{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-12T09:16:17Z",
    "providers": [
      "Codex"
    ],
    "breadth": "recalled by Codex without web access - no source was read",
    "missingProviders": [],
    "pass": 2,
    "cost": {
      "grok": {
        "seconds": 22.2,
        "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a094e6-1bb4-7220-9f8c-742e95242a5c\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: DNA replication factor A complex\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n",
        "usd": 0.0,
        "recall": true
      },
      "codex": {
        "seconds": 74.2,
        "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a094e6-1ba1-7d40-8598-60d9cb2462be\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: DNA replication factor A complex\nRegistry id: vr.tr.dna-replication-factor-a-complex\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorde"
      }
    },
    "enrichment": {
      "pass": 3,
      "engine": "claude",
      "producedAt": "2026-10-06T12:00:00Z",
      "ingestedAt": "2026-10-06T08:41:21+00:00",
      "fields": [
        "agent_conduct",
        "ethics",
        "failure_modes_and_hazards",
        "owners",
        "visual_identification"
      ]
    },
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-07T10:10:28+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "2 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q21109588",
    "registryId": "vr.tr.dna-replication-factor-a-complex",
    "name": "DNA replication factor A complex",
    "version": "0.1.0-research.1",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "PHY.MAT"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q21109588/",
  "model": {
    "registry_id": "vr.tr.dna-replication-factor-a-complex",
    "name": "DNA replication factor A complex",
    "purpose": "Enable an agent to recognize a DNA replication factor A complex, assess its assembly and single-stranded DNA-binding state, and judge its suitability for a specified biological interpretation or experiment.",
    "definition": "DNA replication factor A complex, usually called replication protein A (RPA), is a eukaryotic heterotrimeric protein complex that binds single-stranded DNA, protects it from degradation and secondary-structure formation, and coordinates proteins involved in DNA replication, repair and recombination.",
    "scope_statement": "This model owns the molecular identity, composition, assembly, DNA engagement, regulatory state and experimental fitness of the complex registered as vr.tr.dna-replication-factor-a-complex, provisionally interpreted as replication protein A (RPA), with organism and construct boundaries explicit.",
    "in_scope": [
      "Organism-specific identity and correspondence to replication protein A nomenclature",
      "Subunit composition, sequence variants and intact-complex assembly",
      "Single-stranded DNA binding, occupancy and exchange",
      "Complex-associated modifications and interactions in replication, repair and recombination",
      "Preparation integrity and evidence supporting functional assessments"
    ],
    "out_of_scope": [
      "Standalone models of constituent genes and isolated subunits",
      "Complete DNA replication, repair or recombination pathways",
      "DNA polymerases, helicases and replication factor C complexes",
      "Bacterial single-stranded DNA-binding proteins and other distinct binding complexes",
      "Commercial reagent formulations, packaging and supplier operations"
    ],
    "distinguishing_features": [
      "Require evidence of an assembled RPA complex rather than detection of one constituent subunit; a human RPA structural record identifies a heterotrimer with 1:1:1 stoichiometry. [RCSB PDB 8RK2](https://www.rcsb.org/structure/8RK2)",
      "Test preferential engagement of single-stranded DNA under stated conditions; ssDNA binding and coating are documented for yeast RPA. [RCSB PDB 6I52](https://www.rcsb.org/structure/6i52)",
      "Use subunit sequence identities and assembly evidence to distinguish RPA from other single-stranded DNA-binding proteins; binding alone does not establish identity.",
      "Distinguish the complex from replication factor C, DNA polymerase and helicase by constituent identities and measured activity rather than the shared word replication.",
      "Identify whether evidence concerns a full complex or an engineered fragment; an isolated RPA large-subunit DNA-binding domain is not evidence for complete-complex assembly. [RCSB PDB 1FGU](https://www.rcsb.org/structure/1FGU)"
    ],
    "characteristics": [
      {
        "name": "Organism and molecular identity",
        "kind": "relation",
        "unit_or_values": "Taxonomy identifier, complex accession and constituent sequence accessions",
        "why_it_matters": "Prevents transfer of species-specific composition or behavior without justification."
      },
      {
        "name": "Subunit composition and stoichiometry",
        "kind": "category",
        "unit_or_values": "Named subunits with copy counts; canonical, variant or unresolved composition",
        "why_it_matters": "Distinguishes an intact complex from partial assemblies or alternative forms."
      },
      {
        "name": "Construct coverage",
        "kind": "category",
        "unit_or_values": "Full-length, truncated, tagged or mutated; residue boundaries for each subunit",
        "why_it_matters": "Defines which binding and interaction properties can reasonably be assessed."
