{ "model": { "rank": 16700, "code": "thing-q33123", "model_id": "vr.tr.proteolysis", "name": "proteolysis", "purpose": "Let an agent explain proteolysis and its kinds, relay enzymes, mechanisms and regulation from biochemistry references, describe roles in physiology, disease and drug design, and distinguish proteolysis from protein denaturation, degradation of other molecules and non-enzymatic hydrolysis.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q33123/", "tier": 2, "score": 32, "payload": { "layer": "wikidata", "aliases": [ "protein modification by small protein removal", "protein processing", "proteolysis involved in cellular protein catabolic process", "membrane protein proteolysis", "limited proteolysis", "self proteolysis" ], "aliasCount": 6, "merged": 6, "knownIn": 32, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": "vr.tr.proteolysis", "source": { "dataset": "wikidata", "item": "Q33123", "url": "https://www.wikidata.org/wiki/Q33123", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T05:16:08Z", "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": 3, "engine": "claude" }, "metaModel": { "id": "THING-Q33123", "registryId": "vr.tr.proteolysis", "name": "proteolysis", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q33123/", "model": { "registry_id": "vr.tr.proteolysis", "name": "proteolysis", "purpose": "Let an agent explain proteolysis and its kinds, relay enzymes, mechanisms and regulation from biochemistry references, describe roles in physiology, disease and drug design, and distinguish proteolysis from protein denaturation, degradation of other molecules and non-enzymatic hydrolysis.", "definition": "The breakdown of proteins into smaller polypeptides or amino acids by hydrolysis of peptide bonds, carried out by proteases and peptidases, occurring as digestion in the gut, as intracellular protein turnover through the proteasome and lysosomes, as limited proteolysis that activates enzymes, hormones and signalling proteins by cleaving specific sites, as removal of small protein modifiers such as ubiquitin, as membrane protein cleavage, and as self-proteolysis or autolysis; proteolysis regulates the cell cycle, apoptosis and immunity and is targeted by drugs.", "what_it_is_for": "Not applicable; a biochemical process.", "affordances": [ "explain kinds and mechanisms", "relay enzymes and regulation", "describe roles and applications", "distinguish related processes" ], "distinguishing_features": [ "Peptide bond hydrolysis", "Enzyme catalysed", "Complete or limited", "Regulatory roles" ], "appearance": "Not a visible object; peptide bond cleavage.", "visual_identification": [ "Enzymatic breakdown of proteins", "Digestive proteolysis, proteasomal and lysosomal degradation, limited proteolysis, deubiquitination, membrane protein proteolysis, autolysis", "Denaturation unfolds without cleavage; glycolysis and lipolysis break other molecules" ], "physical_properties": [ { "quantity": "protease classes", "typical_range": "serine, cysteine, aspartic, metallo, threonine, glutamic", "unit": "list", "note": "" }, { "quantity": "human proteases", "typical_range": "about 600", "unit": "count", "note": "degradome estimates" } ], "families_and_kinds": [ "digestive proteolysis by pepsin, trypsin and chymotrypsin", "intracellular protein catabolism via proteasome and lysosome", "limited proteolysis and protein processing such as zymogen activation", "removal of small protein modifiers such as ubiquitin and SUMO", "membrane protein proteolysis including regulated intramembrane proteolysis", "self-proteolysis and autolysis" ], "related_models": [ { "relation": "is a kind of", "target": "protein metabolic process", "why": "in registry terms" }, { "relation": "is catalysed by", "target": "protease", "why": "of several classes" }, { "relation": "is carried out by", "target": "proteasome", "why": "for tagged proteins" }, { "relation": "is contrasted with", "target": "protein denaturation", "why": "which does not cleave bonds" } ], "identifiers": [ { "scheme": "GO", "value_or_pattern": "GO:0006508", "note": "proteolysis" }, { "scheme": "MeSH", "value_or_pattern": "D011487", "note": "proteolysis" } ], "standards_and_regulation": [ "Gene Ontology and enzyme nomenclature", "No regulation" ], "failure_modes_and_hazards": [ "Confusing proteolysis with denaturation", "Overgeneralising digestive proteolysis to cellular regulation", "Agents giving personal medical advice on protease inhibitors" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What proteolysis is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is proteolysis, and how does it differ from denaturation and other degradation?", "kind": "definition" }, { "text": "Is the question about proteolysis in general, a specific kind or a protease?", "kind": "boundary" } ] } ] }, { "id": "kinds", "name": "Kinds", "description": "Kinds.", "findings": [ { "id": "kinds-finding", "name": "Kinds", "description": "Kinds.", "questions": [ { "text": "How do digestive, proteasomal, lysosomal, limited, deubiquitinating, membrane and self-proteolysis differ?", "kind": "definition" }, { "text": "Which entry fits the specific kind?", "kind": "action" } ] } ] } ] }, { "id": "mechanism", "name": "Mechanism", "description": "Enzymes and regulation.", "rationale": "Science.", "layers": [ { "id": "enzymes", "name": "Enzymes", "description": "Proteases.", "findings": [ { "id": "enzymes-finding", "name": "Enzymes", "description": "Enzymes.", "questions": [ { "text": "How do the protease classes cleave peptide bonds, and how is specificity determined?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "regulation", "name": "Regulation", "description": "Regulation.", "findings": [ { "id": "regulation-finding", "name": "Regulation", "description": "Regulation.", "questions": [ { "text": "How is proteolysis controlled by zymogens, inhibitors, compartments and ubiquitin tagging?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "roles", "name": "Roles", "description": "Roles.", "rationale": "Application.", "layers": [ { "id": "physiology", "name": "Physiology", "description": "Physiology.", "findings": [ { "id": "physiology-finding", "name": "Physiology", "description": "Physiology.", "questions": [ { "text": "What roles does proteolysis play in digestion, cell cycle, apoptosis, blood clotting and immunity?", "kind": "provenance" }, { "text": "Which entry fits the specific role?", "kind": "action" } ] } ] }, { "id": "medicine", "name": "Medicine", "description": "Disease and drugs.", "findings": [ { "id": "medicine-finding", "name": "Medicine", "description": "Medicine.", "questions": [ { "text": "How do proteolysis errors cause disease, and how do protease inhibitors and proteasome inhibitors work, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about their own treatment, 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 is proteolysis studied and used in proteomics and food science?", "kind": "provenance" }, { "text": "Which entry fits proteomics?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were proteases and the ubiquitin-proteasome system discovered?", "kind": "provenance" }, { "text": "Which entry fits the history of biochemistry?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should the proteasome and limited proteolysis be separate primary entries?", "How should biochemistry references be linked?", "The registry entry has merged aliases naming Gene Ontology subterms; 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": "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 proteolysis, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain proteolysis and its kinds, relay enzymes, mechanisms and regulation from biochemistry references, describe roles in physiology, disease and drug design, and distinguish proteolysis from protein denaturation, degradation of other molecules and non-enzymatic hydrolysis.", "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: protein modification by small protein removal, protein processing, proteolysis involved in cellular protein catabolic process, membrane protein proteolysis, limited proteolysis, self proteolysis.", "6 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 proteolysis, 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": [ "protein modification by small protein removal", "protein processing", "proteolysis involved in cellular protein catabolic process", "membrane protein proteolysis", "limited proteolysis", "self proteolysis" ] } ], "standing": "Described in 32 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 6 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 proteolysis from another, and a proteolysis 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 proteolysis, 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 proteolysis, 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 proteolysis 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 proteolysis, 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 proteolysis, 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 proteolysis 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 proteolysis 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 proteolysis, 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 proteolysis, 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 proteolysis 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 proteolysis from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a proteolysis, 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 proteolysis, 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 proteolysis 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 proteolysis 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 proteolysis between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a proteolysis, 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 proteolysis, 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 proteolysis 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 proteolysis, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a proteolysis 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 proteolysis, 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 proteolysis, 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 proteolysis 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 proteolysis 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 proteolysis, 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 proteolysis and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a proteolysis, 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 proteolysis, 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 proteolysis 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 proteolysis consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a proteolysis 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 proteolysis, 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 proteolysis, 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 proteolysis 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 proteolysis 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 proteolysis 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 proteolysis 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 proteolysis 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 proteolysis?", "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 proteolysis?", "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 proteolysis 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 proteolysis and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a proteolysis, 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 proteolysis, 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 proteolysis 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 proteolysis is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a proteolysis, 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 proteolysis, 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 proteolysis 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 } } } }