{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-10-22T10:18:19Z",
    "providers": [
      "Claude"
    ],
    "breadth": "researched by Claude against the sources listed below",
    "pass": 2,
    "wave": 5,
    "engine": "claude",
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-22T10:34:33+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "7 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q14876077",
    "registryId": "vr.tr.protein-catabolic-process",
    "name": "protein catabolic process",
    "version": "0.2.0-wave.5",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "ACT.PRC"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q14876077/",
  "model": {
    "registry_id": "vr.tr.protein-catabolic-process",
    "name": "protein catabolic process",
    "purpose": "Let an agent explain protein breakdown pathways, find Gene Ontology annotations, and relate protein degradation to physiology and disease with sources.",
    "definition": "The chemical reactions and pathways resulting in the breakdown of a protein by destruction of its native, active configuration, with or without hydrolysis of peptide bonds (Gene Ontology GO:0030163); in eukaryotes mainly through the ubiquitin-proteasome system and lysosomal or vacuolar pathways, and in bacteria through ATP-dependent proteases.",
    "what_it_is_for": "Removing damaged or unneeded proteins, regulating protein levels and recycling amino acids.",
    "affordances": [
      "explain main degradation pathways",
      "give Gene Ontology terms",
      "relate degradation to disease and drugs with sources",
      "describe experimental methods"
    ],
    "distinguishing_features": [
      "The ubiquitin-proteasome system degrades most short-lived proteins.",
      "Autophagy delivers proteins and organelles to lysosomes.",
      "Denaturation without hydrolysis also counts as catabolism in the GO definition."
    ],
    "appearance": null,
    "visual_identification": [
      "Not visible; measured by protein turnover experiments"
    ],
    "physical_properties": [],
    "families_and_kinds": [
      "ubiquitin-dependent and ubiquitin-independent proteasomal degradation",
      "ER-associated degradation (ERAD)",
      "lysosomal, vacuolar and autophagic degradation",
      "organellar and bacterial protease degradation",
      "non-proteolytic denaturation"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "catabolic process",
        "why": "metabolism"
      },
      {
        "relation": "uses",
        "target": "proteasome",
        "why": "machinery"
      },
      {
        "relation": "uses",
        "target": "lysosome",
        "why": "organelle"
      },
      {
        "relation": "is described by",
        "target": "Gene Ontology",
        "why": "annotation"
      }
    ],
    "identifiers": [
      {
        "scheme": "Gene Ontology",
        "value_or_pattern": "GO:0030163",
        "note": "protein catabolic process"
      }
    ],
    "standards_and_regulation": [
      "Gene Ontology definitions"
    ],
    "failure_modes_and_hazards": [
      "Protein aggregation diseases when degradation fails"
    ],
    "agent_conduct": {
      "may": [
        "explain processes and point to databases"
      ],
      "must_not": [
        "give medical advice"
      ],
      "requires_human": []
    },
    "ethics": {
      "considerations": [
        "accuracy"
      ],
      "affected_parties": [
        "researchers",
        "students"
      ]
    },
    "owners": {
      "steward": "nobody; a biological process",
      "master_systems": [
        "Gene Ontology"
      ]
    },
    "facets_not_applicable": {
      "properties": "A process has no physical properties; half-lives are recorded under physiology.",
      "hazards": "A cellular process poses no hazards; disease links are listed as failure modes."
