{ "model": { "rank": 16687, "code": "thing-q898362", "model_id": "vr.tr.post-translational-protein-modification", "name": "post-translational protein modification", "purpose": "Let an agent explain post-translational modifications and their main kinds, describe their roles in regulation and disease, relay databases and methods of detection, and route detailed biochemical or clinical questions to the right resources.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q898362/", "tier": 2, "score": 32, "payload": { "layer": "wikidata", "aliases": [ "palmitoylation", "protein carbamylation", "enzyme interconversion", "Side chain modification", "post-translational protein acetylation", "C-terminal protein amino acid modification", "N-terminal protein amino acid propionylation", "CAAX-box protein modification", "myristoylation", "Tyrosine sulfation", "dolichylation", "protein carbonylation" ], "aliasCount": 12, "merged": 12, "knownIn": 32, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q898362", "url": "https://www.wikidata.org/wiki/Q898362", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T21:17:39Z", "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-Q898362", "registryId": "vr.tr.post-translational-protein-modification", "name": "post-translational protein modification", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q898362/", "model": { "registry_id": "vr.tr.post-translational-protein-modification", "name": "post-translational protein modification", "purpose": "Let an agent explain post-translational modifications and their main kinds, describe their roles in regulation and disease, relay databases and methods of detection, and route detailed biochemical or clinical questions to the right resources.", "definition": "The chemical modification of a protein after it has been synthesised by the ribosome, by adding groups such as phosphate, acetyl, methyl, lipid, sugar or ubiquitin, by cleaving the chain or by forming bonds between residues; these modifications control protein activity, location, stability and interactions and are central to signalling, regulation and disease.", "what_it_is_for": "Regulating proteins after synthesis.", "affordances": [ "explain the main kinds and their effects", "describe roles in signalling and disease", "relay databases and detection methods", "route detailed questions" ], "distinguishing_features": [ "Occurs after translation", "Enzyme-mediated in most cases", "Reversible in many cases", "Regulates function and fate" ], "appearance": "Not visible; chemical changes to protein molecules detected by mass spectrometry and antibodies.", "visual_identification": [ "Covalent change to a protein after translation", "Kinds by added group or cleavage", "Co-translational and genetic changes are different processes" ], "physical_properties": [ { "quantity": "known modification types", "typical_range": "hundreds", "unit": "types", "note": "catalogued in databases" } ], "families_and_kinds": [ "phosphorylation", "acetylation and methylation", "glycosylation", "lipidation such as palmitoylation", "ubiquitination and related modifications", "proteolytic cleavage and terminal modifications", "non-enzymatic modifications such as carbamylation" ], "related_models": [ { "relation": "is a kind of", "target": "protein modification process", "why": "the category" }, { "relation": "regulates", "target": "protein", "why": "the target" }, { "relation": "is detected by", "target": "mass spectrometry", "why": "the main method" }, { "relation": "is catalysed by", "target": "enzyme", "why": "kinases, transferases and ligases" } ], "identifiers": [ { "scheme": "Gene Ontology", "value_or_pattern": "GO:0043687", "note": "post-translational protein modification" }, { "scheme": "PSI-MOD", "value_or_pattern": "per modification", "note": "ontology of protein modifications" } ], "standards_and_regulation": [ "Gene Ontology and PSI-MOD definitions", "Proteomics data standards from the HUPO Proteomics Standards Initiative" ], "failure_modes_and_hazards": [ "Misassignment of modification sites", "Confusing modifications with sequence variants", "Agents giving clinical advice" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "concept", "name": "Concept", "description": "What the modifications are.", "rationale": "Definition.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and kinds.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What are post-translational modifications, and what main kinds exist?", "kind": "definition" }, { "text": "Is the question about a modification or about a sequence variant or co-translational event?", "kind": "boundary" } ] } ] }, { "id": "enzymes", "name": "Enzymes", "description": "Writers, readers and erasers.", "findings": [ { "id": "enzymes-finding", "name": "Enzymes", "description": "Enzymes.", "questions": [ { "text": "Which enzymes add, recognise and remove modifications?", "kind": "definition" }, { "text": "Which entry fits a specific modification?", "kind": "action" } ] } ] } ] }, { "id": "function", "name": "Function", "description": "Roles.", "rationale": "Biology.", "layers": [ { "id": "regulation", "name": "Regulation", "description": "Regulation and signalling.", "findings": [ { "id": "regulation-finding", "name": "Regulation", "description": "Regulation.", "questions": [ { "text": "How do modifications control activity, localisation, stability and interactions?", "kind": "provenance" }, { "text": "Which entry fits cell signalling?", "kind": "action" } ] } ] }, { "id": "disease", "name": "Disease", "description": "Disease relevance.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "How are modifications involved in disease and drug targets, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about their own condition, which needs a clinician?", "kind": "boundary" } ] } ] } ] }, { "id": "detect", "name": "Detect", "description": "Methods and data.", "rationale": "Method.", "layers": [ { "id": "methods", "name": "Methods", "description": "Detection.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How are modifications detected and quantified?", "kind": "measurement" }, { "text": "Which entry fits proteomics?", "kind": "action" } ] } ] }, { "id": "databases", "name": "Databases", "description": "Databases.", "findings": [ { "id": "databases-finding", "name": "Databases", "description": "Databases.", "questions": [ { "text": "Which databases catalogue modifications and sites?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] } ] }, { "id": "learn", "name": "Learn", "description": "Teaching.", "rationale": "Study.", "layers": [ { "id": "teach", "name": "Teach", "description": "Teaching.", "findings": [ { "id": "teach-finding", "name": "Teach", "description": "Teaching.", "questions": [ { "text": "How are post-translational modifications taught, and which misconceptions arise?", "kind": "provenance" }, { "text": "Which entry fits protein biochemistry?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were key modifications discovered, and how did the field develop?", "kind": "provenance" }, { "text": "Which entry fits the history of biochemistry?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should each major modification be a separate entry?", "How should modification databases be linked?", "The registry entry has merged aliases naming specific modifications; 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 post-translational protein modification, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain post-translational modifications and their main kinds, describe their roles in regulation and disease, relay databases and methods of detection, and route detailed biochemical or clinical questions to the right resources.", "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: palmitoylation, protein carbamylation, enzyme interconversion, Side chain modification, post-translational protein acetylation, C-terminal protein amino acid modification, N-terminal protein amino acid propionylation, CAAX-box protein modification, myristoylation, Tyrosine sulfation, dolichylation, protein carbonylation.", "12 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 post-translational protein modification, 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": [ "palmitoylation", "protein carbamylation", "enzyme interconversion", "Side chain modification", "post-translational protein acetylation", "C-terminal protein amino acid modification", "N-terminal protein amino acid propionylation", "CAAX-box protein modification", "myristoylation", "Tyrosine sulfation", "dolichylation", "protein carbonylation" ] } ], "standing": "Described in 32 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 post-translational protein modification from another, and a post-translational protein modification 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 post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 post-translational protein modification 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 post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 post-translational protein modification from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 post-translational protein modification 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 post-translational protein modification between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 post-translational protein modification, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a post-translational protein modification 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 post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 post-translational protein modification 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 post-translational protein modification, 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 post-translational protein modification and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 post-translational protein modification consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a post-translational protein modification 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 post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 post-translational protein modification 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 post-translational protein modification 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 post-translational protein modification 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 post-translational protein modification 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 post-translational protein modification?", "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 post-translational protein modification?", "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 post-translational protein modification 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 post-translational protein modification and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 post-translational protein modification is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a post-translational protein modification, 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 post-translational protein modification, 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 post-translational protein modification 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 } } } }