{ "model": { "rank": 16598, "code": "thing-q68685", "model_id": "vr.tr.metabolic-pathway", "name": "metabolic pathway", "purpose": "Let an agent explain metabolic pathways and their regulation, support learning and research with pathway databases, and relate pathway defects to health at a general level.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q68685/", "tier": 2, "score": 32, "payload": { "layer": "wikidata", "aliases": [ "De novo lipogenesis", "photorespiratory bypass", "ATP-ADP-AMP cycle", "metabolic network", "Mitochondrial shuttle", "biosynthetic pathway", "MAP kinase signaling system", "lipolysis", "ubiquitin-proteasome system", "lipid mobilization" ], "aliasCount": 10, "merged": 10, "knownIn": 32, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q68685", "url": "https://www.wikidata.org/wiki/Q68685", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T19:25:36Z", "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": 2, "engine": "claude" }, "metaModel": { "id": "THING-Q68685", "registryId": "vr.tr.metabolic-pathway", "name": "metabolic pathway", "version": "0.2.0-wave.2", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q68685/", "model": { "registry_id": "vr.tr.metabolic-pathway", "name": "metabolic pathway", "purpose": "Let an agent explain metabolic pathways and their regulation, support learning and research with pathway databases, and relate pathway defects to health at a general level.", "definition": "A linked series of chemical reactions in a cell, catalysed by enzymes, that converts substrates into products, such as glycolysis, the citric acid cycle, fatty acid synthesis and photosynthetic pathways, organised into catabolic and anabolic routes and interconnected into metabolic networks; pathways are regulated and their defects cause metabolic diseases.", "what_it_is_for": "Cellular energy, biosynthesis and biochemistry.", "affordances": [ "explain a pathway and its steps", "describe regulation and integration", "find pathway databases", "relate pathway defects to diseases in general terms" ], "distinguishing_features": [ "Enzyme-catalysed steps", "Catabolic or anabolic", "Regulated", "Networked" ], "appearance": "Not visible; drawn as pathway maps.", "visual_identification": [ "Sequences of enzyme-catalysed reactions", "Maps with substrates and products", "Signalling pathways transmit information rather than mass" ], "physical_properties": [], "families_and_kinds": [ "central carbon pathways such as glycolysis and the citric acid cycle", "lipid pathways such as de novo lipogenesis", "amino acid and nucleotide pathways", "photosynthetic and photorespiratory pathways", "shuttles and cycles such as mitochondrial shuttles" ], "related_models": [ { "relation": "is a kind of", "target": "biological pathway", "why": "category" }, { "relation": "is a kind of", "target": "chemical reaction", "why": "category" }, { "relation": "uses", "target": "hydrolysis", "why": "reaction type" }, { "relation": "is related to", "target": "cellular transport", "why": "metabolite transport" } ], "identifiers": [ { "scheme": "KEGG pathway ID", "value_or_pattern": "map number", "note": "database" } ], "standards_and_regulation": [ "Pathway databases such as KEGG, Reactome and MetaCyc", "Gene Ontology biological process terms" ], "failure_modes_and_hazards": [ "Oversimplified pathway diagrams", "Agents giving medical advice on metabolic disease", "Confusing metabolic and signalling pathways" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "steps", "name": "Steps", "description": "Pathway structure.", "rationale": "Steps and enzymes.", "layers": [ { "id": "sequence", "name": "Sequence", "description": "Reactions.", "findings": [ { "id": "sequence-finding", "name": "Sequence", "description": "Reactions.", "questions": [ { "text": "What are the steps, enzymes and intermediates of this pathway?", "kind": "definition" }, { "text": "Where in the cell does it occur?", "kind": "definition" } ] } ] }, { "id": "energy", "name": "Energy", "description": "Energy balance.", "findings": [ { "id": "energy-finding", "name": "Energy", "description": "Energy balance.", "questions": [ { "text": "What is the ATP and cofactor yield or cost of the pathway?", "kind": "measurement" }, { "text": "Which steps are irreversible?", "kind": "definition" } ] } ] } ] }, { "id": "regulation", "name": "Regulation", "description": "Control.", "rationale": "Pathways are controlled.", "layers": [ { "id": "control", "name": "Control", "description": "Regulatory points.", "findings": [ { "id": "control-finding", "name": "Control", "description": "Regulation.", "questions": [ { "text": "Which enzymes are regulatory, and how are they controlled?", "kind": "provenance" }, { "text": "How do hormones affect the pathway?", "kind": "provenance" } ] } ] }, { "id": "network", "name": "Network", "description": "Integration.", "findings": [ { "id": "network-finding", "name": "Network", "description": "Integration.", "questions": [ { "text": "How does this pathway connect to others in the metabolic network?", "kind": "definition" }, { "text": "How are shuttles and cycles used to link compartments?", "kind": "definition" } ] } ] } ] }, { "id": "health", "name": "Health", "description": "Disease links.", "rationale": "General information.", "layers": [ { "id": "defects", "name": "Defects", "description": "Inborn errors.", "findings": [ { "id": "defects-finding", "name": "Defects", "description": "Defects.", "questions": [ { "text": "Which diseases result from defects in this pathway, according to medical genetics sources?", "kind": "provenance" }, { "text": "Is the user asking about their own condition?", "kind": "boundary" } ] } ] }, { "id": "drugs", "name": "Drugs", "description": "Pathway targets.", "findings": [ { "id": "drugs-finding", "name": "Drugs", "description": "Drug targets.", "questions": [ { "text": "Which drugs target enzymes in this pathway, in general terms?", "kind": "provenance" }, { "text": "What research is under way?", "kind": "provenance" } ] } ] } ] }, { "id": "learn", "name": "Learn", "description": "Study.", "rationale": "Resources exist.", "layers": [ { "id": "databases", "name": "Databases", "description": "Pathway resources.", "findings": [ { "id": "databases-finding", "name": "Databases", "description": "Databases.", "questions": [ { "text": "Which databases map this pathway, and how can they be used?", "kind": "provenance" }, { "text": "Which identifiers apply?", "kind": "provenance" } ] } ] }, { "id": "teach", "name": "Teach", "description": "Teaching.", "findings": [ { "id": "teach-finding", "name": "Teach", "description": "Teaching.", "questions": [ { "text": "How can this pathway be taught without rote memorisation?", "kind": "action" }, { "text": "Which misconceptions arise?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should each pathway be a separate entry?", "How should databases be linked?", "How should disease links be handled?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "abstract concept", "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 metabolic pathway, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain metabolic pathways and their regulation, support learning and research with pathway databases, and relate pathway defects to health at a general level.", "characteristics": { "substance": "activity", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: De novo lipogenesis, photorespiratory bypass, ATP-ADP-AMP cycle, metabolic network, Mitochondrial shuttle, biosynthetic pathway, MAP kinase signaling system, lipolysis, ubiquitin-proteasome system, lipid mobilization.", "10 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 32 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a metabolic pathway, and on what evidence are they told apart?" ], "whatItIsMadeOf": "something that happens over time", "physicalCharacter": [ "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" ], "howItIsRecognised": [ "Nothing to see. What is recognised is an instance of it, and which instances count is exactly what is argued about." ], "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": [ "De novo lipogenesis", "photorespiratory bypass", "ATP-ADP-AMP cycle", "metabolic network", "Mitochondrial shuttle", "biosynthetic pathway", "MAP kinase signaling system", "lipolysis", "ubiquitin-proteasome system", "lipid mobilization" ] } ], "standing": "Described in 32 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 10 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 metabolic pathway from another, and a metabolic pathway 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 metabolic pathway, 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 metabolic pathway, 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 metabolic pathway 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 metabolic pathway, 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 metabolic pathway, 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 metabolic pathway 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 metabolic pathway 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 metabolic pathway, 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 metabolic pathway, 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 metabolic pathway 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 metabolic pathway from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a metabolic pathway, 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 metabolic pathway, 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 metabolic pathway 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 metabolic pathway 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 metabolic pathway between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a metabolic pathway, 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 metabolic pathway, 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 metabolic pathway 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 metabolic pathway, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a metabolic pathway 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 metabolic pathway, 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 metabolic pathway, 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 metabolic pathway is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "process-and-outcome", "name": "Process, inputs and outcome", "description": "How a metabolic pathway proceeds, what it needs and what it leaves behind.", "rationale": "An activity is known by its