      },
      {
        "name": "Assembly integrity",
        "kind": "state",
        "unit_or_values": "Intact, partially dissociated, aggregated or unresolved, with method and conditions",
        "why_it_matters": "Controls whether a preparation represents the registered complex."
      },
      {
        "name": "Apparent ssDNA-binding affinity",
        "kind": "measurement",
        "unit_or_values": "Kd in nM or µM, with substrate, buffer, temperature and binding model",
        "why_it_matters": "Supports comparisons only when assay conditions and substrate properties are compatible."
      },
      {
        "name": "DNA-binding footprint",
        "kind": "measurement",
        "unit_or_values": "Nucleotides per bound complex under specified conditions",
        "why_it_matters": "Relates complex abundance to DNA coverage without assuming a universal footprint."
      },
      {
        "name": "DNA association and dissociation kinetics",
        "kind": "measurement",
        "unit_or_values": "Association rate in M^-1 s^-1, dissociation rate in s^-1, or residence time in s",
        "why_it_matters": "Distinguishes stable occupancy from rapid exchange that an equilibrium measurement may conceal."
      },
      {
        "name": "Modification state",
        "kind": "state",
        "unit_or_values": "Subunit, residue, modification and occupancy; unmeasured recorded separately from absent",
        "why_it_matters": "Allows functional differences to be evaluated against a defined molecular state."
      },
      {
        "name": "DNA and protein partners",
        "kind": "relation",
        "unit_or_values": "Partner identity, directness of interaction, occupancy and experimental context",
        "why_it_matters": "Separates intrinsic complex properties from properties of larger assemblies."
      },
      {
        "name": "Active preparation fraction",
        "kind": "measurement",
        "unit_or_values": "Percentage or molar fraction competent in a specified binding assay",
        "why_it_matters": "Prevents total protein concentration from being treated as functional complex concentration."
      }
    ],
    "affordances": [
      "Resolve a named RPA preparation to its organism, constituent sequences and construct boundaries.",
      "Assess whether a sample contains an intact complex suitable for a specified assay.",
      "Compare ssDNA binding and exchange measurements under compatible conditions.",
      "Evaluate whether modification or partner-binding evidence supports a proposed functional state.",
      "Select or reject a preparation for replication, repair or recombination experiments using recorded acceptance criteria.",
      "Flag interpretations that extrapolate from isolated domains, incomplete assemblies or another species."
    ],
    "agent_conduct": {
      "may": [
        "Explain the role of replication protein A in DNA replication and repair from cited sources.",
        "Annotate RPA subunits and genes in datasets the agent is authorized to edit."
      ],
      "must_not": [
        "Confuse the RPA complex with unrelated proteins or abbreviations.",
        "Present research findings on RPA as clinical guidance.",
        "Fabricate or alter experimental data about the complex."
      ],
      "requires_human": [
        "Publishing interpretations of RPA variants found in a person's genome."
      ]
    },
    "ethics": {
      "considerations": [
        "Research on DNA repair underlies cancer studies, where overstatement misleads patients.",
        "Genetic findings about individuals carry privacy risk."
      ],
      "affected_parties": [
        "Researchers",
        "Patients in studies",
        "Readers of research"
      ]
    },
    "owners": {
      "steward": "Nobody owns the molecule; the laboratory answers for its samples and data.",
      "master_systems": [
        "Protein and gene databases"
      ]
    },
    "visual_identification": [
      "Not visible to the eye; identified by its three subunits in protein gels and by sequence in databases.",
      "Structural models show oligonucleotide-binding folds wrapped around single-stranded DNA."
    ],
    "failure_modes_and_hazards": [
      "Misannotation of subunits spreads errors through databases.",
      "Overinterpreting laboratory results can mislead clinical expectations."
    ],
    "what_it_is_for": [
      "Replication protein A functions in eukaryotic cells wherever exposed single-stranded DNA requires protection and coordination with DNA processing proteins.",
      "It is studied in research on DNA replication, repair, recombination and cellular responses to replication stress.",
      "Purified complexes are used in biochemical experiments that examine DNA binding and interactions among DNA metabolism proteins."
    ],
    "standards_and_regulation": [
      "The Gene Ontology cellular component classification, maintained by the Gene Ontology Consortium, includes the DNA replication factor A complex for biological annotation."
    ]
  },
  "sources": [
    {
      "id": "wikidata",
      "title": "Wikidata item Q21109588: DNA replication factor A complex",
      "url": "https://www.wikidata.org/wiki/Q21109588",
      "url_status": "live",
      "what_it_supports": "identity and sense of the item",
      "checked_by": "wikidata-api"
    },
    {
      "id": "wikipedia-en",
      "title": "Wikipedia: Replication protein A",
      "url": "https://en.wikipedia.org/wiki/Replication_protein_A",
      "url_status": "live",
      "what_it_supports": "general description of the item",
      "checked_by": "wikidata-api sitelink"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "rpa-identity-and-composition",
        "name": "RPA identity and composition",
        "description": "Resolve what molecular assembly the registry name denotes and which constituents instantiate it.",
        "rationale": "The registry has no definition, and a name containing replication factor is insufficient to establish molecular identity.",
        "layers": [
          {
            "id": "name-and-taxon-resolution",
            "name": "Name and taxon resolution",
            "description": "Connect the registry entry to authoritative complex terminology and organism-specific records.",
            "findings": [
              {
                "id": "registered-complex-correspondence",
                "name": "Registered complex correspondence",
                "description": "Establish whether DNA replication factor A complex denotes canonical RPA and document the supported taxonomic scope.",
                "questions": [
                  {
                    "text": "Which authoritative complex or ontology record explicitly connects this registry name to replication protein A?",
                    "kind": "definition",
                    "id": "registered-complex-correspondence-q01"
                  },
                  {
                    "text": "Does the supporting record define a cross-species complex class or an organism-specific assembly?",
                    "kind": "boundary",
                    "id": "registered-complex-correspondence-q02"
                  }
                ]
              }
            ]
          },
          {
            "id": "constituent-resolution",
            "name": "Constituent resolution",
            "description": "Identify the actual subunits and distinguish canonical composition from substitutions or incomplete assemblies.",
            "findings": [
              {
                "id": "subunit-membership-and-copy-number",
                "name": "Subunit membership and copy number",
                "description": "Record constituent accessions, sequence versions and experimentally supported stoichiometry.",
                "questions": [
                  {
                    "text": "Which sequence-identified subunits and copy numbers constitute the complex in this organism?",
                    "kind": "definition",
                    "id": "subunit-membership-and-copy-number-q01"
                  },
                  {
                    "text": "What evidence distinguishes the assembled complex from co-detected free subunits?",
                    "kind": "measurement",
                    "id": "subunit-membership-and-copy-number-q02"
                  },
                  {
                    "text": "Does a paralog substitution remain a variant of this registry thing or require a link to a distinct complex?",
                    "kind": "boundary",
                    "id": "subunit-membership-and-copy-number-q03"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "assembly-and-domain-integrity",
        "name": "Assembly and domain integrity",
        "description": "Describe constituent completeness, domain organization and the physical integrity of the assembly.",
        "rationale": "A domain construct can retain DNA binding while omitting functions required of the complete complex.",
        "layers": [
          {
            "id": "construct-and-domain-coverage",
            "name": "Construct and domain coverage",
            "description": "Map the experimental material to complete subunit sequences and relevant domains.",
            "findings": [
              {
                "id": "represented-rpa-regions",
                "name": "Represented RPA regions",
                "description": "Identify retained and missing regions before applying structural or functional observations to the full complex.",
                "questions": [
                  {
                    "text": "Which residue ranges, tags and mutations are present in each constituent?",
                    "kind": "provenance",
                    "id": "represented-rpa-regions-q01"
                  },
                  {
                    "text": "Which DNA-binding, assembly or partner-interaction regions are absent or altered?",
                    "kind": "boundary",
                    "id": "represented-rpa-regions-q02"
                  }
                ]
              }
            ]
          },
          {
            "id": "physical-assembly-state",
            "name": "Physical assembly state",
            "description": "Assess whether the expected assembly persists under the conditions of use.",
            "findings": [
              {
                "id": "intact-complex-fraction",
                "name": "Intact complex fraction",
                "description": "Separate intact complexes from dissociated constituents, aggregates and mixtures.",
                "questions": [
                  {
                    "text": "What measurements establish assembly size, constituent ratios and sample homogeneity?",
                    "kind": "measurement",
                    "id": "intact-complex-fraction-q01"
                  },
                  {
                    "text": "Under which concentration, buffer and temperature conditions does the assembly remain intact?",
                    "kind": "measurement",
                    "id": "intact-complex-fraction-q02"
                  },
                  {
                    "text": "What loss of assembly integrity disqualifies the preparation for the intended experiment?",
                    "kind": "action",
