{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-11T05:28:49Z", "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": 1, "engine": "claude", "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-05T16:30:00Z", "ingestedAt": "2026-10-05T13:20:29+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "revisions": [ { "at": "2026-10-06T22:59:39+00:00", "engine": "codex", "fields": [ "definition", "distinguishing_features" ], "answering_review": "253c40ee673b98e2a78981d519114e1cae8509dee31d561aa89d43966252c018" } ], "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-Q8054", "registryId": "vr.tr.protein", "name": "protein", "version": "0.2.0-wave.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q8054/", "model": { "registry_id": "vr.tr.protein", "name": "protein", "purpose": "Let an agent handle proteins by identity, sequence, structure, function and organism, using standard identifiers, and nutrition as a separate sense.", "definition": "A biomolecule or biomolecule complex largely consisting of one or more chains of amino acid residues, with folded regions, intrinsically disordered regions or both, carrying out functions such as catalysis, structure, transport and signalling.", "what_it_is_for": "Proteins do most of the work in cells; in diets, protein supplies amino acids.", "affordances": [ "identify it, by sequence and accession", "determine its structure", "study its function", "produce it, recombinantly, under biosafety rules" ], "distinguishing_features": [ "Proteins consist largely of amino acid chains that may be folded, intrinsically disordered or both.", "Function depends on sequence, structure and molecular dynamics.", "Proteins are encoded by genes.", "Dietary protein is a nutrition concept." ], "appearance": "Invisible to the eye; shown as structure models, sequences or bands on gels.", "visual_identification": [ "UniProt accession and gene name", "PDB structures", "Dietary protein on labels is a nutrient, not a specific protein" ], "physical_properties": [ { "quantity": "length", "typical_range": "50-35000", "unit": "amino acids", "note": "titin is the largest" }, { "quantity": "mass", "typical_range": "5-3800", "unit": "kDa", "note": "" } ], "families_and_kinds": [ "enzymes", "structural proteins", "transport proteins", "signalling proteins and receptors", "antibodies" ], "related_models": [ { "relation": "is made of", "target": "amino acids", "why": "monomers" }, { "relation": "is encoded by", "target": "gene", "why": "DNA" }, { "relation": "works in", "target": "cell", "why": "context" }, { "relation": "is a nutrient in", "target": "food", "why": "dietary protein" } ], "identifiers": [ { "scheme": "UniProt accession", "value_or_pattern": "for example P69905", "note": "protein sequence and function" }, { "scheme": "PDB id", "value_or_pattern": "four characters", "note": "structures" } ], "standards_and_regulation": [ "Biosafety rules for recombinant proteins", "Medicines regulation for protein therapeutics", "Food labelling rules on protein content" ], "failure_modes_and_hazards": [ "Allergenic proteins in food", "Misfolding diseases", "Confusing orthologs across species" ], "in_scope": [], "out_of_scope": [], "characteristics": [], "agent_conduct": { "may": [ "Describe proteins' structure and function from cited databases and literature.", "Report dietary protein content from food composition data." ], "must_not": [ "Assist in designing or producing proteins intended to harm people, such as toxins.", "Present predicted structures as experimentally confirmed.", "Give personal dietary or supplement advice to a person with a medical condition.", "Misattribute data from shared databases." ], "requires_human": [ "Releasing designs or data for proteins with possible dual use." ] }, "ethics": { "considerations": [ "Protein science serves medicine but some proteins are toxins with misuse potential.", "Shared databases rely on honest attribution and accuracy." ], "affected_parties": [ "Patients", "Researchers", "The public" ] }, "owners": { "steward": "Nobody owns proteins in nature; protein data banks curate shared records.", "master_systems": [ "Protein sequence and structure databases" ] } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q8054: protein", "url": "https://www.wikidata.org/wiki/Q8054", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Protein", "url": "https://en.wikipedia.org/wiki/Protein", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "identity", "name": "Identity", "description": "Which protein.", "rationale": "Accessions prevent confusion.", "layers": [ { "id": "accession", "name": "Accession", "description": "UniProt and gene.", "findings": [ { "id": "accession-finding", "name": "Accession", "description": "Identifiers.", "questions": [ { "text": "What is its UniProt accession and gene name?", "kind": "provenance" }, { "text": "Which organism?", "kind": "definition" } ] } ] }, { "id": "sequence", "name": "Sequence", "description": "Amino acid sequence.", "findings": [ { "id": "sequence-finding", "name": "Sequence", "description": "The sequence.", "questions": [ { "text": "What is its sequence and length?", "kind": "measurement" }, { "text": "Which isoform?", "kind": "boundary" } ] } ] } ] }, { "id": "structure", "name": "Structure", "description": "Shape.", "rationale": "Structure explains function.", "layers": [ { "id": "experimental", "name": "Experimental", "description": "PDB.", "findings": [ { "id": "experimental-finding", "name": "Structure", "description": "Experimental structures.", "questions": [ { "text": "Is there an experimental structure, at what resolution?", "kind": "provenance" }, { "text": "Which method?", "kind": "provenance" } ] } ] }, { "id": "predicted", "name": "Predicted", "description": "Models.", "findings": [ { "id": "predicted-finding", "name": "Prediction", "description": "Predicted models.", "questions": [ { "text": "Is a predicted model available, and how confident is it?", "kind": "measurement" }, { "text": "Where might it be wrong?", "kind": "boundary" } ] } ] } ] }, { "id": "function", "name": "Function", "description": "What it does.", "rationale": "Function is what matters in biology and medicine.", "layers": [ { "id": "role", "name": "Role", "description": "Molecular function.", "findings": [ { "id": "role-finding", "name": "Function", "description": "Molecular and biological role.", "questions": [ { "text": "What does the protein do?", "kind": "definition" }, { "text": "How is that known?", "kind": "provenance" } ] } ] }, { "id": "disease", "name": "Disease", "description": "Links to disease.", "findings": [ { "id": "disease-finding", "name": "Disease links", "description": "Disease associations.", "questions": [ { "text": "Is it linked to disease?", "kind": "provenance" }, { "text": "Is it a drug target?", "kind": "provenance" } ] } ] } ] }, { "id": "use", "name": "Use", "description": "Production and diet.", "rationale": "Proteins are made and eaten.", "layers": [ { "id": "production", "name": "Production", "description": "Recombinant.", "findings": [ { "id": "production-finding", "name": "Production", "description": "How it is produced.", "questions": [ { "text": "How is it produced for use?", "kind": "definition" }, { "text": "Which rules apply?", "kind": "provenance" } ] } ] }, { "id": "diet", "name": "Diet", "description": "Nutrition and allergy.", "findings": [ { "id": "diet-finding", "name": "Nutrition", "description": "Dietary aspects.", "questions": [ { "text": "Is it a food allergen?", "kind": "boundary" }, { "text": "How much dietary protein is recommended, by whom?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Should proteins be instances with UniProt accessions?", "How should dietary and biochemical senses be separated?", "How should predicted structures be marked?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }