{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T23:13:43Z", "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", "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T10:00:00Z", "ingestedAt": "2026-10-06T07:00:50+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-06T19:51:59+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q375795", "registryId": "vr.tr.glycoside-hydrolase-superfamily", "name": "glycoside hydrolase superfamily", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q375795/", "model": { "registry_id": "vr.tr.glycoside-hydrolase-superfamily", "name": "glycoside hydrolase superfamily", "purpose": "Let an agent explain glycoside hydrolases and their classification, identify major enzyme kinds and their substrates, relay biological roles and industrial uses, and distinguish them from other carbohydrate-active enzymes.", "definition": "A large group of enzymes that hydrolyse glycosidic bonds in carbohydrates and glycoconjugates, classified into families by sequence in the CAZy database and including amylases, cellulases, inulinases, dextranases, pectinases, alpha-glucosidases, beta-galactosidases and debranching enzymes such as amylo-alpha-1,6-glucosidase; glycoside hydrolases are essential in digestion, cell wall turnover and glycan processing, and are used industrially in food, biofuel and textile processing.", "what_it_is_for": "Breaking down carbohydrates and glycans.", "affordances": [ "explain the superfamily and classification", "identify enzyme kinds and substrates", "relay biological roles and uses", "distinguish from related enzymes" ], "distinguishing_features": [ "Glycosidic bond hydrolysis", "Sequence-based families", "Retaining and inverting mechanisms", "Wide biological and industrial roles" ], "appearance": "Not visible; enzyme structures shown as protein folds in databases.", "visual_identification": [ "Enzymes hydrolysing glycosidic bonds", "Families by sequence in CAZy", "Glycosyltransferases build bonds; lyases and esterases act differently" ], "physical_properties": [ { "quantity": "CAZy glycoside hydrolase families", "typical_range": "over 180", "unit": "count", "note": "" }, { "quantity": "EC class", "typical_range": "EC 3.2.1", "unit": "code", "note": "glycosidases" } ], "families_and_kinds": [ "amylases and glucosidases", "cellulases and hemicellulases", "inulinases and dextranases", "pectinases", "beta-galactosidases including lactase", "debranching enzymes such as amylo-alpha-1,6-glucosidase", "lysozymes and chitinases" ], "related_models": [ { "relation": "is a kind of", "target": "glycosidase", "why": "in registry terms" }, { "relation": "is a kind of", "target": "hydrolase", "why": "EC 3" }, { "relation": "is classified in", "target": "CAZy database", "why": "by family" }, { "relation": "is contrasted with", "target": "glycosyltransferase", "why": "which forms bonds" } ], "identifiers": [ { "scheme": "EC", "value_or_pattern": "3.2.1", "note": "glycosidases" }, { "scheme": "CAZy", "value_or_pattern": "GH families", "note": "sequence-based" } ], "standards_and_regulation": [ "IUBMB enzyme nomenclature", "Food enzyme regulations", "Biosafety rules for enzyme production organisms" ], "failure_modes_and_hazards": [ "Enzyme deficiencies causing disease, such as lactase deficiency and glycogen storage disease", "Allergenicity of industrial enzymes", "Confusing families and mechanisms" ], "in_scope": [], "out_of_scope": [], "characteristics": [], "agent_conduct": { "may": [ "Describe the enzyme families and their functions from biochemical databases.", "Annotate sequences into families using recognised classification." ], "must_not": [ "Fabricate activity or classification data.", "Present enzyme supplements as cures for health conditions without evidence.", "Ignore safety rules when handling enzyme powders that can cause allergy." ], "requires_human": [ "Using enzyme preparations in food or medicine for people." ] }, "ethics": { "considerations": [ "Enzyme dusts are a recognised cause of occupational asthma.", "Classification databases are shared resources; errors spread to every user." ], "affected_parties": [ "Researchers", "Workers handling enzyme products", "Consumers" ] }, "owners": { "steward": "Nobody owns the group; curators of carbohydrate enzyme databases maintain the classification.", "master_systems": [ "Carbohydrate-active enzyme databases" ] } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q375795: glycoside hydrolase superfamily", "url": "https://www.wikidata.org/wiki/Q375795", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Glycoside hydrolase", "url": "https://en.wikipedia.org/wiki/Glycoside_hydrolase", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What the superfamily is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and classification.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What are glycoside hydrolases, and how are they classified by family and mechanism?", "kind": "definition" }, { "text": "Is the enzyme a glycoside hydrolase or another carbohydrate-active enzyme?", "kind": "boundary" } ] } ] }, { "id": "kinds", "name": "Kinds", "description": "Kinds and substrates.", "findings": [ { "id": "kinds-finding", "name": "Kinds", "description": "Kinds.", "questions": [ { "text": "What major kinds exist, and which substrates does each act on?", "kind": "definition" }, { "text": "Which entry fits the specific enzyme?", "kind": "action" } ] } ] } ] }, { "id": "biology", "name": "Biology", "description": "Biological roles.", "rationale": "Science.", "layers": [ { "id": "roles", "name": "Roles", "description": "Roles.", "findings": [ { "id": "roles-finding", "name": "Roles", "description": "Roles.", "questions": [ { "text": "What roles do glycoside hydrolases play in digestion, cell walls and glycan processing?", "kind": "provenance" }, { "text": "Which entry fits carbohydrate metabolism?", "kind": "action" } ] } ] }, { "id": "disease", "name": "Disease", "description": "Deficiencies and disease.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "Which diseases arise from deficiencies, such as lactose intolerance and glycogen storage disease type III?", "kind": "provenance" }, { "text": "Is the user asking about a personal condition, which needs a clinician?", "kind": "boundary" } ] } ] } ] }, { "id": "use", "name": "Use", "description": "Industrial uses.", "rationale": "Application.", "layers": [ { "id": "industry", "name": "Industry", "description": "Industry.", "findings": [ { "id": "industry-finding", "name": "Industry", "description": "Industry.", "questions": [ { "text": "How are these enzymes used in food, brewing, biofuel, textiles and detergents?", "kind": "provenance" }, { "text": "Which entry fits industrial enzyme?", "kind": "action" } ] } ] }, { "id": "regulation", "name": "Regulation", "description": "Regulation.", "findings": [ { "id": "regulation-finding", "name": "Regulation", "description": "Regulation.", "questions": [ { "text": "How are food and industrial enzymes regulated?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] } ] }, { "id": "study", "name": "Study", "description": "Structure and research.", "rationale": "Study.", "layers": [ { "id": "mechanism", "name": "Mechanism", "description": "Mechanisms.", "findings": [ { "id": "mechanism-finding", "name": "Mechanism", "description": "Mechanism.", "questions": [ { "text": "How do retaining and inverting mechanisms work, and how are structures studied?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] }, { "id": "research", "name": "Research", "description": "Research.", "findings": [ { "id": "research-finding", "name": "Research", "description": "Research.", "questions": [ { "text": "What are current research directions, such as enzyme discovery and engineering?", "kind": "provenance" }, { "text": "Which entry fits enzyme engineering?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should each major enzyme kind be a separate entry?", "How should CAZy and EC databases be linked?", "The registry entry has merged aliases naming specific enzymes; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }