{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-13T22:29:47Z",
    "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": "2026-10-06T07:42:37+00:00",
      "fields": [
        "agent_conduct",
        "ethics",
        "owners"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q417379",
    "registryId": "vr.tr.post-transcriptional-modification",
    "name": "post-transcriptional modification",
    "version": "0.2.0-wave.4",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "ACT.PRC"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q417379/",
  "model": {
    "registry_id": "vr.tr.post-transcriptional-modification",
    "name": "post-transcriptional modification",
    "purpose": "Let an agent explain post-transcriptional modification, relay capping, splicing, polyadenylation, editing and tRNA and rRNA processing from molecular biology sources, describe disease links and therapies that target splicing, flag the misfiled protein alias, and distinguish post-transcriptional from transcriptional and post-translational modification and from epigenetic DNA modification.",
    "definition": "The set of chemical changes made to a primary RNA transcript after transcription to produce mature functional RNA, including in eukaryotic messenger RNA the addition of a 5 prime cap, splicing to remove introns, including alternative splicing that yields multiple proteins from one gene, 3 prime cleavage and polyadenylation, and RNA editing such as adenosine-to-inosine editing, as well as processing and nucleotide modifications of transfer and ribosomal RNA; the registry alias arginylation names the addition of arginine to proteins, a post-translational modification, and appears misfiled. Errors in processing, such as splicing mutations, cause diseases including spinal muscular atrophy.",
    "what_it_is_for": "Producing mature functional RNA.",
    "affordances": [
      "explain processing steps",
      "relay splicing and editing",
      "describe disease links",
      "flag misfiled aliases"
    ],
    "distinguishing_features": [
      "Acts on RNA",
      "Nuclear processing in eukaryotes",
      "Alternative splicing diversity",
      "Therapeutic target"
    ],
    "appearance": "Not visible; studied through sequencing and biochemical methods.",
    "visual_identification": [
      "RNA processing after transcription",
      "Arginylation, RNA processing, mRNA maturation",
      "Transcriptional regulation controls RNA synthesis; post-translational modification changes proteins; epigenetic marks modify DNA or histones"
    ],
    "physical_properties": [
      {
        "quantity": "split genes discovered",
        "typical_range": "1977",
        "unit": "year",
        "note": "Nobel Prize 1993 to Roberts and Sharp"
      },
      {
        "quantity": "poly(A) tail length",
        "typical_range": "about 50-250",
        "unit": "nucleotides",
        "note": "varies"
      },
      {
        "quantity": "nusinersen approval",
        "typical_range": "2016",
        "unit": "year",
        "note": "splicing-modifying therapy for SMA"
      }
    ],
    "families_and_kinds": [
      "5 prime capping",
      "splicing and alternative splicing",
      "polyadenylation",
      "RNA editing",
      "tRNA and rRNA modification"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "biochemical process",
        "why": "in registry terms"
      },
      {
        "relation": "includes",
        "target": "RNA splicing",
        "why": ""
      },
      {
        "relation": "is contrasted with",
        "target": "post-translational modification",
        "why": ""
      },
      {
        "relation": "is contrasted with",
        "target": "arginylation",
        "why": "misfiled alias"
      }
    ],
    "identifiers": [],
    "standards_and_regulation": [
      "No direct regulation; drug approval rules for RNA-targeting therapies"
    ],
    "failure_modes_and_hazards": [
      "Confusing RNA and protein modifications",
      "Oversimplifying gene expression",
      "Misfiled protein alias"
    ],
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": [],
    "agent_conduct": {
      "may": [
        "Explain RNA capping, splicing, polyadenylation and editing from molecular biology sources.",
        "Distinguish RNA processing from protein modification."
      ],
      "must_not": [
        "Confuse post-transcriptional RNA changes with post-translational protein changes.",
        "Oversimplify gene expression as one gene making one protein.",
        "Present preliminary research on RNA-based therapies as established treatment.",
        "File protein modification aliases under RNA processing."
