{ "model": { "rank": 5081, "code": "thing-q162657", "model_id": "vr.tr.neurotransmitter", "name": "neurotransmitter", "purpose": "Enable an agent to identify a substance acting as a neurotransmitter, evaluate evidence for that role in a defined biological context, and determine appropriate interpretation, measurement and handling.", "family": "Thing Registry", "category": "Physical world and living systems", "status": "research-draft", "kind": "thing", "plane": "PHY", "domain": "PHY.MAT", "industry": "", "version": "", "url": "/models/thing/q162657/", "tier": 2, "score": 70, "payload": { "layer": "wikidata", "aliases": [ "gasotransmitter", "cotransmitter", "catecholamine", "Glycinergic", "Catecholine", "cysteinyldopa (unspecified stereochemistry)", "norepinephrine", "epinephrine", "(±)-adrenaline", "beta,3-Dihydroxytyrosine", "droxidopa", "5-S-Cysteinyldopa" ], "aliasCount": 12, "merged": 12, "knownIn": 70, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": "vr.tr.neurotransmitter", "source": { "dataset": "wikidata", "item": "Q162657", "url": "https://www.wikidata.org/wiki/Q162657", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-09T21:37:22Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 20.5, "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: 01a08819-b89a-7610-96bc-382474a8f100\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: neurotransmitter\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: 100", "usd": 0, "recall": true }, "codex": { "seconds": 61, "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: 01a08819-b8a0-7052-a04e-b68ad1ed4584\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: neurotransmitter\nRegistry id: vr.tr.neurotransmitter\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry:" } } }, "metaModel": { "id": "THING-Q162657", "registryId": "vr.tr.neurotransmitter", "name": "neurotransmitter", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q162657/", "model": { "registry_id": "vr.tr.neurotransmitter", "name": "neurotransmitter", "purpose": "Enable an agent to identify a substance acting as a neurotransmitter, evaluate evidence for that role in a defined biological context, and determine appropriate interpretation, measurement and handling.", "definition": "A neurotransmitter is an endogenous chemical messenger released by a neuron that acts on receptors of another cell to transmit or modulate a signal.", "scope_statement": "This model owns neurotransmitter as a biological role of a chemical substance in neuronal communication, connecting molecular identity to release, target action and signal termination without treating all neurotransmitters as one material or assuming that a substance has the same role everywhere.", "in_scope": [ "Chemical identity, molecular form and material preparation when applicable", "Evidence that a substance serves as a neurotransmitter in a specified organism, circuit and target", "Synthesis, availability, storage and release mechanisms", "Receptor or molecular target engagement and context-dependent effects", "Transport, degradation, diffusion and other signal-termination mechanisms", "Measurement validity and constraints on experimental use" ], "out_of_scope": [ "Complete models of neurons, synapses, neural circuits or nervous systems", "Hormonal or metabolic functions unrelated to the specified neurotransmission context", "Drug products and therapeutic prescribing decisions", "Diseases attributed to altered neurotransmission", "Industrial production processes and laboratory equipment design" ], "distinguishing_features": [ "A neurotransmitter is identified by evidence of a signaling role involving neuronal release and target action; chemical identity alone does not establish that role.", "A substance detected in neural tissue is not thereby a neurotransmitter: its participation in communication must be distinguished from metabolic presence or experimental contamination.", "A receptor agonist can mimic a transmitter without being an endogenous neurotransmitter in the system examined.", "Hormone, neurotransmitter and neuromodulator labels can overlap for the same substance; classify the particular source, delivery route and action rather than requiring mutually exclusive substance classes.", "Vesicular storage and a postsynaptic membrane receptor are not universal requirements; evaluate alternative release routes and intracellular targets where relevant." ], "characteristics": [ { "name": "Chemical identity and form", "kind": "category", "unit_or_values": "Chemical name; structure or peptide sequence; stereochemistry; protonation or salt form; applicable CAS, PubChem or other identifiers", "why_it_matters": "Separates the biologically active entity from salts, precursors, metabolites and experimental preparations." }, { "name": "Neurotransmitter role evidence", "kind": "state", "unit_or_values": "Proposed; supported in a specified context; disputed; insufficiently assessed, with supporting evidence", "why_it_matters": "Prevents a context-specific or tentative assignment from becoming a universal classification." }, { "name": "Biological signaling context", "kind": "relation", "unit_or_values": "Organism, tissue, circuit, source cell, target cell or compartment, developmental stage and experimental condition", "why_it_matters": "Defines where claims about release and action apply." }, { "name": "Release mechanism", "kind": "category", "unit_or_values": "Vesicular exocytosis; nonvesicular release; production followed by diffusion; other documented mechanism; unresolved", "why_it_matters": "Determines which evidence and interventions can establish signal delivery." }, { "name": "Target and response coupling", "kind": "relation", "unit_or_values": "Receptor subtype or other molecular target linked to a measured cellular response", "why_it_matters": "Avoids assigning a fixed excitatory or inhibitory effect to the molecule independently of its target." }, { "name": "Local transmitter concentration", "kind": "measurement", "unit_or_values": "mol/L with compartment, sampling volume, time resolution and measurement method", "why_it_matters": "Distinguishes local signaling exposure from bulk tissue abundance." }, { "name": "Signal time course", "kind": "measurement", "unit_or_values": "Onset, peak latency and decay in ms or s, with the measured chemical or biological endpoint", "why_it_matters": "Separates transmitter clearance from receptor activation and downstream response duration." }, { "name": "Signal termination route", "kind": "relation", "unit_or_values": "Transporter, enzyme, uptake cell, diffusion pathway or chemical reaction with supporting context", "why_it_matters": "Explains how exposure ends and where perturbations may change signaling." }, { "name": "Preparation quality and stability", "kind": "state", "unit_or_values": "Purity, concentration, solvent, pH, storage conditions, degradation assessment and expiry when applicable", "why_it_matters": "Connects experimental usability and handling decisions to the actual material." } ], "affordances": [ "Assess whether a candidate substance has sufficient evidence for a neurotransmitter role in a particular system.", "Trace a signaling episode from transmitter availability through release, target action and termination.", "Compare receptor-dependent responses without assuming a universal effect for the substance.", "Select measurements that distinguish tissue abundance, extracellular release and functional response.", "Assess whether a proposed experimental perturbation isolates synthesis, release, target engagement or clearance.", "Check whether a material preparation is suitable for the intended assay and handling conditions." ] }, "sources": [], "structure": { "bundles": [ { "id": "identity-and-role", "name": "Identity and neurotransmitter role", "description": "Connect the chemical entity to evidence for its role in neuronal communication.", "rationale": "Neurotransmitter is a functional classification spanning different chemical entities, not a single composition or universal behavior.", "layers": [ { "id": "molecular-identity", "name": "Molecular identity", "description": "Resolve the active molecule and distinguish related chemical forms.", "findings": [ { "id": "active-entity-and-preparation", "name": "Active entity and preparation", "description": "Record which molecular entity is implicated and how it relates to the material measured or supplied.", "questions": [ { "text": "What structure, stereochemistry or peptide sequence identifies the proposed transmitter?", "kind": "definition", "id": "active-entity-and-preparation-q01" }, { "text": "Does the recorded identifier refer to the active entity, a salt, a precursor, a metabolite or a mixture?", "kind": "boundary", "id": "active-entity-and-preparation-q02" } ] } ] }, { "id": "contextual-role-evidence", "name": "Contextual role evidence", "description": "Assess neurotransmitter status within an explicitly bounded biological system.", "findings": [ { "id": "evidence-for-neuronal-communication", "name": "Evidence for neuronal communication", "description": "Separate observed presence from evidence of release and causally relevant target action.", "questions": [ { "text": "Which observations establish neuronal release and a target response attributable to this substance in the specified system?", "kind": "provenance", "id": "evidence-for-neuronal-communication-q01" }, { "text": "In this context, how is its neurotransmitter role distinguished from or combined with endocrine, metabolic or neuromodulatory roles?", "kind": "boundary", "id": "evidence-for-neuronal-communication-q02" } ] } ] } ] }, { "id": "availability-and-release", "name": "Availability and release", "description": "Describe how a neuron obtains the transmitter and makes it available to targets.", "rationale": "A signaling model must distinguish production and storage capacity from actual release.", "layers": [ { "id": "synthesis-and-pools", "name": "Synthesis and available pools", "description": "Locate production, processing and storage relevant to signaling.", "findings": [ { "id": "signaling-pool-maintenance", "name": "Signaling pool maintenance", "description": "Record how precursors, processing, transport and compartmentation support transmitter availability.", "questions": [ { "text": "Which cells, precursors and processing steps supply the transmitter used in this signaling context?", "kind": "provenance", "id": "signaling-pool-maintenance-q01" }, { "text": "Is the relevant supply stored in vesicles, present in another pool or synthesized on demand, and how is that established?", "kind": "measurement", "id": "signaling-pool-maintenance-q02" } ] } ] }, { "id": "release-and-delivery", "name": "Release and delivery", "description": "Characterize the trigger, mechanism and spatial route of transmitter delivery.", "findings": [ { "id": "release-event", "name": "Release event", "description": "Distinguish physiological signal delivery from leakage, injury and externally applied substance.", "questions": [ { "text": "What triggers release or production, and what evidence identifies the mechanism rather than cell damage or leakage?", "kind": "provenance", "id": "release-event-q01" }, { "text": "Does delivery occur across a synaptic cleft, through extrasynaptic space or by another route, and over what measured distance?", "kind": "measurement", "id": "release-event-q02" } ] } ] } ] }, { "id": "target-action", "name": "Target action", "description": "Connect transmitter exposure to molecular engagement and cellular or circuit effects.", "rationale": "The effect of a transmitter depends on target expression, coupling and physiological conditions.", "layers": [ { "id": "molecular-recognition", "name": "Molecular recognition", "description": "Identify receptors or other molecular targets mediating the response.", "findings": [ { "id": "target-engagement-evidence", "name": "Target engagement evidence", "description": "Associate the transmitter with specific targets while distinguishing binding from functional activation.", "questions": [ { "text": "Which receptor subtypes or other molecular targets mediate the response, and where are they located?", "kind": "definition", "id": "target-engagement-evidence-q01" }, { "text": "Which binding or functional measurements support engagement, and under what concentration and assay conditions?", "kind": "measurement", "id": "target-engagement-evidence-q02" } ] } ] }, { "id": "context-dependent-response", "name": "Context-dependent response", "description": "Describe the response at the level actually measured.", "findings": [ { "id": "response-sign-and-scale", "name": "Response sign and scale", "description": "Separate molecular, cellular and circuit outcomes and preserve conditions affecting their interpretation.", "questions": [ { "text": "What changes in conductance, membrane potential, intracellular signaling or release probability follow exposure?", "kind": "measurement", "id": "response-sign-and-scale-q01" }, { "text": "Which target properties and physiological conditions determine whether the observed effect increases, decreases or otherwise modifies activity?", "kind": "boundary", "id": "response-sign-and-scale-q02" } ] } ] } ] }, { "id": "termination-and-adaptation", "name": "Termination and adaptation", "description": "Track removal of the transmitter and changes in responsiveness during repeated exposure.", "rationale": "Signal duration depends on both extracellular availability and the response machinery.", "layers": [ { "id": "clearance-and-fate", "name": "Clearance and chemical fate", "description": "Identify mechanisms ending local transmitter exposure.", "findings": [ { "id": "termination-pathways", "name": "Termination pathways", "description": "Record uptake, degradation, diffusion or reaction pathways and the fate of resulting material.", "questions": [ { "text": "Which transporters, enzymes, cells or physical processes reduce transmitter availability at the target?", "kind": "definition", "id": "termination-pathways-q01" }, { "text": "What measurements establish clearance kinetics, and do resulting metabolites or recycled pools contribute to subsequent signaling?", "kind": "measurement", "id": "termination-pathways-q02" } ] } ] }, { "id": "feedback-and-responsiveness", "name": "Feedback and responsiveness", "description": "Represent regulation of release and target sensitivity over time.", "findings": [ { "id": "repeated-exposure-effects", "name": "Repeated exposure effects", "description": "Distinguish changes in transmitter supply from feedback, desensitization and downstream adaptation.", "questions": [ { "text": "What evidence shows feedback on transmitter synthesis or release, including any autoreceptor involvement?", "kind": "provenance", "id": "repeated-exposure-effects-q01" }, { "text": "How does the response change with repeated exposure, and which measurements distinguish depletion, target desensitization and clearance changes?", "kind": "measurement", "id": "repeated-exposure-effects-q02" } ] } ] } ] }, { "id": "measurement-and-experimental-use", "name": "Measurement and experimental use", "description": "Establish what measurements support and which preparations