{ "model": { "rank": 10258, "code": "thing-q62536", "model_id": "vr.tr.ion-channel-complex", "name": "ion channel complex", "purpose": "Let an agent explain ion channel complexes and their structure, relay classes, gating and physiology from biochemistry references, describe the families and proteins the registry aliases name at the level of published biology, and distinguish channel complexes from transporters, pumps and single channel subunits.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q62536/", "tier": 2, "score": 45, "payload": { "layer": "wikidata", "aliases": [ "Bestrophin/UPF0187", "Ectatomin", "Archaeal/bacterial/fungal rhodopsins", "SARS coronavirus accessory protein, Orf3/3a", "G protein-coupled inwardly-rectifying potassium channel", "Ion transport domain, protein family", "Potassium channel, voltage-dependent, beta subunit, KCNAB", "Calcium homeostasis modulator protein 1", "Synthetic ion channels", "cation diffusion facilitator", "Potassium channel, calcium-activated, BK, beta subunit", "Potassium channel, voltage-dependent, beta subunit, KCNE", "cysteine loop ligand-gated ion channel receptor", "voltage-gated ion channel", "G protein-gated ion channel", "P2X6 purinoceptor", "P2X4 purinoceptor", "P2X7 purinoceptor", "P2X5 purinoceptor", "P2X1 purinoceptor", "P2X2 purinoceptor", "P2X3 purinoceptor", "Neurotransmitter-gated ion-channel", "Potassium channel, voltage-dependent, beta subunit, KCNAB3", "Potassium channel, voltage-dependent, beta subunit, KCNAB2", "potassium channel", "voltage-gated sodium channel", "prokaryotic proton-gated ion channel GLIC", "Glycine receptor alpha 3", "Glycine receptor alpha 1", "Glycine receptor beta", "GABA type A receptor-associated protein", "5-hydroxytryptamine receptor 3A", "Cholinergic receptor nicotinic alpha 1 subunit", "Cholinergic receptor nicotinic gamma subunit", "Cholinergic receptor nicotinic beta 1 subunit", "Cholinergic receptor nicotinic beta 2 subunit", "Cholinergic receptor nicotinic epsilon subunit", "Cholinergic receptor nicotinic delta subunit", "Gamma-aminobutyric acid type A receptor subunit gamma2" ], "aliasCount": 173, "merged": 175, "knownIn": 45, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q62536", "url": "https://www.wikidata.org/wiki/Q62536", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T14:33:26Z", "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-Q62536", "registryId": "vr.tr.ion-channel-complex", "name": "ion channel complex", "version": "0.2.0-wave.4", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q62536/", "model": { "registry_id": "vr.tr.ion-channel-complex", "name": "ion channel complex", "purpose": "Let an agent explain ion channel complexes and their structure, relay classes, gating and physiology from biochemistry references, describe the families and proteins the registry aliases name at the level of published biology, and distinguish channel complexes from transporters, pumps and single channel subunits.", "definition": "A protein complex embedded in a membrane that forms a pore allowing ions to pass, including G protein-coupled inwardly rectifying potassium channels, bestrophin chloride channels, microbial rhodopsin light-driven channels and pumps, and viral and toxin proteins that form ion-conducting pores such as the SARS coronavirus Orf3a protein and the ant venom peptide ectatomin, together with protein families defined by the ion transport domain; ion channel complexes underlie nerve signalling, muscle contraction and cell homeostasis.", "what_it_is_for": "Not applicable; a protein complex class.", "affordances": [ "explain structure and gating", "relay classes and physiology", "describe named families", "distinguish related proteins" ], "distinguishing_features": [ "Pore formation", "Selective conduction", "Gated", "Multi-subunit" ], "appearance": "Not a visible object; multi-subunit pores in membranes.", "visual_identification": [ "Membrane protein complex forming an ion pore", "GIRK channels, bestrophins, microbial rhodopsins, SARS Orf3a, ectatomin, ion transport domain families", "Transporters bind and move ions; pumps use ATP; a subunit is one protein of the complex" ], "physical_properties": [ { "quantity": "human ion channel genes", "typical_range": "over 400", "unit": "count", "note": "" }, { "quantity": "conduction rate", "typical_range": "up to millions of ions per second", "unit": "note", "note": "" }, { "quantity": "gating types", "typical_range": "voltage, ligand, mechanical, light", "unit": "list", "note": "" } ], "families_and_kinds": [ "voltage-gated channel complexes", "ligand-gated channels including GIRK channels", "chloride channels such as bestrophins", "light-gated channels and pumps such as microbial rhodopsins", "viroporins such as SARS coronavirus Orf3a", "pore-forming toxins such as ectatomin", "families with the ion transport domain" ], "related_models": [ { "relation": "is a kind of", "target": "transmembrane transporter complex", "why": "in registry terms" }, { "relation": "is a kind of", "target": "ion transmembrane transporter", "why": "in registry terms" }, { "relation": "is a kind of", "target": "porin", "why": "in registry terms, loosely" }, { "relation": "is contrasted with", "target": "ion pump", "why": "which uses ATP" } ], "identifiers": [ { "scheme": "GO", "value_or_pattern": "GO:0034702", "note": "ion channel complex" } ], "standards_and_regulation": [ "No regulation; biosafety rules for toxin and viral protein research" ], "failure_modes_and_hazards": [ "Agents providing toxin or pathogen manipulation detail", "Confusing channels with transporters", "Registry aliases mixing families, viral proteins and a toxin" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What an ion channel complex is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is an ion channel complex, and how does it differ from transporters, pumps and single subunits?", "kind": "definition" }, { "text": "Is the question about structure, a family, physiology or pathogen and toxin detail the model does not provide?", "kind": "boundary" } ] } ] }, { "id": "families", "name": "Families", "description": "Named families.", "findings": [ { "id": "families-finding", "name": "Families", "description": "Families.", "questions": [ { "text": "What are GIRK channels, bestrophins, microbial rhodopsins, SARS Orf3a, ectatomin and ion transport domain families, at the level of published biology?", "kind": "definition" }, { "text": "Which entry fits the specific family?", "kind": "action" } ] } ] } ] }, { "id": "biology", "name": "Biology", "description": "Structure and gating.", "rationale": "Science.", "layers": [ { "id": "structure", "name": "Structure", "description": "Structure.", "findings": [ { "id": "structure-finding", "name": "Structure", "description": "Structure.", "questions": [ { "text": "How do subunits assemble into pores, and how is selectivity achieved?