{ "model": { "rank": 5592, "code": "thing-q188928", "model_id": "vr.tr.messenger-rna", "name": "messenger RNA", "purpose": "Enable an agent to recognise messenger RNA, assess its molecular and functional state, and determine suitable handling, analysis and translation-related uses.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q188928/", "tier": 2, "score": 66, "payload": { "layer": "wikidata", "aliases": [ "nucleoside-modified messenger RNA", "ribosome-bound mRNA", "subgenomic mRNA", "stored messenger RNA", "polycistronic mRNA" ], "aliasCount": 5, "merged": 5, "knownIn": 66, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q188928", "url": "https://www.wikidata.org/wiki/Q188928", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T22:43:15Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22, "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: 01a08856-0ff4-7ad3-90b5-da1e46881747\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: messenger RNA\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 188 things:\n# Batch 006: 1001 re", "usd": 0, "recall": true }, "codex": { "seconds": 59.5, "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: 01a08856-0ff8-75f2-8c22-d0db0ab280ed\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: messenger RNA\nRegistry id: vr.tr.messenger-rna\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none" } } }, "metaModel": { "id": "THING-Q188928", "registryId": "vr.tr.messenger-rna", "name": "messenger RNA", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q188928/", "model": { "registry_id": "vr.tr.messenger-rna", "name": "messenger RNA", "purpose": "Enable an agent to recognise messenger RNA, assess its molecular and functional state, and determine suitable handling, analysis and translation-related uses.", "definition": "Messenger RNA (mRNA) is a class of ribonucleic acid molecules whose nucleotide sequences serve as templates for ribosomal synthesis of proteins.", "scope_statement": "This model owns messenger RNA as a class of physical RNA molecules and as particular transcripts or preparations, including sequence identity, coding organisation, maturation, translation competence, integrity and handling requirements.", "in_scope": [ "Transcript identity, sequence variants and natural or engineered origin", "Protein-coding regions, untranslated regions and translation-relevant architecture", "Processing, terminal structures and nucleotide modifications", "Integrity, abundance, purity and translation competence in a specified context", "Molecular stability, storage conditions and compatibility with intended use" ], "out_of_scope": [ "DNA genes, genomes and transcriptional regulatory systems as independently modelled things", "Transfer RNA, ribosomal RNA and noncoding RNA classes", "Encoded proteins and their downstream biological effects", "Cells, ribosomes and translation machinery as independent systems", "Delivery carriers, formulated medicines and clinical treatment protocols", "Manufacturing processes and laboratory instruments as independent things" ], "distinguishing_features": [ "Establish that the material is RNA rather than DNA using sequence chemistry or suitable analytical evidence.", "Identify an evidenced or intended role as a protein-translation template; an apparent open reading frame alone does not establish messenger RNA identity.", "Distinguish messenger RNA from transfer RNA and ribosomal RNA by its coding-template role rather than merely its presence near ribosomes.", "Distinguish precursor, mature and degraded transcript states without assuming that every messenger RNA requires the same processing steps.", "Separate the RNA molecule from a carrier or finished product containing it; carrier properties do not establish transcript identity or integrity." ], "characteristics": [ { "name": "Transcript identity and sequence", "kind": "relation", "unit_or_values": "Reference accession and version, organism or construct identifier, sequence and documented differences", "why_it_matters": "Names alone cannot distinguish transcript isoforms, engineered variants or sequence revisions." }, { "name": "Molecular length", "kind": "measurement", "unit_or_values": "Nucleotides, with treatment of variable tails and incomplete molecules specified", "why_it_matters": "Length supports identity and integrity assessment when compared with the expected transcript." }, { "name": "Coding organisation", "kind": "category", "unit_or_values": "Coding-region coordinates, reading frames, expected products and monocistronic or polycistronic organisation", "why_it_matters": "Translation expectations depend on which coding regions the transcript contains." }, { "name": "Topology and terminal architecture", "kind": "category", "unit_or_values": "Linear or circular; applicable 5' and 3' structures, cap identity and tail identity", "why_it_matters": "Architecture affects recognition, translation and degradation and must be interpreted in context." }, { "name": "Processing state", "kind": "state", "unit_or_values": "Precursor, partially processed, mature for the relevant biological system, or unresolved", "why_it_matters": "A transcript can have the expected sequence origin without being ready for its intended function." }, { "name": "Nucleotide modifications", "kind": "category", "unit_or_values": "Modification identity, location or distribution, occupancy and detection method where known", "why_it_matters": "Modification patterns can distinguish preparations and affect their functional behaviour." }, { "name": "Integrity", "kind": "measurement", "unit_or_values": "Full-length fraction in percent and fragment-size distribution, with assay and reference", "why_it_matters": "RNA quantity alone does not establish the amount of intact coding template." }, { "name": "Abundance or concentration", "kind": "measurement", "unit_or_values": "Copies