    },
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": []
  },
  "sources": [
    {
      "id": "SRC-001",
      "title": "Q14876077",
      "publisher": "Wikidata",
      "url": "https://www.wikidata.org/wiki/Q14876077",
      "what_it_supports": "identity of the registry item, labels and sitelinks",
      "url_status": "live"
    },
    {
      "id": "SRC-002",
      "title": "Proteolysis",
      "publisher": "Wikipedia",
      "url": "https://en.wikipedia.org/wiki/Proteolysis",
      "what_it_supports": "protein breakdown",
      "url_status": "live"
    },
    {
      "id": "SRC-003",
      "title": "GO:0030163 - protein catabolic process",
      "publisher": "PomBase",
      "url": "https://www.pombase.org/term/GO%3A0030163",
      "what_it_supports": "Identifier, definition including loss of native configuration without peptide-bond hydrolysis, and parent terms.",
      "url_status": "live"
    },
    {
      "id": "SRC-004",
      "title": "Protein Degradation",
      "publisher": "Sinauer Associates, The Cell: A Molecular Approach, via NCBI Bookshelf",
      "url": "https://www.ncbi.nlm.nih.gov/books/NBK9957/",
      "what_it_supports": "Eukaryotic degradation pathways, ubiquitin targeting, lysosomes, autophagy and protein turnover.",
      "url_status": "live"
    },
    {
      "id": "SRC-005",
      "title": "Regulated Proteolysis in Bacteria",
      "publisher": "Annual Reviews, via PubMed Central",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6013389/",
      "what_it_supports": "Bacterial protein degradation through ATP-dependent proteases including Lon, ClpXP and FtsH.",
      "url_status": "live"
    },
    {
      "id": "SRC-006",
      "title": "Protein degrons and degradation: Exploring substrate recognition and pathway selection in plants",
      "publisher": "The Plant Cell, indexed by PubMed",
      "url": "https://pubmed.ncbi.nlm.nih.gov/38701343/",
      "what_it_supports": "Plant degradation pathways, substrate signals, autophagy and organellar proteases.",
      "url_status": "live"
    },
    {
      "id": "SRC-007",
      "title": "Introduction to GO annotations",
      "publisher": "Gene Ontology Consortium",
      "url": "https://www.geneontology.org/docs/go-annotations/",
      "what_it_supports": "Meaning of biological process annotations, gene product participation, references and evidence codes.",
      "url_status": "live"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "pathway",
        "name": "Pathway",
        "description": "Which route.",
        "rationale": "Pathways differ.",
        "layers": [
          {
            "id": "route",
            "name": "Route",
            "description": "Proteasome or lysosome.",
            "findings": [
              {
                "id": "route",
                "name": "Route",
                "description": "Pathway and machinery.",
                "questions": [
                  {
                    "text": "Which pathway degrades the protein?",
                    "kind": "provenance"
                  },
                  {
                    "text": "What evidence shows it?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "signal",
            "name": "Signal",
            "description": "Degrons and tags.",
            "findings": [
              {
                "id": "signal",
                "name": "Signal",
                "description": "Tag.",
                "questions": [
                  {
                    "text": "Which signal targets it, such as ubiquitin chains?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which enzymes add it?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "annotation",
        "name": "Annotation",
        "description": "Databases.",
        "rationale": "Annotations need evidence.",
        "layers": [
          {
            "id": "go-terms",
            "name": "GO terms",
            "description": "Ontology.",
            "findings": [
              {
                "id": "go-term",
                "name": "GO term",
                "description": "ID and evidence.",
                "questions": [
                  {
                    "text": "Which GO terms apply?",
                    "kind": "provenance"
                  },
                  {
                    "text": "With which evidence codes?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "protein-records",
            "name": "Protein records",
            "description": "UniProt.",
            "findings": [
              {
                "id": "record",
                "name": "Record",
                "description": "Organism, the substrate protein degraded, and proteins that take part in degradation, kept distinct.",
                "questions": [
                  {
                    "text": "Which protein is degraded?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which record describes it?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "physiology",
        "name": "Physiology",
        "description": "Roles.",
        "rationale": "Degradation regulates cells.",
        "layers": [
          {
            "id": "regulation",
            "name": "Regulation",
            "description": "Turnover.",
            "findings": [
              {
                "id": "turnover",
                "name": "Turnover",
                "description": "Half-life.",
                "questions": [
                  {
                    "text": "What is the protein's half-life?",
                    "kind": "measurement"
                  },
                  {
                    "text": "In which cells?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "disease",
            "name": "Disease",
            "description": "Failure.",
            "findings": [
              {
                "id": "disease-link",
                "name": "Disease link",
                "description": "Condition and evidence.",
                "questions": [
                  {
                    "text": "Which diseases involve failed degradation?",
                    "kind": "provenance"
                  },
                  {
                    "text": "What evidence?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "methods",
        "name": "Methods",
        "description": "Measurement.",
        "rationale": "Methods shape results.",
        "layers": [
          {
            "id": "assays",
            "name": "Assays",
            "description": "Turnover assays.",
            "findings": [
              {
                "id": "assay",
                "name": "Assay",
                "description": "Method.",
                "questions": [
                  {
                    "text": "How was degradation measured?",
                    "kind": "provenance"
                  },
                  {
                    "text": "With which controls?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "drugs",
            "name": "Drugs",
            "description": "Pharmacology.",
            "findings": [
              {
                "id": "drug",
                "name": "Drug",
                "description": "Agent and target.",
                "questions": [
                  {
                    "text": "Which drugs act on these pathways?",
                    "kind": "provenance"
                  },
                  {
                    "text": "At which step?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "The registry merges many substrate-specific catabolic processes; they should be separate entries."
  ],
  "statistics": {
    "bundles": 4,
    "layers": 8,
    "findings": 8,
    "questions": 16
  }
}