{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-14T02:35:30Z",
    "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": 4,
    "engine": "claude",
    "enrichment": {
      "pass": 3,
      "engine": "claude",
      "producedAt": "2026-10-06T11:00:00Z",
      "ingestedAt": "2026-10-06T07:43:18+00:00",
      "fields": [
        "agent_conduct",
        "ethics",
        "owners"
      ]
    },
    "revisions": [
      {
        "at": "2026-10-06T22:57:18+00:00",
        "engine": "codex",
        "fields": [
          "definition",
          "failure_modes_and_hazards",
          "purpose",
          "visual_identification"
        ],
        "answering_review": "5deb5cc9dbca6b2c256afeb536519f872fce728c36ae2a2a21932eaeea2e1194"
      }
    ],
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-07T10:10:32+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "2 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q67201373",
    "registryId": "vr.tr.glycosyltransferases",
    "name": "glycosyltransferases",
    "version": "0.2.0-wave.4",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "PHY.MAT"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q67201373/",
  "model": {
    "registry_id": "vr.tr.glycosyltransferases",
    "name": "glycosyltransferases",
    "purpose": "Let an agent explain glycosyltransferases, relay their reaction, classification, biological roles and examples from biochemistry sources, describe the named enzymes and the inclusion of ADP-ribosyltransferases within the EC glycosyltransferase classification, and distinguish glycosyltransferases from glycosidases and other transferase classes.",
    "definition": "A large class of enzymes that transfer a glycosyl group from a donor, usually a nucleotide sugar, to an acceptor such as another sugar, a protein, a lipid or a small molecule, building the glycans and glycoconjugates central to biology; the registry aliases name specific glycosyltransferases such as protein O-GlcNAc transferase and protein xylosyltransferase, along with ADP-ribosyltransferases including diphtheria toxin, which transfer ADP-ribosyl groups and belong within the EC glycosyltransferase classification. Glycosyltransferases underlie blood group antigens, cell signalling and drug and vaccine glycosylation, and are studied in glycobiology.",
    "what_it_is_for": "Building glycans by transferring sugars.",
    "affordances": [
      "explain the reaction and classification",
      "relay biological roles",
      "describe named enzymes",
      "flag misfiled aliases"
    ],
    "distinguishing_features": [
      "Transfer sugars",
      "Build glycans",
      "Many families",
      "Central to glycobiology"
    ],
    "appearance": "Not visible; proteins studied as reagents and in structures.",
    "visual_identification": [
      "These enzymes transfer a glycosyl group to an acceptor.",
      "Examples include diphtheria toxin ADP-ribosyltransferase, Skp1-hydroxyproline N-acetylglucosaminyltransferase, alpha-1,4-glucan-protein synthase, dolichyl-phosphate-mannose-protein mannosyltransferase, protein O-GlcNAc transferase and protein xylosyltransferase.",
      "Glycosidases break glycosidic bonds, other transferase classes move different groups, and ADP-ribosyltransferases transfer ADP-ribosyl groups within the EC glycosyltransferase classification."
    ],
    "physical_properties": [
      {
        "quantity": "donor",
        "typical_range": "usually a nucleotide sugar",
        "unit": "note",
        "note": ""
      },
      {
        "quantity": "CAZy classification",
        "typical_range": "many GT families",
        "unit": "note",
        "note": ""
      },
      {
        "quantity": "registry parent",
        "typical_range": "transferase",
        "unit": "note",
        "note": ""
      }
    ],
    "families_and_kinds": [
      "nucleotide-sugar-dependent glycosyltransferases",
      "protein glycosyltransferases such as OGT",
      "lipid glycosyltransferases",
      "polysaccharide synthases"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "transferase",
        "why": "in registry terms"
      },
      {
        "relation": "builds",
        "target": "glycan",
        "why": ""
      },
      {
        "relation": "is contrasted with",
        "target": "glycoside hydrolase",
        "why": ""
      },
      {
        "relation": "is contrasted with",
        "target": "ADP-ribosyltransferase",
        "why": "misfiled alias"
      }
    ],
    "identifiers": [],
    "standards_and_regulation": [
      "Enzyme Commission nomenclature",
      "CAZy database classification"
    ],
    "failure_modes_and_hazards": [
      "Incorrectly excluding ADP-ribosyltransferases from the EC glycosyltransferase classification can mislead users.",
      "Glycosyltransferases can be confused with glycosidases.",
      "Glycobiology can be oversimplified."
    ],
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": [],
    "agent_conduct": {
      "may": [
        "Describe glycosyltransferase families and their roles from scientific databases.",
        "Look up enzyme classification and sequence entries in public databases."
