{ "model": { "rank": 16834, "code": "thing-q424204", "model_id": "vr.tr.transmembrane-protein", "name": "transmembrane protein", "purpose": "Let an agent explain transmembrane proteins and their structure, relay classes, functions and study methods from biochemistry references, describe membrane-active toxins and peptides at the level of published biology, and distinguish transmembrane proteins from peripheral membrane proteins, lipid-anchored proteins and secreted proteins.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q424204/", "tier": 2, "score": 32, "payload": { "layer": "wikidata", "aliases": [ "pore-forming toxin", "snake three-finger toxin", "insect/fungal defensin", "plant defensin", "Tachyplesin", "Oxyopinin", "Membrane attack complex component/perforin/complement C9", "prion protein family", "Vacuolating cytotoxin", "Pro-islet amyloid polypeptide", "Hemolytic lectin CEL-III, C-terminal domain superfamily", "gasdermin", "Pentraxin", "Mastoparan family", "Pleurocidin", "Moricin family", "Aerolysin", "Aurein antibiotic peptide family", "cecropin", "Epsilon toxin", "Lipid binding protein BPI/LBP", "Bacteriocin, lactococcin 972", "Pleurotolysin", "Clostridial Cytotoxin family", "dermaseptins", "ESAT-6-like superfamily", "Arenicin", "beta defensin", "cholesterol-dependent cytolysin", "Cytolethal distending toxin", "Haemolysin E", "yeast killer toxin family", "diphtheria toxin family", "RTX toxin", "Cytohemolysin", "Melittin family", "Amoebapore family", "Type III-Target Cell Pore", "Equinatoxin", "tripartite haemolysin BL" ], "aliasCount": 319, "merged": 319, "knownIn": 32, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q424204", "url": "https://www.wikidata.org/wiki/Q424204", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T14:10:43Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 4, "engine": "claude" }, "metaModel": { "id": "THING-Q424204", "registryId": "vr.tr.transmembrane-protein", "name": "transmembrane protein", "version": "0.2.0-wave.4", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q424204/", "model": { "registry_id": "vr.tr.transmembrane-protein", "name": "transmembrane protein", "purpose": "Let an agent explain transmembrane proteins and their structure, relay classes, functions and study methods from biochemistry references, describe membrane-active toxins and peptides at the level of published biology, and distinguish transmembrane proteins from peripheral membrane proteins, lipid-anchored proteins and secreted proteins.", "definition": "A protein that spans the whole cell membrane, with domains on both sides, forming channels, transporters, receptors and enzymes essential to cell function, and including membrane-inserting proteins listed in the registry aliases such as pore-forming toxins, snake three-finger toxins that bind receptors, defensins of insects, fungi and plants, and antimicrobial peptides such as tachyplesin and oxyopinin that disrupt membranes; the model covers structure and biology without any guidance on toxin production or use.", "what_it_is_for": "Not applicable; a protein class.", "affordances": [ "explain structure and classes", "relay functions and methods", "describe membrane-active molecules", "distinguish related proteins" ], "distinguishing_features": [ "Spans the bilayer", "Alpha-helical or beta-barrel", "Channels and receptors", "Toxin and peptide relatives" ], "appearance": "Not a visible object; proteins spanning the lipid bilayer.", "visual_identification": [ "Protein spanning the membrane", "Channels, transporters, receptors; pore-forming toxins, three-finger toxins, defensins, tachyplesin, oxyopinin", "Peripheral proteins attach to the surface; lipid-anchored proteins are tethered; secreted proteins leave the cell" ], "physical_properties": [ { "quantity": "share of human genes", "typical_range": "about 25-30", "unit": "percent", "note": "encode membrane proteins" }, { "quantity": "main folds", "typical_range": "alpha-helical bundles and beta-barrels", "unit": "list", "note": "" }, { "quantity": "drug targets", "typical_range": "over half of drugs target membrane proteins", "unit": "note", "note": "" } ], "families_and_kinds": [ "ion channels and transporters", "G protein-coupled and other receptors", "membrane enzymes", "beta-barrel outer membrane proteins", "pore-forming toxins and membrane-active peptides such as defensins, tachyplesin and oxyopinin", "three-finger toxins that target membrane receptors" ], "related_models": [ { "relation": "is a kind of", "target": "integral membrane protein", "why": "in registry terms" }, { "relation": "is embedded in", "target": "cell membrane", "why": "the lipid bilayer" }, { "relation": "is contrasted with", "target": "peripheral membrane protein", "why": "attached to the surface" }, { "relation": "is exemplified by", "target": "ion channel", "why": "a major class" } ], "identifiers": [ { "scheme": "GO", "value_or_pattern": "GO:0016021", "note": "membrane, integral component" } ], "standards_and_regulation": [ "No regulation of the protein class; biosafety rules apply to toxin research" ], "failure_modes_and_hazards": [ "Agents providing toxin production or use guidance", "Confusing transmembrane with peripheral proteins", "Registry aliases naming toxins and peptides as if kinds of transmembrane protein" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What a transmembrane protein is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and structure.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is a transmembrane protein, and how does it differ from peripheral, lipid-anchored and secreted proteins?", "kind": "definition" }, { "text": "Is the question about structure, function, a class, or toxin use, which the model does not assist?", "kind": "boundary" } ] } ] }, { "id": "classes", "name": "Classes", "description": "Classes.", "findings": [ { "id": "classes-finding", "name": "Classes", "description": "Classes.", "questions": [ { "text": "What are channels, transporters, receptors, membrane enzymes and beta-barrel proteins?", "kind": "definition" }, { "text": "Which entry fits the specific class?", "kind": "action" } ] } ] } ] }, { "id": "biology", "name": "Biology", "description": "Biology.", "rationale": "Science.", "layers": [ { "id": "function", "name": "Function", "description": "Function.", "findings": [ { "id": "function-finding", "name": "Function", "description": "Function.", "questions": [ { "text": "How do transmembrane proteins transport ions and molecules, transmit signals and catalyse reactions?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "folding", "name": "Folding", "description": "Insertion and folding.", "findings": [ { "id": "folding-finding", "name": "Folding", "description": "Folding.", "questions": [ { "text": "How are transmembrane proteins inserted and folded in the membrane?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "active", "name": "Active", "description": "Membrane-active molecules.", "rationale": "Science.", "layers": [ { "id": "toxins", "name": "Toxins", "description": "Toxins.", "findings": [ { "id": "toxins-finding", "name": "Toxins", "description": "Toxins.", "questions": [ { "text": "What are pore-forming toxins and three-finger toxins, and how do they act, at the level of published biology?", "kind": "provenance" }, { "text": "Is the presentation limited to biology without production or use detail?", "kind": "boundary" } ] } ] }, { "id": "peptides", "name": "Peptides", "description": "Antimicrobial peptides.", "findings": [ { "id": "peptides-finding", "name": "Peptides", "description": "Peptides.", "questions": [ { "text": "What are defensins, tachyplesin and oxyopinin, and why are they studied for antimicrobials?", "kind": "provenance" }, { "text": "Which entry fits antimicrobial peptide?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Methods and medicine.", "rationale": "Context.", "layers": [ { "id": "methods", "name": "Methods", "description": "Study methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How are membrane proteins studied by cryo-EM, crystallography and prediction?", "kind": "provenance" }, { "text": "Which entry fits membrane protein structure?", "kind": "action" } ] } ] }, { "id": "medicine", "name": "Medicine", "description": "Drug targets.", "findings": [ { "id": "medicine-finding", "name": "Medicine", "description": "Medicine.", "questions": [ { "text": "Why are membrane proteins major drug targets, and what diseases involve them?", "kind": "provenance" }, { "text": "Which entry fits G protein-coupled receptor?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should pore-forming toxin and defensin be separate primary entries?", "How should biochemistry references be linked?", "The registry entry has merged aliases naming toxins and antimicrobial peptides; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "chemical substance or material", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a transmembrane protein, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain transmembrane proteins and their structure, relay classes, functions and study methods from biochemistry references, describe membrane-active toxins and peptides at the level of published biology, and distinguish transmembrane proteins from peripheral membrane proteins, lipid-anchored proteins and secreted proteins.", "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: pore-forming toxin, snake three-finger toxin, insect/fungal defensin, plant defensin, Tachyplesin, Oxyopinin, Membrane attack complex component/perforin/complement C9, prion protein family, Vacuolating cytotoxin, Pro-islet amyloid polypeptide, Hemolytic lectin CEL-III, C-terminal domain superfamily, gasdermin.", "319 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 32 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 transmembrane protein, 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": [ "pore-forming toxin", "snake three-finger toxin", "insect/fungal defensin", "plant defensin", "Tachyplesin", "Oxyopinin", "Membrane attack complex component/perforin/complement C9", "prion protein family", "Vacuolating cytotoxin", "Pro-islet amyloid polypeptide", "Hemolytic lectin CEL-III, C-terminal domain superfamily", "gasdermin" ] } ], "standing": "Described in 32 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 319 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 transmembrane protein from another, and a transmembrane protein 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 transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a transmembrane protein 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 transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a transmembrane protein performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a transmembrane protein at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 transmembrane protein is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a transmembrane protein, 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 transmembrane protein, 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 transmembrane protein 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 } } } }