per cell, copies per volume, ng/µL or mol/L, with sampling context and method", "why_it_matters": "Biological abundance and preparation concentration answer different operational questions." }, { "name": "Preparation purity", "kind": "measurement", "unit_or_values": "Assay-specific amounts or fractions of unwanted RNA species, DNA, proteins and other relevant residuals", "why_it_matters": "Impurities can affect interpretation and suitability independently of transcript identity." }, { "name": "Translation competence", "kind": "state", "unit_or_values": "Untested, demonstrated, reduced or undetected in a named translation system with controls", "why_it_matters": "Functional conclusions require a compatible system and cannot follow from sequence alone." } ], "affordances": [ "Identify a transcript and compare it with a reference or engineered specification.", "Map coding regions and assess whether processing and architecture suit a specified translation context.", "Quantify transcript abundance, intact material and preparation impurities.", "Select compatible handling and analytical conditions using preparation-specific evidence.", "Evaluate translation competence in a defined assay.", "Determine whether evidence supports an intended use or whether further characterisation is required." ] }, "sources": [], "structure": { "bundles": [ { "id": "transcript-identity", "name": "Transcript identity", "description": "Establish which messenger RNA is being represented and at what level.", "rationale": "Messenger RNA is a heterogeneous molecular class, so a class name cannot substitute for transcript or preparation identity.", "layers": [ { "id": "reference-and-origin", "name": "Reference and origin", "description": "Connect the RNA to its sequence reference and biological or engineered origin.", "findings": [ { "id": "sequence-grounding", "name": "Sequence grounding", "description": "Record the evidence needed to identify the transcript without treating a gene name as an exact RNA sequence.", "questions": [ { "text": "Which accession, version or explicit sequence identifies this transcript, and which differences are documented?", "kind": "definition", "id": "sequence-grounding-q01" }, { "text": "Was this RNA observed in a biological source or produced from an engineered template, and what evidence establishes that origin?", "kind": "provenance", "id": "sequence-grounding-q02" } ] } ] }, { "id": "identity-boundaries", "name": "Identity boundaries", "description": "Separate the molecular class, transcript variant and physical preparation.", "findings": [ { "id": "transcript-versus-preparation", "name": "Transcript versus preparation", "description": "Clarify whether assertions apply to a sequence-defined transcript or to material that may contain multiple RNA species.", "questions": [ { "text": "Does the represented thing denote the messenger RNA class, a transcript isoform, an engineered construct or a particular preparation?", "kind": "boundary", "id": "transcript-versus-preparation-q01" }, { "text": "Which sequence, tail-length or modification differences are included within this identity, and which require a separately identified variant?", "kind": "boundary", "id": "transcript-versus-preparation-q02" } ] } ] } ] }, { "id": "coding-and-maturation", "name": "Coding and maturation", "description": "Describe the architecture that makes the RNA a candidate translation template.", "rationale": "Coding sequence, processing and terminal structures must be interpreted together and in the relevant biological system.", "layers": [ { "id": "coding-architecture", "name": "Coding architecture", "description": "Locate coding regions and translation-relevant noncoding portions.", "findings": [ { "id": "translation-template-map", "name": "Translation template map", "description": "Capture coding-region assignments and their supporting evidence without equating every possible reading frame with an expressed product.", "questions": [ { "text": "Which coding regions, initiation sites, termination sites and expected products are supported, and which remain predictions?", "kind": "definition", "id": "translation-template-map-q01" }, { "text": "Which untranslated regions or other sequence elements must be retained for the intended translation context?", "kind": "action", "id": "translation-template-map-q02" } ] } ] }, { "id": "processing-and-chemistry", "name": "Processing and chemistry", "description": "Characterise maturation, topology, termini and nucleotide modifications.", "findings": [ { "id": "contextual-maturity", "name": "Contextual maturity", "description": "Assess maturity against the requirements of the particular transcript and system rather than a universal checklist.", "questions": [ { "text": "Which processing steps are applicable, and what evidence distinguishes precursor, partially processed and mature material?", "kind": "measurement", "id": "contextual-maturity-q01" }, { "text": "What topology, cap or other terminal chemistry, tail distribution and nucleotide modifications are measured or specified?", "kind": "measurement", "id": "contextual-maturity-q02" } ] } ] } ] }, { "id": "molecular-and-functional-state", "name": "Molecular and functional state", "description": "Assess how much relevant RNA is present and whether it performs its template function.", "rationale": "Sequence identity and bulk RNA concentration do not establish intactness, purity or functional translation.", "layers": [ { "id": "quantity-and-integrity", "name": "Quantity and integrity", "description": "Distinguish total detected RNA from intact target transcript.", "findings": [ { "id": "intact-target-assessment", "name": "Intact target assessment", "description": "Relate abundance measurements to transcript specificity, fragmentation and unwanted material.", "questions": [ { "text": "How much target RNA is present, in which units, and can the assay distinguish it from fragments and other RNA species?", "kind": "measurement", "id": "intact-target-assessment-q01" }, { "text": "What evidence establishes full-length fraction and relevant impurities, including unwanted double-stranded RNA where applicable?", "kind": "measurement", "id": "intact-target-assessment-q02" } ] } ] }, { "id": "translation-evidence", "name": "Translation evidence", "description": "Link functional claims to a specified translation system and readout.", "findings": [ { "id": "context-bound-competence", "name": "Context-bound competence", "description": "Record whether the transcript produces the expected product under tested conditions and what limits that conclusion.", "questions": [ { "text": "In which cellular or cell-free system was translation tested, and how were product identity and output assessed?", "kind": "measurement", "id": "context-bound-competence-q01" }, { "text": "Which controls distinguish a transcript defect from delivery failure, assay limitations or incompatibility with the translation system?", "kind": "measurement", "id": "context-bound-competence-q02" } ] } ] } ] }, { "id": "stability-and-use", "name": "Stability and use", "description": "Connect preparation history and stability evidence to handling and use decisions.", "rationale": "Messenger RNA suitability depends on its present condition and preparation context, not just its original specification.", "layers": [ { "id": "handling-and-persistence", "name": "Handling and persistence", "description": "Track conditions and events that may change integrity or function.", "findings": [ { "id": "condition-dependent-stability", "name": "Condition-dependent stability", "description": "Record stability evidence for the actual RNA preparation and distinguish it from cellular turnover measurements.", "questions": [ { "text": "What temperature, buffer, RNase-control measures and storage duration are supported for this preparation?", "kind": "action", "id": "condition-dependent-stability-q01" }, { "text": "What handling history, freeze-thaw exposure or measured degradation limits confidence in its current condition?", "kind": "provenance", "id": "condition-dependent-stability-q02" } ] } ] }, { "id": "intended-use-qualification", "name": "Intended-use qualification", "description": "Determine whether the characterised RNA meets the needs of a particular use.", "findings": [ { "id": "use-specific-evidence", "name": "Use-specific evidence", "description": "Tie acceptance decisions to transcript properties while linking formulation and product-level decisions to neighbouring models.", "questions": [ { "text": "Which identity, integrity, purity and functional acceptance criteria must this RNA meet for the intended use?", "kind": "action", "id": "use-specific-evidence-q01" }, { "text": "Which handling or use constraints arise from the RNA sequence and encoded product, and which belong to the carrier, formulation or finished product?", "kind": "boundary", "id": "use-specific-evidence-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "This is recall without source consultation; length and half-life ranges are broad biological generalizations.", "mRNA is a sequence-diverse molecular class, so a single molecular formula, molecular mass, purity specification or hazard classification would be misleading.", "A 5' cap, poly(A) tail and removal of introns are common features of mature nuclear-encoded eukaryotic mRNA, not universal requirements for all mRNA." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of messenger RNA 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": [ "Monocistronic mRNA, containing one principal protein-coding region", "Polycistronic mRNA, containing multiple protein-coding regions", "Nuclear-encoded eukaryotic mRNA", "Organelle-encoded mRNA", "Viral mRNA", "Synthetic mRNA produced by in vitro transcription" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of messenger RNA this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "NCBI RefSeq", "value_or_pattern": "NM_. or XM_.", "note": "Identifies individual protein-coding transcript reference sequences; NM_ denotes curated records and XM_ denotes computational model records. These are not identifiers for mRNA as a material class." }, { "scheme": "INSDC sequence accession", "value_or_pattern": "Accession followed by a numeric sequence version", "note": "GenBank, ENA and DDBJ share this system for nucleotide sequence records, including deposited mRNA sequences." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of messenger RNA 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": [ "Carries coding information to ribosomes during cellular protein synthesis.", "Transcript abundance and sequence are measured to investigate gene expression.", "Synthetic mRNA directs production of antigens in mRNA vaccines.", "Introduced mRNA enables transient protein expression in research and biotechnology.", "Detection of particular transcripts supports molecular diagnostic assays." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of messenger RNA 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": "Transcript length", "typical_range": "Commonly hundreds to several thousand nucleotides; some transcripts are much longer", "unit": "nucleotide" }, { "quantity": "Intracellular half-life", "typical_range": "Often minutes in bacteria and minutes to many hours in eukaryotes; strongly dependent on transcript and conditions", "unit": "minute or hour" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of messenger RNA 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": [ "RNase contamination and chemical hydrolysis fragment mRNA and reduce its usefulness as a translation template.", "Sequence errors, incorrect processing or unsuitable untranslated regions can alter the protein produced or impair expression.", "Unprotected extracellular mRNA is vulnerable to degradation and generally enters cells inefficiently.", "Introduced RNA can activate innate immune responses; effects depend on sequence, chemical modifications, impurities and delivery.", "Double-stranded RNA by-products in synthetic preparations can contribute to unwanted immune activation; toxicity can also arise from the encoded protein or delivery formulation." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of messenger RNA 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": "RNA", "difference": "RNA is the broader molecular class; mRNA is distinguished by its role as a protein-coding translation template." }, { "name": "Pre-mRNA", "difference": "Pre-mRNA is a precursor requiring processing to form mature mRNA, commonly including splicing in eukaryotes." }, { "name": "Transfer RNA", "difference": "Transfer RNA delivers amino acids and decodes mRNA codons rather than supplying the protein-coding template." }, { "name": "Ribosomal RNA", "difference": "Ribosomal RNA forms structural and catalytic components of ribosomes rather than serving as their protein-coding template." }, { "name": "Complementary DNA", "difference": "Complementary DNA is DNA copied from an RNA template; its sugar chemistry and molecular role differ from those of mRNA." }, { "name": "mRNA vaccine", "difference": "An mRNA vaccine is a formulated medicinal product containing antigen-encoding mRNA; mRNA itself is a much broader molecular class." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of messenger RNA this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should this registry entry include precursor messenger RNA directly, or represent it through a related precursor model and maturation relation?", "How should circular translation templates and engineered self-amplifying RNA constructs relate to this entry without conflating distinct molecular categories?", "What evidence threshold distinguishes a messenger RNA from an RNA with a predicted but unverified coding region?", "Which assay-specific integrity and translation criteria can be shared across transcript types, and which must remain preparation-specific?", "Which identifiers and handling classifications meaningfully apply to the broad messenger RNA class versus an exact sequence, preparation or formulated product?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 15, "questions": 23 } }, "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 messenger RNA, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an agent to recognise messenger RNA, assess its molecular and functional state, and determine suitable handling, analysis and translation-related uses.", "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: nucleoside-modified messenger RNA, ribosome-bound mRNA, subgenomic mRNA, stored messenger RNA, polycistronic mRNA.", "5 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 66 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 messenger 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": [ "nucleoside-modified messenger RNA", "ribosome-bound mRNA", "subgenomic mRNA", "stored messenger RNA", "polycistronic mRNA" ] } ], "standing": "Described in 66 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 5 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 messenger RNA from another, and a messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger RNA from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger RNA is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a messenger 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 messenger 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 messenger 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 messenger RNA is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a messenger 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 messenger 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 messenger 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 messenger 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 messenger RNA is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger RNA between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a messenger 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 messenger 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 messenger 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 messenger RNA, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger RNA is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a messenger RNA performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a messenger 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 messenger 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 messenger 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 messenger RNA.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a messenger RNA at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a messenger 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 messenger 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 messenger 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 messenger RNA there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger 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 messenger RNA and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a messenger 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 messenger 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 messenger 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 messenger RNA is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a messenger 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 messenger 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 messenger 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 } } } }