      ],
      "must_not": [
        "Present research findings on these enzymes as approved treatments.",
        "Claim a link between an enzyme variant and a disease in a specific person.",
        "Misrepresent database entries or invent enzyme functions.",
        "Share identifiable genetic data from research participants."
      ],
      "requires_human": [
        "Using enzyme variant data in a clinical decision for a person."
      ]
    },
    "ethics": {
      "considerations": [
        "Defects in glycosylation cause rare diseases that families need honest information about.",
        "Research data can identify participants if handled carelessly."
      ],
      "affected_parties": [
        "Patients with glycosylation disorders",
        "Research participants",
        "Researchers"
      ]
    },
    "owners": {
      "steward": "Nobody owns the enzymes; curators of enzyme and carbohydrate databases keep the reference entries.",
      "master_systems": [
        "Enzyme classification and carbohydrate-active enzyme databases"
      ]
    }
  },
  "sources": [
    {
      "id": "wikidata",
      "title": "Wikidata item Q67201373: glycosyltransferases",
      "url": "https://www.wikidata.org/wiki/Q67201373",
      "url_status": "live",
      "what_it_supports": "identity and sense of the item",
      "checked_by": "wikidata-api"
    },
    {
      "id": "wikipedia-en",
      "title": "Wikipedia: Glycosyltransferase",
      "url": "https://en.wikipedia.org/wiki/Glycosyltransferase",
      "url_status": "live",
      "what_it_supports": "general description of the item",
      "checked_by": "wikidata-api sitelink"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "understand",
        "name": "Understand",
        "description": "What glycosyltransferases are.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "definition",
            "name": "Definition",
            "description": "Definition.",
            "findings": [
              {
                "id": "definition-finding",
                "name": "Definition",
                "description": "Definition.",
                "questions": [
                  {
                    "text": "What is a glycosyltransferase, and how does it differ from glycosidases, other transferases and ADP-ribosyltransferases?",
                    "kind": "definition"
                  },
                  {
                    "text": "Is the question about biochemistry, glycobiology or a specific enzyme?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          },
          {
            "id": "enzymes",
            "name": "Enzymes",
            "description": "Named enzymes.",
            "findings": [
              {
                "id": "enzymes-finding",
                "name": "Enzymes",
                "description": "Enzymes.",
                "questions": [
                  {
                    "text": "What are protein O-GlcNAc transferase and xylosyltransferase, and why are the diphtheria toxin and other ADP-ribosyltransferases different?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which entry fits the specific enzyme?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "biochemistry",
        "name": "Biochemistry",
        "description": "Reaction.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "reaction",
            "name": "Reaction",
            "description": "Sugar transfer.",
            "findings": [
              {
                "id": "reaction-finding",
                "name": "Reaction",
                "description": "Reaction.",
                "questions": [
                  {
                    "text": "How do glycosyltransferases transfer sugars from donors to acceptors?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which references are standard?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "classification",
            "name": "Classification",
            "description": "Classification.",
            "findings": [
              {
                "id": "classification-finding",
                "name": "Classification",
                "description": "Classification.",
                "questions": [
                  {
                    "text": "How are glycosyltransferases classified in CAZy families?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which sources are cited?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "biology",
        "name": "Biology",
        "description": "Roles.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "glycans",
            "name": "Glycans",
            "description": "Building glycans.",
            "findings": [
              {
                "id": "glycans-finding",
                "name": "Glycans",
                "description": "Glycans.",
                "questions": [
                  {
                    "text": "How do glycosyltransferases build glycans and glycoconjugates?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits glycosylation?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "bloodgroups",
            "name": "Blood groups",
            "description": "Blood group antigens.",
            "findings": [
              {
                "id": "bloodgroups-finding",
                "name": "Blood groups",
                "description": "Blood groups.",
                "questions": [
                  {
                    "text": "How do glycosyltransferases determine ABO blood group antigens?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Is the information accurate?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "context",
        "name": "Context",
        "description": "Applications.",
        "rationale": "Sources.",
        "layers": [
          {
            "id": "drugs",
            "name": "Drugs",
            "description": "Drug and vaccine glycosylation.",
            "findings": [
              {
                "id": "drugs-finding",
                "name": "Drugs",
                "description": "Drugs.",
                "questions": [
                  {
                    "text": "How does glycosylation affect biologic drugs and vaccines?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits biopharmaceutical?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "research",
            "name": "Research",
            "description": "Glycobiology.",
            "findings": [
              {
                "id": "research-finding",
                "name": "Research",
                "description": "Research.",
                "questions": [
                  {
                    "text": "How are glycosyltransferases studied in glycobiology?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Is the presentation neutral and attributed?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "The registry ADP-ribosyltransferase aliases should be reviewed as a different class",
    "How should CAZy families be linked?",
    "Should protein glycosyltransferases be a separate entry?"
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}