules for laboratory work" ], "failure_modes_and_hazards": [ "Sample degradation by contaminating RNases", "Off-target gene editing", "Partisan framing of germline editing debates" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What a nuclease is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is a nuclease, and how does it differ from polymerases, ligases, proteases and helicases?", "kind": "definition" }, { "text": "Is the question about biology, laboratory methods or medical gene therapies, whose status needs current sources?", "kind": "boundary" } ] } ] }, { "id": "enzymes", "name": "Enzymes", "description": "Named enzymes.", "findings": [ { "id": "enzymes-finding", "name": "Enzymes", "description": "Enzymes.", "questions": [ { "text": "What are ribonuclease T, ribonuclease V1, rRNA endonucleases and PR-4 proteins?", "kind": "definition" }, { "text": "Which entry fits the specific enzyme?", "kind": "action" } ] } ] } ] }, { "id": "biology", "name": "Biology", "description": "Biological roles.", "rationale": "Science.", "layers": [ { "id": "repair", "name": "Repair", "description": "DNA repair and replication.", "findings": [ { "id": "repair-finding", "name": "Repair", "description": "Repair.", "questions": [ { "text": "How do nucleases act in DNA repair and replication?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "defence", "name": "Defence", "description": "Immune defence.", "findings": [ { "id": "defence-finding", "name": "Defence", "description": "Defence.", "questions": [ { "text": "How do restriction systems and CRISPR defend bacteria?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "tools", "name": "Tools", "description": "Laboratory tools.", "rationale": "Regulation.", "layers": [ { "id": "restriction", "name": "Restriction enzymes", "description": "Restriction enzymes.", "findings": [ { "id": "restriction-finding", "name": "Restriction enzymes", "description": "Restriction enzymes.", "questions": [ { "text": "How did restriction enzymes enable recombinant DNA?", "kind": "provenance" }, { "text": "Which entry fits restriction enzyme?", "kind": "action" } ] } ] }, { "id": "editing", "name": "Gene editing", "description": "Genome editing.", "findings": [ { "id": "editing-finding", "name": "Gene editing", "description": "Gene editing.", "questions": [ { "text": "How do CRISPR-Cas9, TALENs and zinc-finger nucleases edit genomes?", "kind": "provenance" }, { "text": "Which entry fits CRISPR gene editing?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Ethics.", "rationale": "Attribution.", "layers": [ { "id": "germline", "name": "Germline", "description": "Germline editing debate.", "findings": [ { "id": "germline-finding", "name": "Germline", "description": "Germline.", "questions": [ { "text": "What do scientific academies, ethicists and advocates argue about heritable genome editing, with positions attributed?", "kind": "provenance" }, { "text": "Is the presentation neutral and attributed?", "kind": "boundary" } ] } ] }, { "id": "therapy", "name": "Therapy", "description": "Approved therapies.", "findings": [ { "id": "therapy-finding", "name": "Therapy", "description": "Therapy.", "questions": [ { "text": "Which nuclease-based therapies have regulators approved, checked against current sources?", "kind": "provenance" }, { "text": "Is the information current?", "kind": "boundary" } ] } ] } ] } ] }, "openQuestions": [ "Should pathogenesis-related protein 4 be moved to plant defence entries?", "Should programmable nucleases be a separate entry?", "How should enzyme databases be linked?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "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 nuclease, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain nucleases, relay classes, biological roles and laboratory and gene-editing uses from biochemistry sources with ethical debates attributed, describe the named enzymes, and distinguish nucleases from polymerases, ligases, proteases and helicases.", "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: ribonuclease, deoxyribonuclease, Pathogenesis-related protein-4, RRNA endonuclease, Ribonuclease T, Ribonuclease V1, VapC family, Ribonuclease/ribotoxin, Protein of unknown function DUF86, Ribonuclease E/G, Ribonuclease II/ribonuclease R, Ribonuclease E.", "131 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 36 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 nuclease, 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": [ "ribonuclease", "deoxyribonuclease", "Pathogenesis-related protein-4", "RRNA endonuclease", "Ribonuclease T", "Ribonuclease V1", "VapC family", "Ribonuclease/ribotoxin", "Protein of unknown function DUF86", "Ribonuclease E/G", "Ribonuclease II/ribonuclease R", "Ribonuclease E" ] } ], "standing": "Described in 36 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 131 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 nuclease from another, and a nuclease 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 nuclease, 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 nuclease, 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 nuclease 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 nuclease, 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 nuclease, 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 nuclease 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 nuclease 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 nuclease, 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 nuclease, 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 nuclease 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 nuclease from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a nuclease, 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 nuclease, 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 nuclease 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 nuclease 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 nuclease, 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 nuclease, 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 nuclease 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 nuclease is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a nuclease, 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 nuclease, 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 nuclease 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 nuclease is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a nuclease, 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 nuclease, 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 nuclease 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 nuclease 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 nuclease is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a nuclease, 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 nuclease, 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 nuclease 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 nuclease 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 nuclease, 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 nuclease, 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 nuclease 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 nuclease 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 nuclease between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a nuclease, 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 nuclease, 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 nuclease 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 nuclease, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a nuclease 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 nuclease, 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 nuclease, 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 nuclease 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 nuclease 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 nuclease is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a nuclease performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a nuclease, 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 nuclease, 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 nuclease 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 nuclease.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a nuclease at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a nuclease, 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 nuclease, 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 nuclease 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 nuclease there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a nuclease, 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 nuclease, 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 nuclease 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 nuclease 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 nuclease 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 nuclease 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 nuclease 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 nuclease, 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 nuclease 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 nuclease 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 nuclease 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 nuclease, 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 nuclease 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 nuclease and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a nuclease, 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 nuclease, 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 nuclease 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 nuclease is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a nuclease, 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 nuclease, 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 nuclease 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 } } } }