and interventions are fit for purpose.", "rationale": "Bulk abundance, local release and biological activity are different observables, while experimental materials can differ from the endogenous entity.", "layers": [ { "id": "assay-interpretation", "name": "Assay interpretation", "description": "Match analytical claims to specificity, sampling and temporal resolution.", "findings": [ { "id": "observable-and-assay-limits", "name": "Observable and assay limits", "description": "Record whether an assay measures the chemical itself, a proxy or a downstream response.", "questions": [ { "text": "Does the method measure total tissue content, extracellular concentration, release events, target occupancy or a functional response?", "kind": "measurement", "id": "observable-and-assay-limits-q01" }, { "text": "What calibration, selectivity controls and spatial and temporal limits constrain attribution to this transmitter?", "kind": "measurement", "id": "observable-and-assay-limits-q02" } ] } ] }, { "id": "preparations-and-perturbations", "name": "Preparations and perturbations", "description": "Connect experimental actions to material identity and interpretable effects.", "findings": [ { "id": "fit-for-purpose-intervention", "name": "Fit-for-purpose intervention", "description": "Assess preparation quality and intervention specificity before interpreting experimental outcomes.", "questions": [ { "text": "What purity, solvent, pH, stability and substance-specific handling information apply to the exact preparation being used?", "kind": "action", "id": "fit-for-purpose-intervention-q01" }, { "text": "Which controls are needed to attribute an intervention's effect to transmitter synthesis, release, target action or clearance rather than other mechanisms?", "kind": "action", "id": "fit-for-purpose-intervention-q02" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "This describes a biological role shared by many substances, not one material with a common formula, purity specification, melting point, or hazard classification.", "No universal concentration or kinetic range applies; measurements require a named transmitter, compartment, organism, and method.", "Definitions differ in their treatment of gaseous and other nonclassical messengers; vesicular storage and release are not universal across the broader category." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of neurotransmitter 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": [ "Amino acid transmitters, such as glutamate and glycine", "Monoamines, such as dopamine and serotonin", "Acetylcholine", "Purines, such as ATP", "Neuropeptides, such as substance P", "Gaseous transmitters, such as nitric oxide" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of neurotransmitter 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": "CAS Registry Number", "value_or_pattern": "Two to seven digits, a hyphen, two digits, a hyphen, and one check digit", "note": "Identifies individual chemical substances; neurotransmitter is a functional category with no single CAS number. Salts and other chemical forms may have separate records." }, { "scheme": "PubChem Compound ID (CID)", "value_or_pattern": "Positive integer", "note": "Identifies individual chemical structures rather than neurotransmitter function as a category." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of neurotransmitter 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": [ "Mediates communication between neurons and from neurons to muscle or gland cells.", "Supports experimental investigation of receptors, synapses, and neural circuits.", "Provides targets for medicines that alter transmitter synthesis, release, receptor activation, reuptake, or degradation.", "Selected neurotransmitters, including dopamine and norepinephrine, are also administered as medicines." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of neurotransmitter 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": [ "Excessive glutamate receptor activation can cause excitotoxic neuronal injury.", "Disrupted synthesis, release, clearance, or receptor function can impair neural signaling.", "Effects depend on receptor subtype and target cell; a transmitter cannot always be classified as intrinsically excitatory or inhibitory.", "Chemical handling hazards depend on the particular molecule, formulation, concentration, and route of exposure." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of neurotransmitter this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-regional-variation", "name": "Regional variation", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Norepinephrine and noradrenaline name the same molecule; epinephrine and adrenaline likewise name the same molecule, with usage varying between naming systems and regions." ], "questions": [ { "id": "evidence-regional-variation-q01", "text": "Which of these regional variation hold for the sense of neurotransmitter 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": "Hormone", "difference": "Hormonal signaling typically reaches targets through circulation; neurotransmission originates from neuronal release onto or near target cells. A molecule can serve both roles." }, { "name": "Neuromodulator", "difference": "Emphasizes changes to neuronal excitability or synaptic effectiveness; it overlaps with neurotransmitter rather than defining a mutually exclusive chemical class." }, { "name": "Neuropeptide", "difference": "Defined by peptide composition and neuronal production or use; only a subset of neurotransmitters are peptides." }, { "name": "Neurotransmitter receptor", "difference": "The receptor is the molecular target that recognizes a transmitter and initiates a cellular response, rather than the released messenger." }, { "name": "Neurotransmitter precursor", "difference": "A precursor is used to synthesize a transmitter but does not qualify as a transmitter solely because of that role." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of neurotransmitter this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "What operational evidence threshold should this catalogue adopt for neurotransmitter status, particularly for unconventional candidates?", "Which existing Vercy models already own chemical identity, receptor function or neuronal signaling, and should be referenced to avoid duplicate ownership?", "How should the catalogue express overlapping neurotransmitter and neuromodulator roles without imposing an unsupported categorical boundary?", "Which organism, circuit and developmental differences require separate contextual findings for each represented substance?", "Which authoritative sources and assay standards should establish substance-specific identifiers, material properties, handling requirements and confidence in release measurements?" ], "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 neurotransmitter, record what state it is in, and decide what may be done with it.", "whatItIs": "Enable an agent to identify a substance acting as a neurotransmitter, evaluate evidence for that role in a defined biological context, and determine appropriate interpretation, measurement and handling.", "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: gasotransmitter, cotransmitter, catecholamine, Glycinergic, Catecholine, cysteinyldopa (unspecified stereochemistry), norepinephrine, epinephrine, (±)-adrenaline, beta,3-Dihydroxytyrosine, droxidopa, 5-S-Cysteinyldopa.", "12 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 70 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 neurotransmitter, 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": [ "gasotransmitter", "cotransmitter", "catecholamine", "Glycinergic", "Catecholine", "cysteinyldopa (unspecified stereochemistry)", "norepinephrine", "epinephrine", "(±)-adrenaline", "beta,3-Dihydroxytyrosine", "droxidopa", "5-S-Cysteinyldopa" ] } ], "standing": "Described in 70 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 12 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 neurotransmitter from another, and a neurotransmitter 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 neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter is built from and which parts are replaceable.", "questions": [ { "id": "parts-and-materials-q01", "text": "What identifies and describes the composition of a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter is judged and by whom.", "questions": [ { "id": "condition-assessment-q01", "text": "What identifies and describes the condition of a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter is, and what that position is measured against.", "questions": [ { "id": "position-and-frame-q01", "text": "What identifies and describes the location of a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a neurotransmitter 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 neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter is for, and what it is used for anyway.", "findings": [ { "id": "function-and-purpose", "name": "Function, purpose and misuse", "description": "The function a neurotransmitter performs and the uses that fall outside it.", "questions": [ { "id": "function-and-purpose-q01", "text": "What identifies and describes the use of a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter.", "findings": [ { "id": "procedures-and-skills", "name": "Procedures, skills and required tools", "description": "What an agent needs before it can act on a neurotransmitter at all.", "questions": [ { "id": "procedures-and-skills-q01", "text": "What identifies and describes handling a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter there is and how fast it goes.", "questions": [ { "id": "consumption-and-stock-q01", "text": "What identifies and describes the supply of a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 neurotransmitter is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a neurotransmitter, 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 neurotransmitter, 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 neurotransmitter 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 } } } }