      ],
      "requires_human": [
        "Using research findings on RNA processing in clinical decisions for a patient."
      ]
    },
    "ethics": {
      "considerations": [
        "Misleading claims about genetics can fuel false hopes and unproven treatments."
      ],
      "affected_parties": [
        "Students and researchers",
        "Patients seeking treatments"
      ]
    },
    "owners": {
      "steward": "Nobody owns the process; it is part of molecular biology.",
      "master_systems": []
    }
  },
  "sources": [],
  "structure": {
    "bundles": [
      {
        "id": "understand",
        "name": "Understand",
        "description": "What post-transcriptional modification is.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "definition",
            "name": "Definition",
            "description": "Definition.",
            "findings": [
              {
                "id": "definition-finding",
                "name": "Definition",
                "description": "Definition.",
                "questions": [
                  {
                    "text": "What is post-transcriptional modification, and how does it differ from transcriptional regulation, post-translational modification and epigenetic marks?",
                    "kind": "definition"
                  },
                  {
                    "text": "Is the question about biology, a disease or a therapy, which a clinician can advise on?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          },
          {
            "id": "alias",
            "name": "Alias",
            "description": "Misfiled alias.",
            "findings": [
              {
                "id": "alias-finding",
                "name": "Alias",
                "description": "Alias.",
                "questions": [
                  {
                    "text": "What is arginylation, and why is it a protein modification?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which entry fits protein arginylation?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "steps",
        "name": "Steps",
        "description": "Processing steps.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "capping",
            "name": "Capping and tailing",
            "description": "Capping and polyadenylation.",
            "findings": [
              {
                "id": "capping-finding",
                "name": "Capping and tailing",
                "description": "Capping and tailing.",
                "questions": [
                  {
                    "text": "How do the 5 prime cap and poly(A) tail protect and regulate mRNA?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which references are standard?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "splicing",
            "name": "Splicing",
            "description": "Splicing.",
            "findings": [
              {
                "id": "splicing-finding",
                "name": "Splicing",
                "description": "Splicing.",
                "questions": [
                  {
                    "text": "How does the spliceosome remove introns, and how does alternative splicing increase diversity?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which sources are cited?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "medicine",
        "name": "Medicine",
        "description": "Disease and therapy.",
        "rationale": "Attribution.",
        "layers": [
          {
            "id": "disease",
            "name": "Disease",
            "description": "Splicing diseases.",
            "findings": [
              {
                "id": "disease-finding",
                "name": "Disease",
                "description": "Disease.",
                "questions": [
                  {
                    "text": "How do splicing errors cause diseases such as spinal muscular atrophy?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits spinal muscular atrophy?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "therapy",
            "name": "Therapy",
            "description": "RNA therapies.",
            "findings": [
              {
                "id": "therapy-finding",
                "name": "Therapy",
                "description": "Therapy.",
                "questions": [
                  {
                    "text": "How do antisense oligonucleotides modify splicing, in general terms?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits nusinersen?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "context",
        "name": "Context",
        "description": "Discovery.",
        "rationale": "Context.",
        "layers": [
          {
            "id": "discovery",
            "name": "Discovery",
            "description": "Split genes.",
            "findings": [
              {
                "id": "discovery-finding",
                "name": "Discovery",
                "description": "Discovery.",
                "questions": [
                  {
                    "text": "How were split genes and splicing discovered in 1977?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits Phillip Allen Sharp?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "editing",
            "name": "Editing",
            "description": "RNA editing.",
            "findings": [
              {
                "id": "editing-finding",
                "name": "Editing",
                "description": "Editing.",
                "questions": [
                  {
                    "text": "What is A-to-I RNA editing by ADAR enzymes?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits ADAR?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "The registry alias arginylation should be moved to post-translational modification",
    "Should RNA editing be a separate entry?",
    "How should molecular biology references be linked?"
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}