{ "model": { "rank": 4639, "code": "thing-q206229", "model_id": "vr.tr.biomolecule", "name": "biomolecule", "purpose": "Enable an agent to identify a biomolecule, assess its molecular integrity and biological relevance, and determine suitable handling, measurement and use.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q206229/", "tier": 2, "score": 73, "payload": { "layer": "wikidata", "aliases": [], "aliasCount": 0, "merged": 0, "knownIn": 73, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q206229", "url": "https://www.wikidata.org/wiki/Q206229", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T20:40:57Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.5, "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: 01a087e5-fc01-7d62-9d06-5129777f77c9\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: biomolecule\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 005: 1001 reg", "usd": 0, "recall": true }, "codex": { "seconds": 66.5, "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: 01a087e5-fc09-7a21-81d5-39d53d2b8f73\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: biomolecule\nRegistry id: vr.tr.biomolecule\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry: (none)\n\n\n" } } }, "metaModel": { "id": "THING-Q206229", "registryId": "vr.tr.biomolecule", "name": "biomolecule", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q206229/", "model": { "registry_id": "vr.tr.biomolecule", "name": "biomolecule", "purpose": "Enable an agent to identify a biomolecule, assess its molecular integrity and biological relevance, and determine suitable handling, measurement and use.", "definition": "A biomolecule is a molecule produced by living organisms or characteristic of their composition and biological processes, including small metabolites and biological macromolecules.", "scope_statement": "This model owns molecular identity, biological provenance, structure, condition-dependent state and evidenced activity of biomolecules, distinguishing a molecular species from a particular preparation and accommodating synthetic counterparts of biological molecules.", "in_scope": [ "Biomolecular classes, including proteins, nucleic acids, carbohydrates, lipids and small biological molecules", "Chemical identity, sequence where applicable, stereochemistry and molecular modifications", "Biological origin and extraction, synthesis or recombinant production provenance", "Conformation, association, degradation and activity under stated conditions", "Preparation-specific purity, concentration, contaminants and handling constraints", "Identifiers, hazards and use restrictions applicable to the identified molecule or preparation" ], "out_of_scope": [ "Whole organisms, cells and tissues that produce or contain biomolecules", "Complete metabolic pathways and biological systems in which biomolecules participate", "Finished medicines, foods, cosmetics and other formulated products", "Manufacturing processes and laboratory instruments as independently modelled things", "Clinical efficacy or patient-specific treatment decisions", "Bulk biological materials whose constituents have not been resolved into molecular identities" ], "distinguishing_features": [ "Biological production or an explicitly justified relationship to a biological molecule supports inclusion; mere presence in a biological sample does not settle the boundary.", "A biomolecule is a molecular entity, whereas a cell, tissue or extract contains multiple molecular entities.", "Biomolecule does not mean macromolecule: small metabolites can qualify, and a large synthetic polymer does not qualify solely through size.", "For sequence-defined biomolecules, sequence, stereochemistry and modifications can distinguish entities that share a common name or nominal mass.", "A molecular identity can persist across preparations even when purity, conformation, aggregation or measured activity differs." ], "characteristics": [ { "name": "Biomolecular class", "kind": "category", "unit_or_values": "protein or peptide; nucleic acid; carbohydrate; lipid; small molecule; conjugate; other justified class", "why_it_matters": "Determines which identity descriptors, structural measurements and handling questions apply." }, { "name": "Molecular identity and identifier resolution", "kind": "relation", "unit_or_values": "Names and applicable CAS, PubChem, ChEBI, sequence or structure accessions, with the exact entity each identifies", "why_it_matters": "Prevents a family, sequence record, salt or modified form from being mistaken for the specific molecule." }, { "name": "Composition and primary structure", "kind": "category", "unit_or_values": "Molecular formula, sequence, residue composition, bond connectivity and stereochemistry as applicable", "why_it_matters": "Establishes what molecule is present and distinguishes closely related variants." }, { "name": "Modification profile", "kind": "state", "unit_or_values": "Modification type, site and occupancy; resolved or unresolved heterogeneity", "why_it_matters": "Modifications can alter molecular identity, binding, stability and activity." }, { "name": "Molecular mass", "kind": "measurement", "unit_or_values": "Da or kDa; calculated or measured; monoisotopic or average; specified molecular form", "why_it_matters": "Supports