{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T01:37:50Z", "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": "2026-10-06T07:03:10+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-06T19:51:54+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q14886350", "registryId": "vr.tr.rna-modification", "name": "RNA modification", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q14886350/", "model": { "registry_id": "vr.tr.rna-modification", "name": "RNA modification", "purpose": "Let an agent explain RNA modification and its kinds, relay mechanisms, functions and methods from molecular biology references, describe its relevance to vaccines and disease with attribution, and distinguish modification from RNA processing and DNA modification.", "definition": "The chemical alteration of RNA molecules after transcription, including over 170 known modifications such as methylation of adenosine and cytosine, pseudouridine synthesis, editing that converts bases as in adenosine-to-inosine editing, capping and the extensive modification of transfer and ribosomal RNA, together with mRNA modifications that regulate stability and translation; RNA modification is studied as epitranscriptomics, underlies the design of mRNA vaccines, and is implicated in development and disease.", "what_it_is_for": "Regulating RNA function.", "affordances": [ "explain kinds and mechanisms", "relay functions and methods", "describe medical relevance", "distinguish from related processes" ], "distinguishing_features": [ "Diverse chemistry", "Writers, readers and erasers", "Regulation of stability and translation", "Vaccine relevance" ], "appearance": "Not visible; chemical marks on RNA detected by sequencing and mass spectrometry.", "visual_identification": [ "Post-transcriptional chemical changes to RNA", "Methylation, pseudouridine, editing, tRNA and mRNA modifications", "Splicing and capping are processing steps; DNA methylation is epigenetics; RNA timestamps are a labelling technique" ], "physical_properties": [ { "quantity": "known modifications", "typical_range": "over 170", "unit": "count", "note": "MODOMICS database" } ], "families_and_kinds": [ "RNA methylation such as m6A and m5C", "pseudouridine synthesis", "RNA editing by base conversion", "tRNA modifications", "rRNA modifications", "mRNA modifications including the cap", "techniques such as RNA timestamps as related methods" ], "related_models": [ { "relation": "is a kind of", "target": "RNA metabolic process", "why": "in registry terms" }, { "relation": "is a kind of", "target": "macromolecule modification", "why": "in registry terms" }, { "relation": "is studied by", "target": "epitranscriptomics", "why": "the field" }, { "relation": "is used in", "target": "mRNA vaccine", "why": "through modified nucleosides" } ], "identifiers": [ { "scheme": "Gene Ontology", "value_or_pattern": "GO:0009451", "note": "RNA modification" }, { "scheme": "MODOMICS", "value_or_pattern": "database", "note": "" } ], "standards_and_regulation": [ "No regulation of the process; drug and vaccine regulation for modified RNA therapeutics" ], "failure_modes_and_hazards": [ "Overstating disease links", "Confusing modification with processing", "Detection artefacts in methods" ], "in_scope": [], "out_of_scope": [], "characteristics": [], "agent_conduct": { "may": [ "Describe known RNA modifications and the methods used to map them, from scientific literature.", "Analyze sequencing data for modification signals in projects it is authorized to support." ], "must_not": [ "Present a predicted modification site as experimentally confirmed.", "Assist in designing agents meant to harm people, animals or crops.", "Use human sequencing data beyond the consent given by the donors.", "Overstate therapeutic claims about modified RNA to patients or investors." ], "requires_human": [ "Sharing or reusing human genomic and transcriptomic datasets.", "Any clinical application decision." ] }, "ethics": { "considerations": [ "Human sequence data is personal and can identify donors and relatives.", "Hype about RNA therapies can mislead patients and investors." ], "affected_parties": [ "Research participants and their relatives", "Patients", "Researchers" ] }, "owners": { "steward": "The research institution for its data; donors retain rights over their samples.", "master_systems": [ "Sequence and modification databases", "Research ethics approval records" ] } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q14886350: RNA modification", "url": "https://www.wikidata.org/wiki/Q14886350", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: RNA editing", "url": "https://en.wikipedia.org/wiki/RNA_editing", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What RNA modification is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and kinds.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is RNA modification, and what kinds exist?", "kind": "definition" }, { "text": "Is the process modification, processing or DNA epigenetics?", "kind": "boundary" } ] } ] }, { "id": "machinery", "name": "Machinery", "description": "Writers, readers, erasers.", "findings": [ { "id": "machinery-finding", "name": "Machinery", "description": "Machinery.", "questions": [ { "text": "How do enzymes add, read and remove modifications?", "kind": "definition" }, { "text": "Which entry fits the specific modification?", "kind": "action" } ] } ] } ] }, { "id": "function", "name": "Function", "description": "Functions.", "rationale": "Science.", "layers": [ { "id": "regulation", "name": "Regulation", "description": "Regulation of RNA.", "findings": [ { "id": "regulation-finding", "name": "Regulation", "description": "Regulation.", "questions": [ { "text": "How do modifications regulate stability, translation, splicing and localisation, as research shows?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] }, { "id": "trna", "name": "tRNA", "description": "tRNA and rRNA.", "findings": [ { "id": "trna-finding", "name": "tRNA", "description": "tRNA.", "questions": [ { "text": "Why are tRNA and rRNA so heavily modified?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] } ] }, { "id": "medicine", "name": "Medicine", "description": "Medical relevance.", "rationale": "Attribution.", "layers": [ { "id": "vaccines", "name": "Vaccines", "description": "mRNA vaccines and therapeutics.", "findings": [ { "id": "vaccines-finding", "name": "Vaccines", "description": "Vaccines.", "questions": [ { "text": "How did modified nucleosides enable mRNA vaccines, as recognised by the 2023 Nobel Prize?", "kind": "provenance" }, { "text": "Which entry fits mRNA vaccine?", "kind": "action" } ] } ] }, { "id": "disease", "name": "Disease", "description": "Disease.", "findings": [ { "id": "disease-finding", "name": "Disease", "description": "Disease.", "questions": [ { "text": "What roles do RNA modifications play in cancer and other diseases, with findings attributed?", "kind": "provenance" }, { "text": "Is the user asking about a personal condition, which needs a clinician?", "kind": "boundary" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Methods and history.", "rationale": "Context.", "layers": [ { "id": "methods", "name": "Methods", "description": "Methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How are modifications detected by sequencing, mass spectrometry and nanopore methods?", "kind": "provenance" }, { "text": "Which entry fits epitranscriptomic sequencing?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How did the field develop from early tRNA studies to epitranscriptomics?", "kind": "provenance" }, { "text": "Which entry fits the history of molecular biology?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should m6A and RNA editing be separate entries?", "How should databases be linked?", "The registry entry has merged aliases naming specific modifications and a technique; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }