{ "model": { "rank": 15806, "code": "thing-q898365", "model_id": "vr.tr.glycosylation", "name": "glycosylation", "purpose": "Let an agent explain glycosylation and its types, relay mechanisms and biological roles from biochemistry references, describe its relevance to disease and biotechnology, and distinguish enzymatic glycosylation from non-enzymatic glycation.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q898365/", "tier": 2, "score": 33, "payload": { "layer": "wikidata", "aliases": [ "macromolecule glycosylation", "lipid glycosylation", "fucosylation", "mannosylation", "N-linked glycosylation", "O-linked glycosylation", "protein O-linked fucosylation", "N-glycan fucosylation" ], "aliasCount": 8, "merged": 8, "knownIn": 33, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q898365", "url": "https://www.wikidata.org/wiki/Q898365", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T00:46:58Z", "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-Q898365", "registryId": "vr.tr.glycosylation", "name": "glycosylation", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q898365/", "model": { "registry_id": "vr.tr.glycosylation", "name": "glycosylation", "purpose": "Let an agent explain glycosylation and its types, relay mechanisms and biological roles from biochemistry references, describe its relevance to disease and biotechnology, and distinguish enzymatic glycosylation from non-enzymatic glycation.", "definition": "The enzymatic attachment of carbohydrate groups to proteins, lipids or other molecules, chiefly N-linked glycosylation on asparagine and O-linked glycosylation on serine and threonine of proteins, with specific modifications such as fucosylation and mannosylation and lipid glycosylation forming glycolipids; glycosylation occurs in the endoplasmic reticulum and Golgi apparatus, affects protein folding, stability, recognition and immune function, is disrupted in congenital disorders of glycosylation, and is critical to biopharmaceutical production.", "what_it_is_for": "Modifying molecules with sugars for structure and function.", "affordances": [ "explain types and mechanisms", "relay biological roles", "describe disease and biotech relevance", "distinguish from glycation" ], "distinguishing_features": [ "Enzymatic", "ER and Golgi localisation", "Structural diversity", "Functional consequences" ], "appearance": "Not visible; sugar chains on proteins shown in molecular models.", "visual_identification": [ "Enzymatic addition of sugars to molecules", "N-linked, O-linked, lipid glycosylation, fucosylation, mannosylation", "Glycation is non-enzymatic; glycogenesis builds glycogen" ], "physical_properties": [ { "quantity": "human proteins glycosylated", "typical_range": "over 50", "unit": "percent", "note": "estimates" } ], "families_and_kinds": [ "N-linked glycosylation", "O-linked glycosylation including O-GlcNAc", "C-mannosylation and other rare forms", "lipid glycosylation and GPI anchors", "specific modifications such as fucosylation and sialylation", "glycosylation in bacteria and archaea" ], "related_models": [ { "relation": "is a kind of", "target": "metabolism", "why": "in registry terms" }, { "relation": "is a", "target": "post-translational modification", "why": "of proteins" }, { "relation": "occurs in", "target": "Golgi apparatus", "why": "and the endoplasmic reticulum" }, { "relation": "is contrasted with", "target": "glycation", "why": "non-enzymatic sugar attachment" } ], "identifiers": [ { "scheme": "Gene Ontology", "value_or_pattern": "GO:0070085", "note": "glycosylation" } ], "standards_and_regulation": [ "Regulatory guidance on glycosylation of biologic medicines", "Nomenclature conventions for glycans" ], "failure_modes_and_hazards": [ "Confusing glycosylation with glycation", "Congenital disorders of glycosylation", "Variability in biopharmaceutical products" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What glycosylation is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and types.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is glycosylation, and how do N-linked, O-linked and lipid glycosylation differ?", "kind": "definition" }, { "text": "Is the process glycosylation or non-enzymatic glycation?", "kind": "boundary" } ] } ] }, { "id": "mechanism", "name": "Mechanism", "description": "Mechanisms.", "findings": [ { "id": "mechanism-finding", "name": "Mechanism", "description": "Mechanism.", "questions": [ { "text": "How do glycosyltransferases build glycans in the ER and Golgi?", "kind": "definition" }, { "text": "Which entry fits the specific type?", "kind": "action" } ] } ] } ] }, { "id": "function", "name": "Function", "description": "Biological roles.", "rationale": "Science.", "layers": [ { "id": "roles", "name": "Roles", "description": "Roles.", "findings": [ { "id": "roles-finding", "name": "Roles", "description": "Roles.", "questions": [ { "text": "How does glycosylation affect folding, stability, cell recognition and immunity?", "kind": "provenance" }, { "text": "Which entry fits glycobiology?", "kind": "action" } ] } ] }, { "id": "disease", "name": "Disease", "description": "Disease.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "What are congenital disorders of glycosylation, and how does glycosylation change in cancer, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about a personal diagnosis, which needs a clinician?", "kind": "boundary" } ] } ] } ] }, { "id": "apply", "name": "Apply", "description": "Biotechnology.", "rationale": "Application.", "layers": [ { "id": "biologics", "name": "Biologics", "description": "Biologic medicines.", "findings": [ { "id": "biologics-finding", "name": "Biologics", "description": "Biologics.", "questions": [ { "text": "Why does glycosylation matter for antibodies and other biologics, and how is it controlled?