identity checks and amount calculations while exposing ambiguity from adducts or heterogeneous forms." }, { "name": "Biological and production provenance", "kind": "relation", "unit_or_values": "Source organism and biological context where known; extraction, synthesis or recombinant production route", "why_it_matters": "Helps interpret expected variants, modifications and possible contaminants." }, { "name": "Conformation and association state", "kind": "state", "unit_or_values": "Applicable fold or conformational ensemble; monomer, oligomer, complex or aggregate; method and conditions", "why_it_matters": "The same chemical entity can behave differently when folded, associated or aggregated." }, { "name": "Preparation concentration and purity", "kind": "measurement", "unit_or_values": "mol/L or g/L; purity percentage with measurement basis; contaminant-specific amounts and detection limits", "why_it_matters": "Determines usable quantity and whether observed effects can be attributed to the intended molecule." }, { "name": "Environmental and physical state", "kind": "state", "unit_or_values": "Physical form, solvent or matrix, pH, temperature in °C, ionic strength in mol/L and relevant cofactors", "why_it_matters": "Makes solubility, structure, stability and activity observations interpretable." }, { "name": "Biological activity", "kind": "measurement", "unit_or_values": "Assay-specific endpoint and units, reference material, conditions and uncertainty; untested where applicable", "why_it_matters": "Separates demonstrated function from identity-based expectations." }, { "name": "Integrity and stability", "kind": "state", "unit_or_values": "Intact, fragmented, oxidized, hydrolyzed, denatured or otherwise altered; assessment method and time", "why_it_matters": "Supports decisions about storage, retesting and suitability for use." }, { "name": "Hazard and regulatory applicability", "kind": "category", "unit_or_values": "Documented classifications or unresolved status, tied to entity, preparation, jurisdiction and intended use", "why_it_matters": "Prevents biological origin from being treated as evidence of safety or permission to use." } ], "affordances": [ "Resolve names and identifiers to a molecular species and distinguish related variants or preparations.", "Select identity, purity, structural and activity measurements appropriate to the biomolecular class.", "Compare preparations using matched molecular forms, measurement methods and assay conditions.", "Choose supported storage, reconstitution and handling conditions from preparation-specific evidence.", "Evaluate suitability for an assay, binding study, transformation or formulation against explicit requirements.", "Identify when unresolved identity, contamination or degradation requires further characterization before use." ] }, "sources": [], "structure": { "bundles": [ { "id": "molecular-identity", "name": "Molecular identity", "description": "Establishes which biomolecular entity is being represented and how precisely it is resolved.", "rationale": "A common biomolecule name can refer to a family, sequence, modified form or heterogeneous preparation.", "layers": [ { "id": "class-and-boundary", "name": "Class and boundary", "description": "Locates the entity within biomolecular classes and neighbouring kinds of material.", "findings": [ { "id": "biomolecule-inclusion", "name": "Biomolecule inclusion", "description": "Record the reason for treating the entity as a biomolecule and whether the record describes a species, family or preparation.", "questions": [ { "text": "What biological origin or relationship to a biological molecule justifies inclusion?", "kind": "definition", "id": "biomolecule-inclusion-q01" }, { "text": "Does the name denote one molecular species, a biomolecular family, a complex or a mixture requiring constituent records?", "kind": "boundary", "id": "biomolecule-inclusion-q02" } ] } ] }, { "id": "identity-resolution", "name": "Identity resolution", "description": "Captures descriptors that separate molecular variants and resolve external identifiers.", "findings": [ { "id": "resolved-molecular-form", "name": "Resolved molecular form", "description": "Specify applicable sequence, connectivity, stereochemistry and modifications, and establish the scope of each identifier.", "questions": [ { "text": "Which sequence, connectivity, stereochemistry and modification details are necessary to distinguish this molecular form?", "kind": "definition", "id": "resolved-molecular-form-q01" }, { "text": "Which authoritative records identify this exact form, and which refer only to a parent compound, sequence or family?", "kind": "provenance", "id": "resolved-molecular-form-q02" } ] } ] } ] }, { "id": "biological-origin-and-preparation", "name": "Biological origin and preparation", "description": "Connects the molecular entity to its biological context and the preparation being evaluated.", "rationale": "Production route and sample composition can explain differences that molecular naming alone cannot.", "layers": [ { "id": "origin-and-production", "name": "Origin and production", "description": "Separates biological occurrence from the route used to produce a particular preparation.", "findings": [ { "id": "source-dependent-variation", "name": "Source-dependent variation", "description": "Record source organism or context, production route and evidence for resulting molecular variation.", "questions": [ { "text": "What evidence identifies the biological source or reference counterpart and the preparation's production route?", "kind": "provenance", "id": "source-dependent-variation-q01" }, { "text": "Which source- or host-dependent modifications and variants were measured in this preparation?", "kind": "measurement", "id": "source-dependent-variation-q02" } ] } ] }, { "id": "preparation-composition", "name": "Preparation composition", "description": "Describes the amount of target molecule and substances accompanying it.", "findings": [ { "id": "purity-and-contaminants", "name": "Purity and contaminants", "description": "Keep concentration, purity, molecular heterogeneity, additives and contaminants distinct.", "questions": [ { "text": "How were concentration and purity measured, with what calibration, measurement basis and uncertainty?", "kind": "measurement", "id": "purity-and-contaminants-q01" }, { "text": "Which related molecular species, residual production materials or contaminants could affect the intended assay or use?", "kind": "action", "id": "purity-and-contaminants-q02" } ] } ] } ] }, { "id": "structure-and-physical-state", "name": "Structure and physical state", "description": "Describes covalent structure, conformation and molecular association under explicit conditions.", "rationale": "Sequence or formula alone may not establish the structural state responsible for biomolecular behaviour.", "layers": [ { "id": "covalent-architecture", "name": "Covalent architecture", "description": "Captures molecular organization beyond a generic class or common name.", "findings": [ { "id": "architecture-and-heterogeneity", "name": "Architecture and heterogeneity", "description": "Record applicable branching, linkage positions, disulfide connectivity, conjugation and site-specific modifications.", "questions": [ { "text": "Which linkage, branching, crosslink or conjugation features are established, and by which measurements?", "kind": "measurement", "id": "architecture-and-heterogeneity-q01" }, { "text": "Which unresolved structural variants are represented together, and when should they be distinguished as separate molecular forms?", "kind": "boundary", "id": "architecture-and-heterogeneity-q02" } ] } ] }, { "id": "conformation-and-association", "name": "Conformation and association", "description": "Tracks condition-dependent folding, complex formation and aggregation.", "findings": [ { "id": "observed-structural-state", "name": "Observed structural state", "description": "Associate structural observations with solvent, temperature, concentration and relevant partners rather than assuming one universal state.", "questions": [ { "text": "What conformation or association state was observed, by which method and under what conditions?", "kind": "measurement", "id": "observed-structural-state-q01" }, { "text": "Does the observed assembly belong to this molecule's state description or require a linked multicomponent-complex model?", "kind": "boundary", "id": "observed-structural-state-q02" } ] } ] } ] }, { "id": "biological-role-and-activity", "name": "Biological role and activity", "description": "Connects biological roles and molecular interactions to evidence and measurable performance.", "rationale": "An expected biological role does not establish that a particular preparation is active or suitable for an intended use.", "layers": [ { "id": "roles-and-interactions", "name": "Roles and interactions", "description": "Records supported participation in biological processes and interactions with other molecular entities.", "findings": [ { "id": "evidenced-biological-role", "name": "Evidenced biological role", "description": "Distinguish directly demonstrated roles and partners from annotations inferred through similarity.", "questions": [ { "text": "Which biological roles or interaction partners are supported by direct evidence, and in what organism or experimental context?", "kind": "provenance", "id": "evidenced-biological-role-q01" }, { "text": "Which proposed roles rely on sequence similarity, class membership or another inference requiring qualification?", "kind": "provenance", "id": "evidenced-biological-role-q02" } ] } ] }, { "id": "activity-and-fitness-for-use", "name": "Activity and fitness for use", "description": "Relates measured activity to assay design and intended application.", "findings": [ { "id": "assay-grounded-performance", "name": "Assay-grounded performance", "description": "Record relevant catalytic, binding, structural or other functional endpoints without presuming every biomolecule has an enzyme-like activity.", "questions": [ { "text": "Which assay endpoint, units, controls and conditions establish the relevant performance of this preparation?", "kind": "measurement", "id": "assay-grounded-performance-q01" }, { "text": "What evidence-based acceptance criteria must this preparation satisfy for the intended use?", "kind": "action", "id": "assay-grounded-performance-q02" } ] } ] } ] }, { "id": "stability-handling-and-use-constraints", "name": "Stability, handling and use constraints", "description": "Supports preservation of molecular integrity and decisions about permissible, suitable use.", "rationale": "Biomolecular integrity, activity and hazards depend on the specific entity, preparation and exposure conditions.", "layers": [ { "id": "degradation-and-preservation", "name": "Degradation and preservation", "description": "Tracks relevant degradation mechanisms and evidence for storage or handling conditions.", "findings": [ { "id": "integrity-preserving-conditions", "name": "Integrity-preserving conditions", "description": "Connect observed degradation, denaturation or aggregation to handling history and validated preservation measures.", "questions": [ { "text": "Which changes in molecular integrity or activity occur over time under the tested temperature, pH, light and freeze-thaw conditions?", "kind": "measurement", "id": "integrity-preserving-conditions-q01" }, { "text": "What storage, reconstitution and retesting instructions are supported for this preparation?", "kind": "action", "id": "integrity-preserving-conditions-q02" } ] } ] }, { "id": "hazards-and-applicable-restrictions", "name": "Hazards and applicable restrictions", "description": "Attaches documented hazards and use constraints to the appropriate molecule or preparation.", "findings": [ { "id": "entity-specific-use-constraints", "name": "Entity-specific use constraints", "description": "Distinguish intrinsic molecular hazards from contamination risks and application-specific regulatory requirements.", "questions": [ { "text": "Which read sources establish applicable hazards, classifications or exposure limits for the exact entity and preparation?", "kind": "provenance", "id": "entity-specific-use-constraints-q01" }, { "text": "Which handling controls or use restrictions apply in the intended jurisdiction, setting and application?", "kind": "action", "id": "entity-specific-use-constraints-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": [ "Definitions differ over inclusion of water, inorganic biological constituents and synthetic analogues; the intended registry boundary should be checked.", "This category has no single formula, molar mass, melting point, purity specification or hazard classification; these require a specified molecular entity and preparation.", "The listed kinds are conventional and can overlap, especially for conjugates such as glycoproteins; names and identifiers may need sequence, stereochemistry and modification details." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of biomolecule 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": [ "Proteins and peptides", "Nucleic acids", "Carbohydrates", "Lipids", "Small-molecule metabolites" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of biomolecule 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": "ChEBI", "value_or_pattern": "CHEBI:", "note": "Identifies chemical entities of biological interest; entries include individual substances and chemical classes." }, { "scheme": "PubChem CID", "value_or_pattern": "Positive integer", "note": "Identifies a compound record; biomolecule as a broad category has no single compound identifier." }, { "scheme": "UniProtKB accession", "value_or_pattern": "6- or 10-character alphanumeric accession", "note": "Identifies a protein knowledgebase entry; sequence variants and modified forms may require additional specification." }, { "scheme": "CAS Registry Number", "value_or_pattern": "2-7 digits, hyphen, 2 digits, hyphen, check digit", "note": "Available for many specific biomolecular substances, but not a universal identifier for every sequence or molecular form." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of biomolecule this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-standards-and-regulation", "name": "Standards and regulation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "IUPAC-IUBMB biochemical nomenclature recommendations provide naming conventions for classes of biomolecules." ], "questions": [ { "id": "evidence-standards-and-regulation-q01", "text": "Which of these standards and regulation hold for the sense of biomolecule 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": [ "Enzymes catalyse reactions in industrial processing and laboratory assays.", "Proteins, nucleic acids and metabolites serve as diagnostic biomarkers.", "Biomolecules serve as medicines, including therapeutic proteins and nucleic acid medicines.", "DNA, RNA and proteins are used in biotechnology and molecular biology research.", "Polysaccharides and proteins provide materials for gels, scaffolds and other biomaterials." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of biomolecule 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": [ "Hydrolysis, oxidation and enzymatic degradation can alter molecular identity and activity.", "Proteins and some nucleic acids can lose functional structure under unsuitable temperature, pH or solvent conditions.", "Aggregation, precipitation or adsorption to surfaces can reduce usable concentration and distort measurements.", "Biomolecular preparations can contain contaminants such as endotoxins, residual enzymes or unintended molecular variants.", "Some biomolecules are toxins, allergens or otherwise biologically hazardous; biological origin does not establish safety." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of biomolecule 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": "Biological macromolecule", "difference": "A biological macromolecule is a large molecule; biomolecule also includes small molecules such as amino acids and metabolites." }, { "name": "Biopolymer", "difference": "A biopolymer consists of repeated or linked monomer units; many biomolecules, including numerous lipids and metabolites, are not polymers." }, { "name": "Organic compound", "difference": "Organic compound is a chemical classification; biomolecule additionally refers to biological occurrence or role, and many organic compounds have no established biological association." }, { "name": "Biomaterial", "difference": "A biomaterial is defined by its use in interaction with biological systems and may be metallic, ceramic or synthetic; a biomolecule is a molecular entity." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of biomolecule this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "With no registry definition recorded, does biomolecule include water and other inorganic molecules involved in life, or follow a narrower convention?", "Where should the boundary fall for synthetic analogues, extensively engineered molecules and biomolecule-synthetic conjugates?", "Which existing Vercy models already own molecule, chemical substance, biomacromolecule or molecular complex, and what should this model inherit or link to?", "What class-specific rules distinguish a new molecular identity from a modification profile, conformational state or heterogeneous preparation?", "Which authoritative sources and minimum measurements should establish identity, integrity and fitness for use for each biomolecular class?" ], "statistics": { "bundles": 6, "layers": 11, "findings": 17, "questions": 27 } }, "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 biomolecule, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an agent to identify a biomolecule, assess its molecular integrity and biological relevance, and determine suitable handling, measurement and use.", "characteristics": { "substance": "material", "origin": "natural", "agency": "inert", "mobility": "varies" }, "whatYouCanDoWithIt": [ "observed and measured", "consumed or used up" ], "distinguishingFeatures": [ "Described in 73 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 biomolecule, and on what evidence are they told apart?" ], "whatItIsMadeOf": "matter you can touch", "physicalCharacter": [ "Mobility varies between examples.", "Does nothing on its own; everything it does, something else did to it.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state", "use it up, and then need more of it" ], "howItIsRecognised": [ "Not recognisable by sight in any reliable way. Appearance varies with grade, form and additives; identification is by label, by documentation, or by assay." ], "relatedModels": [], "standing": "Described in 73 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one biomolecule from another, and a biomolecule 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 biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule 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 biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule 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 biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule 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 biomolecule is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule 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 biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule 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 biomolecule between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a biomolecule 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 biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule 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 biomolecule is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a biomolecule performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a biomolecule at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule 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 biomolecule 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 biomolecule 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 biomolecule 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 biomolecule, 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 biomolecule 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 biomolecule 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 biomolecule 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 biomolecule, 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 biomolecule 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 biomolecule and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a biomolecule, 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 biomolecule, 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 biomolecule 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 biomolecule is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a biomolecule, 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 biomolecule, 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 biomolecule 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 } } } }