                    "id": "intact-complex-fraction-q03"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "single-stranded-dna-engagement",
        "name": "Single-stranded DNA engagement",
        "description": "Describe substrate-dependent binding, DNA coverage and the dynamics of association and release.",
        "rationale": "An RPA complex's state cannot be assessed from protein identity alone when DNA substrate and occupancy determine its behavior.",
        "layers": [
          {
            "id": "substrate-and-affinity",
            "name": "Substrate and affinity",
            "description": "Define the DNA substrate and conditions required to interpret binding measurements.",
            "findings": [
              {
                "id": "conditional-dna-binding",
                "name": "Conditional DNA binding",
                "description": "Record binding as an assay-specific property rather than a context-free affinity constant.",
                "questions": [
                  {
                    "text": "What are the DNA sequence, length, secondary structure and single-stranded or junction configuration?",
                    "kind": "definition",
                    "id": "conditional-dna-binding-q01"
                  },
                  {
                    "text": "What affinity is measured at the stated salt concentration, temperature and protein-to-DNA ratio?",
                    "kind": "measurement",
                    "id": "conditional-dna-binding-q02"
                  },
                  {
                    "text": "Which controls distinguish ssDNA engagement from nonspecific association or assay interference?",
                    "kind": "measurement",
                    "id": "conditional-dna-binding-q03"
                  }
                ]
              }
            ]
          },
          {
            "id": "occupancy-and-exchange",
            "name": "Occupancy and exchange",
            "description": "Resolve how much DNA is engaged and how rapidly complexes redistribute.",
            "findings": [
              {
                "id": "dna-coverage-and-residence",
                "name": "DNA coverage and residence",
                "description": "Record footprint, occupancy and exchange without assuming a single invariant binding mode.",
                "questions": [
                  {
                    "text": "How many nucleotides are engaged per complex, and how was that footprint inferred?",
                    "kind": "measurement",
                    "id": "dna-coverage-and-residence-q01"
                  },
                  {
                    "text": "What residence time or association and dissociation rates are supported by the experiment?",
                    "kind": "measurement",
                    "id": "dna-coverage-and-residence-q02"
                  },
                  {
                    "text": "Does the evidence resolve individual complexes, neighboring complexes or an averaged DNA-bound population?",
                    "kind": "boundary",
                    "id": "dna-coverage-and-residence-q03"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "regulation-and-pathway-interfaces",
        "name": "Regulation and pathway interfaces",
        "description": "Relate molecular modifications and partner engagement to a bounded functional context.",
        "rationale": "The model must distinguish possession of RPA from evidence that it occupies a particular regulated or pathway-associated state.",
        "layers": [
          {
            "id": "modification-dependent-state",
            "name": "Modification-dependent state",
            "description": "Characterize measured modifications and the evidence connecting them to altered behavior.",
            "findings": [
              {
                "id": "site-resolved-regulatory-state",
                "name": "Site-resolved regulatory state",
                "description": "Record modifications by constituent and residue while separating observation from inferred functional consequences.",
                "questions": [
                  {
                    "text": "Which modification sites and occupancies were measured in this organism and preparation?",
                    "kind": "measurement",
                    "id": "site-resolved-regulatory-state-q01"
                  },
                  {
                    "text": "Does a claimed functional effect derive from a directly modified complex, a substitution mutant or correlation alone?",
                    "kind": "provenance",
                    "id": "site-resolved-regulatory-state-q02"
                  }
                ]
              }
            ]
          },
          {
            "id": "partner-engagement-and-functional-context",
            "name": "Partner engagement and functional context",
            "description": "Record the interfaces through which this complex participates in larger DNA-processing systems.",
            "findings": [
              {
                "id": "supported-partner-and-pathway-assignment",
                "name": "Supported partner and pathway assignment",
                "description": "Link direct interaction, localization and functional evidence without treating them as interchangeable.",
                "questions": [
                  {
                    "text": "Which protein partners interact directly with this complex, and is the interaction dependent on DNA or modification state?",
                    "kind": "measurement",
                    "id": "supported-partner-and-pathway-assignment-q01"
                  },
                  {
                    "text": "What evidence places the observed complex in replication, repair or recombination rather than establishing only colocalization?",
                    "kind": "provenance",
                    "id": "supported-partner-and-pathway-assignment-q02"
                  },
                  {
                    "text": "Which claimed outcome requires additional machinery and therefore belongs to a pathway model?",
                    "kind": "boundary",
                    "id": "supported-partner-and-pathway-assignment-q03"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "preparation-and-functional-fitness",
        "name": "Preparation and functional fitness",
        "description": "Determine whether a particular preparation supports the intended measurement or intervention.",
        "rationale": "Purity and nominal concentration do not establish that a protein complex is intact, DNA-free when required or functionally active.",
        "layers": [
          {
            "id": "preparation-history-and-contaminants",
            "name": "Preparation history and contaminants",
            "description": "Track production and handling factors that can change the interpretation of RPA assays.",
            "findings": [
              {
                "id": "assay-relevant-preparation-quality",
                "name": "Assay-relevant preparation quality",
                "description": "Record sample origin, handling and contaminants that could mimic or obscure DNA-binding behavior.",
                "questions": [
                  {
                    "text": "Was the complex isolated natively or reconstituted, and what purification and storage history is documented?",
                    "kind": "provenance",
                    "id": "assay-relevant-preparation-quality-q01"
                  },
                  {
                    "text": "What residual nucleic acid, nuclease activity or free-subunit contamination was measured?",
                    "kind": "measurement",
                    "id": "assay-relevant-preparation-quality-q02"
                  },
                  {
                    "text": "Which preparation defects require cleanup, requalification or rejection before use?",
                    "kind": "action",
                    "id": "assay-relevant-preparation-quality-q03"
                  }
                ]
              }
            ]
          },
          {
            "id": "functional-qualification",
            "name": "Functional qualification",
            "description": "Tie acceptance of a preparation to a defined assay and the limits of the supporting evidence.",
            "findings": [
              {
                "id": "use-specific-activity-evidence",
                "name": "Use-specific activity evidence",
                "description": "Define what the preparation has demonstrably been qualified to do.",
                "questions": [
                  {
                    "text": "What fraction of the stated complex concentration is active in the reference DNA-binding assay?",
                    "kind": "measurement",
                    "id": "use-specific-activity-evidence-q01"
                  },
                  {
                    "text": "Which positive and negative controls establish suitability for the proposed downstream experiment?",
                    "kind": "action",
                    "id": "use-specific-activity-evidence-q02"
                  },
                  {
                    "text": "Which conclusions remain unsupported because qualification used another substrate, construct or organism?",
                    "kind": "boundary",
                    "id": "use-specific-activity-evidence-q03"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "evidence-and-external-alignment",
        "name": "Evidence and external alignment",
        "description": "What the world already says about this thing, gathered so the model can be checked against it.",
        "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.",
        "layers": [
          {
            "id": "reported-evidence",
            "name": "Reported evidence",
            "description": "Findings from the breadth pass, kept separate from the structural claims.",
            "findings": [
              {
                "id": "evidence-confidence-notes",
                "name": "Check these first",
                "description": "Recalled without web access and unsourced; every item is a lead to verify.",
                "evidence": [
                  "The name is interpreted as the eukaryotic replication protein A complex; no organism is specified.",
                  "Subunit symbols and approximate masses given here are human-specific; other organisms use different gene names.",
                  "Binding footprints describe experimentally distinguished modes, not a fixed occupancy; alternative RPA should not be assumed functionally equivalent to canonical RPA."
                ],
                "questions": [
                  {
                    "id": "evidence-confidence-notes-q01",
                    "text": "Which of these check these first hold for the sense of DNA replication factor A complex this model covers, and on what evidence?",
                    "kind": "provenance"
                  }
                ]
              },
              {
                "id": "evidence-kinds",
                "name": "Kinds and varieties",
                "description": "Recalled without web access and unsourced; every item is a lead to verify.",
                "evidence": [
                  "Canonical RPA complex",
                  "Alternative human RPA complex containing RPA4 in place of RPA2"
                ],
                "questions": [
                  {
                    "id": "evidence-kinds-q01",
                    "text": "Which of these kinds and varieties hold for the sense of DNA replication factor A complex this model covers, and on what evidence?",
                    "kind": "provenance"
                  }
                ]
              },
              {
                "id": "evidence-identifiers",
                "name": "Identifiers and schemes",
                "description": "Recalled without web access and unsourced; every item is a lead to verify.",
                "evidence": [
                  {
                    "scheme": "HGNC gene symbols",
                    "value_or_pattern": "RPA1, RPA2, RPA3",
                    "note": "Identify the genes encoding the three canonical human subunits, not the assembled complex."
                  },
                  {
                    "scheme": "HGNC gene symbols",
                    "value_or_pattern": "RPA4",
                    "note": "Identifies the gene encoding an alternative human subunit that can replace RPA2."