steps and its results, and both have to be recordable while it is still running.", "layers": [ { "id": "steps-and-sequence", "name": "Steps and sequence", "description": "The steps of a metabolic pathway, their order and what may run in parallel.", "findings": [ { "id": "steps-and-preconditions", "name": "Steps, preconditions and completion", "description": "What has to be true before each step of a metabolic pathway and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a metabolic pathway, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "steps-and-preconditions-q02", "text": "Who or what asserted this about a step of a metabolic pathway, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "steps-and-preconditions-q03", "text": "What may an agent decide or do once a step of a metabolic pathway is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "inputs-and-results", "name": "Inputs, resources and results", "description": "What a metabolic pathway consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a metabolic pathway takes and the results it leaves, wanted or not.", "questions": [ { "id": "inputs-and-outputs-q01", "text": "What identifies and describes the inputs and results of a metabolic pathway, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "inputs-and-outputs-q02", "text": "Who or what asserted this about the inputs and results of a metabolic pathway, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "inputs-and-outputs-q03", "text": "What may an agent decide or do once the inputs and results of a metabolic pathway is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "definitions-in-contest", "name": "Definitions and who holds them", "description": "What metabolic pathway is taken to mean, and by whom.", "rationale": "When a field disagrees about a concept, the disagreement is the content. A model that picks one definition silently destroys the information.", "layers": [ { "id": "competing-definitions", "name": "Competing definitions", "description": "The main readings and the traditions behind them.", "findings": [ { "id": "definition-map", "name": "Definitions and their holders", "description": "Each definition with the school or body that holds it.", "questions": [ { "id": "definition-map-q01", "text": "Which definitions of metabolic pathway are in use, and which tradition or body holds each?", "kind": "definition" }, { "id": "definition-map-q02", "text": "What turns on the difference between them in practice?", "kind": "boundary" } ] } ] }, { "id": "operationalisation", "name": "Operationalisation", "description": "How it is measured or applied when it has to be.", "findings": [ { "id": "operational-record", "name": "Measures and proxies", "description": "Instruments and indicators used to stand in for it.", "questions": [ { "id": "operational-record-q01", "text": "How is metabolic pathway operationalised or measured in practice, and by what instrument?", "kind": "measurement" }, { "id": "operational-record-q02", "text": "What does that operationalisation leave out, and when does that matter?", "kind": "boundary" } ] } ] } ] }, { "id": "instances-and-use", "name": "Instances, use and consequence", "description": "What counts as an instance of metabolic pathway and what follows from calling something that.", "rationale": "Applying a concept is an act with consequences, so a model must say what the label licenses and what it does not.", "layers": [ { "id": "instances", "name": "What counts as an instance", "description": "Clear cases, borderline cases and non-cases.", "findings": [ { "id": "instance-tests", "name": "Tests for an instance", "description": "What would settle whether something falls under it.", "questions": [ { "id": "instance-tests-q01", "text": "What would settle whether something is an instance of metabolic pathway?", "kind": "boundary" }, { "id": "instance-tests-q02", "text": "Which borderline cases are argued about, and on what grounds?", "kind": "definition" } ] } ] }, { "id": "consequence", "name": "Consequence of application", "description": "Rights, duties or decisions that follow from the label.", "findings": [ { "id": "consequence-record", "name": "What the label licenses", "description": "What an agent may do once something is classified this way.", "questions": [ { "id": "consequence-record-q01", "text": "What follows practically once something is treated as metabolic pathway?", "kind": "action" }, { "id": "consequence-record-q02", "text": "What must an agent not infer from the label alone?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a metabolic pathway 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 metabolic pathway and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a metabolic pathway, 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 metabolic pathway, 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 metabolic pathway 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 metabolic pathway is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a metabolic pathway, 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 metabolic pathway, 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 metabolic pathway is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 6, "layers": 12, "findings": 14, "questions": 38 } } } }