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "gating", "name": "Gating", "description": "Gating.", "findings": [ { "id": "gating-finding", "name": "Gating", "description": "Gating.", "questions": [ { "text": "How do voltage, ligands, light and mechanical force gate channels?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "physiology", "name": "Physiology", "description": "Physiology and medicine.", "rationale": "Clinical.", "layers": [ { "id": "roles", "name": "Roles", "description": "Roles.", "findings": [ { "id": "roles-finding", "name": "Roles", "description": "Roles.", "questions": [ { "text": "How do ion channels drive nerve impulses, heartbeats and secretion?", "kind": "provenance" }, { "text": "Which entry fits action potential?", "kind": "action" } ] } ] }, { "id": "disease", "name": "Disease", "description": "Channelopathies and drugs.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "What are channelopathies, and how do drugs target channels, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about a personal condition, which needs a clinician?", "kind": "boundary" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Methods and history.", "rationale": "Context.", "layers": [ { "id": "methods", "name": "Methods", "description": "Methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How are channels studied by patch clamp, cryo-EM and optogenetics?", "kind": "provenance" }, { "text": "Which entry fits patch clamp?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were ion channels discovered, from Hodgkin and Huxley to MacKinnon?", "kind": "provenance" }, { "text": "Which entry fits the history of neuroscience?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should GIRK channel, bestrophin and viroporin be separate primary entries?", "How should biochemistry references be linked?", "The registry entry has merged aliases naming families, a viral protein and a toxin; 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 ion channel complex, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain ion channel complexes and their structure, relay classes, gating and physiology from biochemistry references, describe the families and proteins the registry aliases name at the level of published biology, and distinguish channel complexes from transporters, pumps and single channel subunits.", "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: Bestrophin/UPF0187, Ectatomin, Archaeal/bacterial/fungal rhodopsins, SARS coronavirus accessory protein, Orf3/3a, G protein-coupled inwardly-rectifying potassium channel, Ion transport domain, protein family, Potassium channel, voltage-dependent, beta subunit, KCNAB, Calcium homeostasis modulator protein 1, Synthetic ion channels, cation diffusion facilitator, Potassium channel, calcium-activated, BK, beta subunit, Potassium channel, voltage-dependent, beta subunit, KCNE.", "175 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 45 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 ion channel complex, 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": [ "Bestrophin/UPF0187", "Ectatomin", "Archaeal/bacterial/fungal rhodopsins", "SARS coronavirus accessory protein, Orf3/3a", "G protein-coupled inwardly-rectifying potassium channel", "Ion transport domain, protein family", "Potassium channel, voltage-dependent, beta subunit, KCNAB", "Calcium homeostasis modulator protein 1", "Synthetic ion channels", "cation diffusion facilitator", "Potassium channel, calcium-activated, BK, beta subunit", "Potassium channel, voltage-dependent, beta subunit, KCNE" ] } ], "standing": "Described in 45 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 175 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 ion channel complex from another, and a ion channel complex 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 ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex 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 ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex 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 ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex 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 ion channel complex is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex 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 ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex 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 ion channel complex between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a ion channel complex 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 ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex 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 ion channel complex is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a ion channel complex performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a ion channel complex at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex 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 ion channel complex 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 ion channel complex 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 ion channel complex 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 ion channel complex, 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 ion channel complex 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 ion channel complex 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 ion channel complex 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 ion channel complex, 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 ion channel complex 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 ion channel complex and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 ion channel complex is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a ion channel complex, 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 ion channel complex, 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 ion channel complex 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 } } } }