                  }
                ],
                "questions": [
                  {
                    "id": "evidence-identifiers-q01",
                    "text": "Which of these identifiers and schemes hold for the sense of DNA replication factor A complex this model covers, and on what evidence?",
                    "kind": "provenance"
                  }
                ]
              },
              {
                "id": "evidence-real-world-use",
                "name": "Real-world use",
                "description": "Recalled without web access and unsourced; every item is a lead to verify.",
                "evidence": [
                  "Coating exposed single-stranded DNA during chromosomal replication",
                  "Supporting DNA repair and homologous recombination",
                  "Helping recruit and activate replication-stress checkpoint machinery",
                  "Use as a purified reagent in biochemical studies of DNA metabolism",
                  "Measurement of RPA accumulation or phosphorylation in studies of replication stress"
                ],
                "questions": [
                  {
                    "id": "evidence-real-world-use-q01",
                    "text": "Which of these real-world use hold for the sense of DNA replication factor A complex this model covers, and on what evidence?",
                    "kind": "provenance"
                  }
                ]
              },
              {
                "id": "evidence-measurements",
                "name": "Typical measurements",
                "description": "Recalled without web access and unsourced; every item is a lead to verify.",
                "evidence": [
                  {
                    "quantity": "Approximate molecular masses of canonical human subunits",
                    "typical_range": "RPA1: 70; RPA2: 32; RPA3: 14",
                    "unit": "kDa"
                  },
                  {
                    "quantity": "Single-stranded DNA binding footprint",
                    "typical_range": "Approximately 8-30, depending on binding mode and experimental conditions",
                    "unit": "nucleotides per complex"
                  }
                ],
                "questions": [
                  {
                    "id": "evidence-measurements-q01",
                    "text": "Which of these typical measurements hold for the sense of DNA replication factor A complex this model covers, and on what evidence?",
                    "kind": "provenance"
                  }
                ]
              },
              {
                "id": "evidence-failure-modes-and-hazards",
                "name": "Failure modes and hazards",
                "description": "Recalled without web access and unsourced; every item is a lead to verify.",
                "evidence": [
                  "Insufficient functional RPA compromises DNA replication and genome maintenance.",
                  "Exhaustion of available RPA during severe replication stress can leave single-stranded DNA unprotected and promote widespread DNA breakage.",
                  "Defective interactions or regulation can impair DNA repair and checkpoint signaling."
                ],
                "questions": [
                  {
                    "id": "evidence-failure-modes-and-hazards-q01",
                    "text": "Which of these failure modes and hazards hold for the sense of DNA replication factor A complex this model covers, and on what evidence?",
                    "kind": "provenance"
                  }
                ]
              },
              {
                "id": "evidence-neighbours",
                "name": "Neighbouring kinds and how to tell them apart",
                "description": "Recalled without web access and unsourced; every item is a lead to verify.",
                "evidence": [
                  {
                    "name": "RPA1",
                    "difference": "RPA1 is the largest individual subunit; the registered thing is the assembled three-subunit complex."
                  },
                  {
                    "name": "Bacterial single-stranded DNA-binding protein",
                    "difference": "Performs related DNA-protection functions in bacteria but has a different subunit organization from canonical eukaryotic RPA."
                  },
                  {
                    "name": "Replication factor C",
                    "difference": "Replication factor C is an ATP-dependent sliding-clamp loader, whereas RPA principally binds single-stranded DNA."
                  },
                  {
                    "name": "RAD51",
                    "difference": "RAD51 forms recombination filaments that catalyze homology search and strand exchange; RPA coats single-stranded DNA and must be reorganized or displaced during filament assembly."
                  }
                ],
                "questions": [
                  {
                    "id": "evidence-neighbours-q01",
                    "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of DNA replication factor A complex this model covers, and on what evidence?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "Which authoritative identifier establishes the exact correspondence between the registry label DNA replication factor A complex and canonical replication protein A?",
    "Does this registry entry encompass organism-specific and alternative-subunit RPA complexes, or should some be linked as distinct registered things?",
    "Does an existing Vercy world model already own this concept and require this entry to link to it?",
    "Which quantitative binding, footprint and exchange measurements are sufficiently comparable to support reference ranges?",
    "Which modification-dependent and partner-dependent effects are established for each covered organism rather than inferred from another species?"
  ],
  "statistics": {
    "bundles": 6,
    "layers": 11,
    "findings": 17,
    "questions": 34
  }
}