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "analysis", "name": "Analysis", "description": "Analysis.", "findings": [ { "id": "analysis-finding", "name": "Analysis", "description": "Analysis.", "questions": [ { "text": "How are glycans analysed by mass spectrometry and other methods?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Evolution and history.", "rationale": "Context.", "layers": [ { "id": "evolution", "name": "Evolution", "description": "Evolution.", "findings": [ { "id": "evolution-finding", "name": "Evolution", "description": "Evolution.", "questions": [ { "text": "How does glycosylation vary across species and domains of life?", "kind": "provenance" }, { "text": "Which entry fits glycan evolution?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How was glycosylation discovered and the field of glycobiology established?", "kind": "provenance" }, { "text": "Which entry fits the history of biochemistry?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should N-linked and O-linked glycosylation be separate entries?", "How should glycobiology databases be linked?", "The registry entry has merged aliases naming specific types; 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 glycosylation, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain glycosylation and its types, relay mechanisms and biological roles from biochemistry references, describe its relevance to disease and biotechnology, and distinguish enzymatic glycosylation from non-enzymatic glycation.", "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: macromolecule glycosylation, lipid glycosylation, fucosylation, mannosylation, N-linked glycosylation, O-linked glycosylation, protein O-linked fucosylation, N-glycan fucosylation.", "8 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 33 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 glycosylation, 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": [ "macromolecule glycosylation", "lipid glycosylation", "fucosylation", "mannosylation", "N-linked glycosylation", "O-linked glycosylation", "protein O-linked fucosylation", "N-glycan fucosylation" ] } ], "standing": "Described in 33 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 8 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 glycosylation from another, and a glycosylation 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 glycosylation, 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 glycosylation, 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 glycosylation 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 glycosylation, 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 glycosylation, 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 glycosylation 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 glycosylation 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 glycosylation, 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 glycosylation, 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 glycosylation 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 glycosylation from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a glycosylation, 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 glycosylation, 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 glycosylation 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 glycosylation 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 glycosylation between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a glycosylation, 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 glycosylation, 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 glycosylation 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 glycosylation, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a glycosylation 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 glycosylation, 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 glycosylation, 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 glycosylation 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 glycosylation 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 glycosylation, 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 glycosylation and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a glycosylation, 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 glycosylation, 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 glycosylation 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 glycosylation consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a glycosylation 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 glycosylation, 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 glycosylation, 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 glycosylation 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 glycosylation 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 glycosylation 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 glycosylation 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 glycosylation 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 glycosylation?", "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 glycosylation?", "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 glycosylation 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 glycosylation and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a glycosylation, 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 glycosylation, 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 glycosylation 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 glycosylation is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a glycosylation, 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 glycosylation, 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 glycosylation 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 } } } }