{ "model": { "rank": 9001, "code": "thing-q215980", "model_id": "vr.tr.ribosomal-rna", "name": "ribosomal RNA", "purpose": "Let an agent explain ribosomal RNA by type, structure, function, gene organisation and research uses such as microbial identification.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q215980/", "tier": 2, "score": 49, "payload": { "layer": "wikidata", "aliases": [ "self-splicing ribosomal RNA", "5S ribosomal RNA", "16S ribosomal RNA encoded by: VC_RS00270 VC_RS00270", "23S ribosomal RNA encoded by: VC_RS00280 VC_RS00280", "5S ribosomal RNA encoded by: rrf VC_RS00285", "16S ribosomal RNA encoded by: VC_RS00735 VC_RS00735", "23S ribosomal RNA encoded by: VC_RS00745 VC_RS00745", "5S ribosomal RNA encoded by: rrf VC_RS00750", "16S ribosomal RNA encoded by: VC_RS01505 VC_RS01505", "23S ribosomal RNA encoded by: VC_RS01520 VC_RS01520", "5S ribosomal RNA encoded by: rrf VC_RS01525", "16S ribosomal RNA encoded by: VC_RS01940 VC_RS01940", "23S ribosomal RNA encoded by: VC_RS01955 VC_RS01955", "5S ribosomal RNA encoded by: rrf VC_RS01960", "16S ribosomal RNA encoded by: VC_RS03580 VC_RS03580", "23S ribosomal RNA encoded by: VC_RS03590 VC_RS03590", "5S ribosomal RNA encoded by: rrf VC_RS03595", "5S ribosomal RNA encoded by: rrf VC_RS12015", "5S ribosomal RNA encoded by: rrf VC_RS12025", "23S ribosomal RNA encoded by: VC_RS12030 VC_RS12030", "16S ribosomal RNA encoded by: VC_RS12045 VC_RS12045", "5S ribosomal RNA encoded by: rrf VC_RS13260", "23S ribosomal RNA encoded by: VC_RS13265 VC_RS13265", "16S ribosomal RNA encoded by: VC_RS13290 VC_RS13290", "5S ribosomal RNA encoded by: rrf VC_RS13295", "23S ribosomal RNA encoded by: VC_RS13300 VC_RS13300", "16S ribosomal RNA encoded by: VC_RS13320 VC_RS13320", "16S Ribosomal RNA encoded by: SAOUHSC_R0001 SAOUHSC_R0001", "23S Ribosomal RNA encoded by: SAOUHSC_R0006 SAOUHSC_R0006", "5S Ribosomal RNA encoded by: SAOUHSC_R00011 SAOUHSC_R00011", "5S Ribosomal RNA encoded by: SAOUHSC_R00016 SAOUHSC_R00016", "16S Ribosomal RNA encoded by: SAOUHSC_R0002 SAOUHSC_R0002", "23S Ribosomal RNA encoded by: SAOUHSC_R0007 SAOUHSC_R0007", "5S Ribosomal RNA encoded by: SAOUHSC_R00012 SAOUHSC_R00012", "5S Ribosomal RNA encoded by: SAOUHSC_R00013 SAOUHSC_R00013", "23S Ribosomal RNA encoded by: SAOUHSC_R0008 SAOUHSC_R0008", "16S Ribosomal RNA encoded by: SAOUHSC_R0003 SAOUHSC_R0003", "5S Ribosomal RNA encoded by: SAOUHSC_R00014 SAOUHSC_R00014", "23S Ribosomal RNA encoded by: SAOUHSC_R0009 SAOUHSC_R0009", "16S Ribosomal RNA encoded by: SAOUHSC_R0004 SAOUHSC_R0004" ], "aliasCount": 765, "merged": 1886, "knownIn": 49, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q215980", "url": "https://www.wikidata.org/wiki/Q215980", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T13:11:21Z", "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": 1, "engine": "claude" }, "metaModel": { "id": "THING-Q215980", "registryId": "vr.tr.ribosomal-rna", "name": "ribosomal RNA", "version": "0.2.0-wave.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q215980/", "model": { "registry_id": "vr.tr.ribosomal-rna", "name": "ribosomal RNA", "purpose": "Let an agent explain ribosomal RNA by type, structure, function, gene organisation and research uses such as microbial identification.", "definition": "The RNA component of ribosomes, which forms their structural core and catalyses peptide bond formation; prokaryotes have 5S, 16S and 23S rRNAs and eukaryotes have 5S, 5.8S, 18S and 28S rRNAs, and 16S rRNA gene sequencing is widely used to identify bacteria.", "what_it_is_for": "Protein synthesis, microbiology and evolutionary studies.", "affordances": [ "explain rRNA types and ribosome structure", "describe the catalytic role of rRNA", "use 16S rRNA sequencing for identification", "find rRNA sequence databases" ], "distinguishing_features": [ "Structural and catalytic RNA", "Most abundant RNA in cells", "Highly conserved", "Used as a phylogenetic marker" ], "appearance": "Not visible; shown in ribosome structures and sequence data.", "visual_identification": [ "Sedimentation labels such as 16S and 23S", "Folded RNA in ribosome structures", "Messenger RNA carries coding information" ], "physical_properties": [], "families_and_kinds": [ "16S and 18S small-subunit rRNA", "23S and 28S large-subunit rRNA", "5S and 5.8S rRNA", "mitochondrial and chloroplast rRNA" ], "related_models": [ { "relation": "is a kind of", "target": "non-coding RNA", "why": "category" }, { "relation": "is part of", "target": "ribosome", "why": "complex" }, { "relation": "catalyses", "target": "peptide bond formation", "why": "function" }, { "relation": "is used in", "target": "16S rRNA sequencing", "why": "method" } ], "identifiers": [], "standards_and_regulation": [ "Laboratory biosafety rules for handling organisms" ], "failure_modes_and_hazards": [ "Overstating identification from partial sequences", "Contamination in sequencing" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "types", "name": "Types", "description": "rRNA types.", "rationale": "Types differ by organism.", "layers": [ { "id": "which", "name": "Which", "description": "Type.", "findings": [ { "id": "which-finding", "name": "Which", "description": "rRNA type.", "questions": [ { "text": "Which rRNA is meant, and is it prokaryotic, eukaryotic or organellar?", "kind": "definition" }, { "text": "What does the S value mean?", "kind": "definition" } ] } ] }, { "id": "genes", "name": "Genes", "description": "rRNA genes.", "findings": [ { "id": "genes-finding", "name": "Genes", "description": "rRNA genes.", "questions": [ { "text": "How are rRNA genes organised and how many copies are there?", "kind": "provenance" }, { "text": "Which databases annotate them?", "kind": "provenance" } ] } ] } ] }, { "id": "function", "name": "Function", "description": "Protein synthesis.", "rationale": "rRNA is catalytic.", "layers": [ { "id": "catalysis", "name": "Catalysis", "description": "Ribozyme.", "findings": [ { "id": "catalysis-finding", "name": "Catalysis", "description": "Catalytic role.", "questions": [ { "text": "How does rRNA catalyse peptide bond formation?", "kind": "definition" }, { "text": "Which structural studies showed it?", "kind": "provenance" } ] } ] }, { "id": "antibiotics", "name": "Antibiotics", "description": "Drug targets.", "findings": [ { "id": "antibiotics-finding", "name": "Antibiotics", "description": "Antibiotic targets.", "questions": [ { "text": "Which antibiotics act on bacterial ribosomes, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about their own treatment?", "kind": "boundary" } ] } ] } ] }, { "id": "methods", "name": "Methods", "description": "Sequencing.", "rationale": "rRNA is a marker.", "layers": [ { "id": "sequencing", "name": "Sequencing", "description": "16S sequencing.", "findings": [ { "id": "sequencing-finding", "name": "Sequencing", "description": "16S sequencing.", "questions": [ { "text": "How is 16S rRNA sequencing used to identify bacteria?", "kind": "definition" }, { "text": "What are its limits?", "kind": "boundary" } ] } ] }, { "id": "databases", "name": "Databases", "description": "Reference data.", "findings": [ { "id": "databases-finding", "name": "Databases", "description": "Reference databases.", "questions": [ { "text": "Which reference databases hold rRNA sequences, such as SILVA?", "kind": "provenance" }, { "text": "How are they curated?", "kind": "provenance" } ] } ] } ] }, { "id": "evolution", "name": "Evolution", "description": "Phylogeny.", "rationale": "rRNA shaped the tree of life.", "layers": [ { "id": "tree", "name": "Tree", "description": "Tree of life.", "findings": [ { "id": "tree-finding", "name": "Tree", "description": "Tree of life.", "questions": [ { "text": "How did rRNA comparisons reveal the three domains of life?", "kind": "provenance" }, { "text": "Who proposed the domain system?", "kind": "provenance" } ] } ] }, { "id": "teaching", "name": "Teaching", "description": "Explaining.", "findings": [ { "id": "teaching-finding", "name": "Teaching", "description": "Teaching.", "questions": [ { "text": "How can ribosome structure be explained with models?", "kind": "action" }, { "text": "Which structure viewers help?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should each rRNA type be a separate entry?", "How should sequence databases be linked?", "How should gene copy variation be recorded?" ], "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 ribosomal RNA, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain ribosomal RNA by type, structure, function, gene organisation and research uses such as microbial identification.", "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: self-splicing ribosomal RNA, 5S ribosomal RNA, 16S ribosomal RNA encoded by: VC_RS00270 VC_RS00270, 23S ribosomal RNA encoded by: VC_RS00280 VC_RS00280, 5S ribosomal RNA encoded by: rrf VC_RS00285, 16S ribosomal RNA encoded by: VC_RS00735 VC_RS00735, 23S ribosomal RNA encoded by: VC_RS00745 VC_RS00745, 5S ribosomal RNA encoded by: rrf VC_RS00750, 16S ribosomal RNA encoded by: VC_RS01505 VC_RS01505, 23S ribosomal RNA encoded by: VC_RS01520 VC_RS01520, 5S ribosomal RNA encoded by: rrf VC_RS01525, 16S ribosomal RNA encoded by: VC_RS01940 VC_RS01940.", "1886 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 49 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 ribosomal RNA, 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": [ "self-splicing ribosomal RNA", "5S ribosomal RNA", "16S ribosomal RNA encoded by: VC_RS00270 VC_RS00270", "23S ribosomal RNA encoded by: VC_RS00280 VC_RS00280", "5S ribosomal RNA encoded by: rrf VC_RS00285", "16S ribosomal RNA encoded by: VC_RS00735 VC_RS00735", "23S ribosomal RNA encoded by: VC_RS00745 VC_RS00745", "5S ribosomal RNA encoded by: rrf VC_RS00750", "16S ribosomal RNA encoded by: VC_RS01505 VC_RS01505", "23S ribosomal RNA encoded by: VC_RS01520 VC_RS01520", "5S ribosomal RNA encoded by: rrf VC_RS01525", "16S ribosomal RNA encoded by: VC_RS01940 VC_RS01940" ] } ], "standing": "Described in 49 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 1886 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 ribosomal RNA from another, and a ribosomal RNA 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 ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a ribosomal RNA 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 ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a ribosomal RNA performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a ribosomal RNA at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 ribosomal RNA is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a ribosomal RNA, 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 ribosomal RNA, 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 ribosomal RNA 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 } } } }