{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T01:04:35Z", "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": "2026-10-06T07:01:18+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "revisions": [ { "at": "2026-10-06T22:51:51+00:00", "engine": "codex", "fields": [ "definition" ], "answering_review": "248312dafe4ac41a1e4fcd8be3a7a2b423f1dbaa2588defe253b395ef6c9a8c6" }, { "at": "2026-10-07T11:32:14+00:00", "engine": "codex", "fields": [ "definition" ], "answering_review": "932a69a3b333e3475897d37e159b26eff51875cbaa6acf857e9e15a9fddb3078" } ], "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T12:16:32+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q42244", "registryId": "vr.tr.ribosome", "name": "ribosome", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.LIV" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q42244/", "model": { "registry_id": "vr.tr.ribosome", "name": "ribosome", "purpose": "Let an agent explain ribosomes and their structure and function, relay their diversity across cell types and organelles, describe their role as antibiotic targets and in disease, and distinguish ribosomes from other RNA-protein complexes.", "definition": "A large complex of ribosomal RNA and proteins found across all domains of life, but absent from some specialised living cells such as mature mammalian red blood cells, that synthesises proteins by translating messenger RNA, composed of a small and a large subunit, typically 70S in bacteria, archaea and chloroplasts and 80S in the eukaryotic cytosol, with mitochondrial ribosomes varying among organisms and being 55S in mammals, occurring free in the cytoplasm, bound to the endoplasmic reticulum membrane or in polysomes translating one mRNA; ribosomes are the target of many antibiotics and their structure was resolved at atomic level in work recognised by the 2009 Nobel Prize in Chemistry.", "what_it_is_for": "Synthesising proteins.", "affordances": [ "explain structure and function", "relay diversity and localisation", "describe antibiotic targeting and disease", "distinguish from related complexes" ], "distinguishing_features": [ "Ribozyme catalysis", "Two subunits", "Universal across life", "Antibiotic target" ], "appearance": "Not visible; dense particles about 20 to 30 nanometres across in electron micrographs.", "visual_identification": [ "RNA-protein machine for translation", "70S and 80S, free, membrane-bound, organellar, polysomal", "Spliceosomes process RNA; proteasomes degrade proteins" ], "physical_properties": [ { "quantity": "eukaryotic ribosome mass", "typical_range": "about 4.3", "unit": "MDa", "note": "" }, { "quantity": "ribosomes per bacterial cell", "typical_range": "about 10000-70000", "unit": "count", "note": "growth dependent" }, { "quantity": "elongation rate", "typical_range": "about 15-20", "unit": "amino acids per second", "note": "bacteria" } ], "families_and_kinds": [ "bacterial and archaeal 70S ribosomes", "eukaryotic cytosolic 80S ribosomes", "mitochondrial and chloroplast ribosomes", "free and membrane-bound ribosomes", "polysomes", "specialised and heterogeneous ribosomes" ], "related_models": [ { "relation": "is a kind of", "target": "intracellular non-membrane-bounded organelle", "why": "in registry terms" }, { "relation": "is a kind of", "target": "nonmembranous cytoplasmic organelle", "why": "in registry terms" }, { "relation": "performs", "target": "translation", "why": "of mRNA into protein" }, { "relation": "is targeted by", "target": "antibiotic", "why": "such as macrolides and aminoglycosides" } ], "identifiers": [ { "scheme": "Gene Ontology", "value_or_pattern": "GO:0005840", "note": "ribosome" } ], "standards_and_regulation": [ "No regulation of the organelle; research and antibiotic regulation apply" ], "failure_modes_and_hazards": [ "Ribosomopathies from ribosomal protein defects", "Antibiotic resistance through ribosomal mutations", "Confusing ribosome types" ], "in_scope": [], "out_of_scope": [], "characteristics": [], "agent_conduct": { "may": [ "Explain ribosome structure and translation from biochemical sources.", "Analyse ribosome profiling or structural data a user is authorized to work with." ], "must_not": [ "Present laboratory findings on ribosomes as medical advice.", "Advise on using ribosome-targeting antibiotics for a person's infection.", "Encourage antibiotic use that drives resistance, such as without diagnosis or course completion.", "Fabricate structural or sequencing data." ], "requires_human": [ "Any clinical decision involving antibiotics that act on ribosomes." ] }, "ethics": { "considerations": [ "Antibiotic resistance is a shared risk; careless advice costs lives.", "Research integrity matters because structural claims guide drug development." ], "affected_parties": [ "Patients on antibiotics", "Researchers", "The public exposed to resistant infections" ] }, "owners": { "steward": "Nobody owns a cell component.", "master_systems": [] } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q42244: ribosome", "url": "https://www.wikidata.org/wiki/Q42244", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Ribosome", "url": "https://en.wikipedia.org/wiki/Ribosome", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What ribosomes are.", "rationale": "Science.", "layers": [ { "id": "structure", "name": "Structure", "description": "Structure.", "findings": [ { "id": "structure-finding", "name": "Structure", "description": "Structure.", "questions": [ { "text": "How are ribosomes built from rRNA and proteins, and how do subunits differ across domains of life?", "kind": "definition" }, { "text": "Is the complex a ribosome or another RNA-protein machine?", "kind": "boundary" } ] } ] }, { "id": "function", "name": "Function", "description": "Translation.", "findings": [ { "id": "function-finding", "name": "Function", "description": "Function.", "questions": [ { "text": "How do ribosomes translate mRNA through initiation, elongation and termination?", "kind": "definition" }, { "text": "Which entry fits translation?", "kind": "action" } ] } ] } ] }, { "id": "diversity", "name": "Diversity", "description": "Kinds and locations.", "rationale": "Science.", "layers": [ { "id": "locations", "name": "Locations", "description": "Free, bound and organellar.", "findings": [ { "id": "locations-finding", "name": "Locations", "description": "Locations.", "questions": [ { "text": "How do free, membrane-bound, polysomal and organellar ribosomes differ in role?", "kind": "provenance" }, { "text": "Which entry fits the specific kind?", "kind": "action" } ] } ] }, { "id": "biogenesis", "name": "Biogenesis", "description": "Biogenesis.", "findings": [ { "id": "biogenesis-finding", "name": "Biogenesis", "description": "Biogenesis.", "questions": [ { "text": "How are ribosomes assembled in the nucleolus and cytoplasm?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] } ] }, { "id": "medicine", "name": "Medicine", "description": "Antibiotics and disease.", "rationale": "Clinical.", "layers": [ { "id": "antibiotics", "name": "Antibiotics", "description": "Antibiotic targets.", "findings": [ { "id": "antibiotics-finding", "name": "Antibiotics", "description": "Antibiotics.", "questions": [ { "text": "Which antibiotics act on ribosomes, and how does resistance arise, in general terms?", "kind": "provenance" }, { "text": "Which entry fits antibiotic resistance?", "kind": "action" } ] } ] }, { "id": "disease", "name": "Disease", "description": "Ribosomopathies.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "What diseases arise from ribosome defects, in general terms?", "kind": "provenance" }, { "text": "Is the user asking about a personal diagnosis, which needs a clinician?", "kind": "boundary" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "History and methods.", "rationale": "Context.", "layers": [ { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were ribosomes discovered and their structures solved, including the 2009 Nobel work?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] }, { "id": "methods", "name": "Methods", "description": "Methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How are ribosomes studied by cryo-electron microscopy, crystallography and profiling?", "kind": "provenance" }, { "text": "Which entry fits ribosome profiling?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should mitochondrial ribosome be a separate entry?", "How should structural databases be linked?", "The registry entry has merged aliases naming localisations and types; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }