{
  "generated_from": "pipeline/layers.yaml + runs/<paper>/ledger.jsonl",
  "groups": {
    "induction": {
      "question": "What did the readers find, and what survived reconciliation?",
      "title": "Induction"
    },
    "interchange": {
      "question": "What survives when a claim tree leaves this format?",
      "title": "Interchange"
    },
    "measures": {
      "question": "What can be measured over the tree - its coverage, its wording, whether its code re-runs?",
      "title": "Measures"
    },
    "source": {
      "question": "What text did the readers read, and what does the paper itself say?",
      "title": "Source"
    },
    "tree": {
      "question": "What does the paper assert, and how do its claims depend on each other?",
      "title": "Tree"
    }
  },
  "layers": [
    {
      "id": "claim-format",
      "title": "Claim format",
      "question": "What is a claim, and what may be said about one?",
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        "document"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "relation-vocab",
      "title": "Relation semantics",
      "question": "What does each relation assert, and which are oppositions?",
      "kind": "question",
      "scope": "corpus",
      "group": null,
      "needs": [
        "claim-format"
      ],
      "views": [
        "table",
        "comparison"
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      "issue": "zmainen/elife-claim-trees#19",
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "epistemic-vocab",
      "title": "Epistemic vocabulary",
      "question": "Does `epistemic` record support strength, or restate the role?",
      "kind": "question",
      "scope": "corpus",
      "group": null,
      "needs": [
        "claim-format"
      ],
      "views": [
        "table"
      ],
      "issue": "zmainen/claim-graphs#21",
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "prediction-outcome",
      "title": "Prediction outcomes",
      "question": "Did the paper's predictions come out, and does the tree say so?",
      "kind": "question",
      "scope": "corpus",
      "group": null,
      "needs": [
        "claim-format",
        "relation-vocab"
      ],
      "views": [
        "table"
      ],
      "issue": "zmainen/elife-claim-trees#28",
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "evaluation",
      "title": "Evaluation",
      "question": "How well does each model profile recover a paper's claim tree?",
      "kind": "step",
      "scope": "corpus",
      "group": null,
      "needs": [
        "claim-tree"
      ],
      "views": [
        "table"
      ],
      "issue": "zmainen/claim-graphs#24",
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "prepare",
      "title": "Prepared paper",
      "question": "What text did the readers actually read?",
      "kind": "step",
      "scope": "paper",
      "group": "source",
      "needs": [],
      "views": [
        "document"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "article",
      "title": "Article",
      "question": "What does the paper itself say, section by section?",
      "kind": "step",
      "scope": "paper",
      "group": "source",
      "needs": [
        "prepare"
      ],
      "views": [
        "document"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "results-reader",
      "title": "Results reader",
      "question": "What does the Results section assert?",
      "kind": "candidate",
      "scope": "paper",
      "group": "induction",
      "needs": [
        "prepare"
      ],
      "views": [
        "list",
        "table",
        "comparison"
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      "issue": null,
      "open": false,
      "requires_human": false,
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    },
    {
      "id": "caption-reader",
      "title": "Caption reader",
      "question": "What do the figure captions assert?",
      "kind": "candidate",
      "scope": "paper",
      "group": "induction",
      "needs": [
        "prepare"
      ],
      "views": [
        "list",
        "table",
        "comparison"
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      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "structure-reader",
      "title": "Structure reader",
      "question": "What is the paper's argument structure?",
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      "scope": "paper",
      "group": "induction",
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        "prepare"
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        "list",
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      "issue": null,
      "open": false,
      "requires_human": false,
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    },
    {
      "id": "reconcile",
      "title": "Reconciliation",
      "question": "Which candidates survive, and which readers agreed?",
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      "scope": "paper",
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        "results-reader",
        "caption-reader",
        "structure-reader"
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        "table",
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      "issue": null,
      "open": false,
      "requires_human": false,
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    },
    {
      "id": "external-review",
      "title": "External review",
      "question": "What structure did the three readers systematically miss?",
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      "scope": "paper",
      "group": "induction",
      "needs": [
        "reconcile"
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      "views": [
        "table",
        "comparison"
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      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "edge-inference",
      "title": "Edge inference",
      "question": "Which claims depend on which?",
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      "scope": "paper",
      "group": "induction",
      "needs": [
        "reconcile",
        "relation-vocab"
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        "graph",
        "table",
        "comparison"
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      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "claim-tree",
      "title": "Claim tree",
      "question": "What does this paper assert, and how do its assertions depend on each other?",
      "kind": "step",
      "scope": "paper",
      "group": "tree",
      "needs": [
        "reconcile",
        "external-review",
        "edge-inference",
        "claim-format"
      ],
      "views": [
        "graph",
        "list",
        "table",
        "comparison"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "stance",
      "title": "Alternatives and stance",
      "question": "What does this paper rule out, and what does it merely entertain?",
      "kind": "feature",
      "scope": "paper",
      "group": "tree",
      "needs": [
        "claim-tree",
        "prepare",
        "claim-format"
      ],
      "views": [
        "graph",
        "list"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "questions",
      "title": "Research questions",
      "question": "What did this paper set out to answer, and which claim answers each question?",
      "kind": "feature",
      "scope": "paper",
      "group": "tree",
      "needs": [
        "claim-tree",
        "prepare"
      ],
      "views": [
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "parts",
      "title": "Parts",
      "question": "Which claims are components of other claims, and which whole does each belong to?",
      "kind": "feature",
      "scope": "paper",
      "group": "tree",
      "needs": [
        "claim-tree",
        "relation-vocab"
      ],
      "views": [
        "table",
        "graph"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "reference-check",
      "title": "Reference check",
      "question": "Do the cited references resolve, and to what?",
      "kind": "feature",
      "scope": "paper",
      "group": "tree",
      "needs": [
        "claim-tree"
      ],
      "views": [
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "abstract-map",
      "title": "Abstract ↔ claims",
      "question": "Which claims does the abstract carry, and which does it drop?",
      "kind": "step",
      "scope": "paper",
      "group": "tree",
      "needs": [
        "claim-tree",
        "prepare"
      ],
      "views": [
        "document",
        "comparison"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "synthesis",
      "title": "Argument from graph",
      "question": "Restated from the claim graph alone, what does this paper argue — and where does that part from its abstract?",
      "kind": "step",
      "scope": "paper",
      "group": "measures",
      "needs": [
        "claim-tree",
        "abstract-map"
      ],
      "views": [
        "document",
        "comparison"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "summaries",
      "title": "Paper summary",
      "question": "What does this paper argue, in three paragraphs?",
      "kind": "step",
      "scope": "paper",
      "group": "measures",
      "needs": [
        "claim-tree"
      ],
      "views": [
        "document"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "plain-claim",
      "title": "Plain wording",
      "question": "What does each claim say, in one sentence a non-specialist can read?",
      "kind": "step",
      "scope": "paper",
      "group": "measures",
      "needs": [
        "claim-tree"
      ],
      "views": [
        "list",
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "verification",
      "title": "Verification",
      "question": "Did anyone check, and what did they find?",
      "kind": "step",
      "scope": "paper",
      "group": "measures",
      "needs": [
        "claim-tree"
      ],
      "views": [
        "graph",
        "table",
        "comparison"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "coverage",
      "title": "Coverage",
      "question": "What does the paper assert that no claim represents?",
      "kind": "step",
      "scope": "paper",
      "group": "measures",
      "needs": [
        "claim-tree",
        "prepare"
      ],
      "views": [
        "document",
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "adjudication",
      "title": "Coverage adjudication",
      "question": "Of the spans the matcher could not resolve, which are real gaps?",
      "kind": "judgement",
      "scope": "paper",
      "group": "measures",
      "needs": [
        "coverage"
      ],
      "views": [
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": "coverage"
    },
    {
      "id": "marks",
      "title": "Marked paper",
      "question": "Where, in the document itself, is each claim and each gap?",
      "kind": "step",
      "scope": "paper",
      "group": "measures",
      "needs": [
        "adjudication",
        "claim-tree",
        "prepare"
      ],
      "views": [
        "document"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "gap-claim",
      "title": "Gap claims",
      "question": "What claim would close each gap?",
      "kind": "candidate",
      "group": "measures",
      "needs": [
        "adjudication",
        "claim-tree",
        "claim-format"
      ],
      "views": [
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "edge-review",
      "title": "Edge review",
      "question": "What does a claim added after induction depend on and support?",
      "kind": "step",
      "group": null,
      "needs": [
        "claim-tree",
        "relation-vocab"
      ],
      "views": [
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "replication",
      "title": "Replication",
      "question": "Has an independent study found the same thing?",
      "kind": "step",
      "scope": "paper",
      "group": "measures",
      "needs": [
        "claim-tree"
      ],
      "views": [
        "table",
        "comparison"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "mira-export",
      "title": "MIRA export",
      "question": "What does the schema eLife reads carry, and what does it drop?",
      "kind": "step",
      "scope": "paper",
      "group": "interchange",
      "needs": [
        "claim-tree",
        "stance",
        "relation-vocab"
      ],
      "views": [
        "graph",
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "oxa-export",
      "title": "OXA export",
      "question": "What does the open document architecture carry?",
      "kind": "step",
      "scope": "paper",
      "group": "interchange",
      "needs": [
        "claim-tree",
        "stance"
      ],
      "views": [
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "dg-export",
      "title": "Discourse Graphs export",
      "question": "What does the Q/C/E/S ontology carry?",
      "kind": "step",
      "scope": "paper",
      "group": "interchange",
      "needs": [
        "oxa-export"
      ],
      "views": [
        "graph",
        "table"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "formats-report",
      "title": "Formats comparison",
      "question": "Measured from the exports, what did each conversion cost?",
      "kind": "step",
      "scope": "paper",
      "group": "interchange",
      "needs": [
        "mira-export",
        "oxa-export",
        "dg-export"
      ],
      "views": [
        "table",
        "comparison"
      ],
      "issue": null,
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "warrant",
      "title": "Warrant",
      "question": "How well does the tree's argument support each claim?",
      "kind": "feature",
      "scope": "paper",
      "group": "tree",
      "needs": [
        "claim-tree",
        "stance",
        "prediction-outcome"
      ],
      "views": [
        "table"
      ],
      "issue": "zmainen/claim-graphs#21",
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "verification-check",
      "title": "Verification check",
      "question": "Does a re-run stand behind each claim, read beside its warrant?",
      "kind": "feature",
      "scope": "paper",
      "group": "measures",
      "needs": [
        "claim-tree",
        "verification"
      ],
      "views": [
        "table"
      ],
      "issue": "zmainen/claim-graphs#21",
      "open": false,
      "requires_human": false,
      "reviews": null
    },
    {
      "id": "modules",
      "title": "Modules",
      "question": "What are the paper's questions, and which claims answer each?",
      "kind": "feature",
      "scope": "paper",
      "group": "tree",
      "needs": [
        "claim-tree",
        "questions",
        "stance",
        "prediction-outcome"
      ],
      "views": [
        "modules"
      ],
      "issue": "zmainen/claim-graphs#53",
      "open": false,
      "requires_human": false,
      "reviews": null
    }
  ],
  "papers": [
    {
      "slug": "artiushin-2026-spider-atlas",
      "title": "A three-dimensional immunofluorescence atlas of the brain of the hackled-orb weaver spider, Uloborus diversus",
      "fill": {
        "done": 14,
        "total": 31,
        "approved": 0,
        "observed": 8
      },
      "cells": [
        {
          "layer": "prepare",
          "state": "stale",
          "version": 3,
          "ran": "2026-09-13T13:47:24Z",
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/prepare.json"
        },
        {
          "layer": "article",
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          "version": 3,
          "ran": "2026-09-13T13:49:32Z",
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/article.json"
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        {
          "layer": "results-reader",
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          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/results-reader.json"
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          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/caption-reader.json"
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        {
          "layer": "structure-reader",
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          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/structure-reader.json"
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        {
          "layer": "reconcile",
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          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/reconcile.json"
        },
        {
          "layer": "external-review",
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          "version": null,
          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/external-review.json"
        },
        {
          "layer": "edge-inference",
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          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/edge-inference.json"
        },
        {
          "layer": "claim-tree",
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          "version": 1,
          "ran": "2026-09-10T09:48:01Z",
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/claim-tree.json"
        },
        {
          "layer": "stance",
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          "version": null,
          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/stance.json"
        },
        {
          "layer": "questions",
          "state": "absent",
          "version": null,
          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/questions.json"
        },
        {
          "layer": "parts",
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          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/parts.json"
        },
        {
          "layer": "reference-check",
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          "version": null,
          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/reference-check.json"
        },
        {
          "layer": "abstract-map",
          "state": "unrecorded",
          "version": 1,
          "ran": "2026-04-20T03:48:50Z",
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/abstract-map.json"
        },
        {
          "layer": "synthesis",
          "state": "unrecorded",
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          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/synthesis.json"
        },
        {
          "layer": "summaries",
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          "version": null,
          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/summaries.json"
        },
        {
          "layer": "plain-claim",
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          "version": 2,
          "ran": "2026-09-12T13:31:48Z",
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/plain-claim.json"
        },
        {
          "layer": "verification",
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          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/verification.json"
        },
        {
          "layer": "coverage",
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          "ran": "2026-09-13T13:48:13Z",
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/coverage.json"
        },
        {
          "layer": "adjudication",
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          "version": 2,
          "ran": "2026-09-11T19:16:28Z",
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/adjudication.json"
        },
        {
          "layer": "marks",
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          "version": 3,
          "ran": "2026-09-12T12:11:26Z",
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/marks.json"
        },
        {
          "layer": "gap-claim",
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          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/gap-claim.json"
        },
        {
          "layer": "edge-review",
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          "version": null,
          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/edge-review.json"
        },
        {
          "layer": "replication",
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          "version": null,
          "ran": null,
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/replication.json"
        },
        {
          "layer": "mira-export",
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          "version": 3,
          "ran": "2026-09-11T12:14:09Z",
          "data": "/elife-claim-trees/data/artiushin-2026-spider-atlas/mira-export.json"
        },
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    },
    {
      "paper": "kammer-2026-foveal-feedback",
      "layer": "reference-check",
      "command": "cd extract && python3 -m claim_graphs.cli verify-refs --paper kammer-2026-foveal-feedback"
    },
    {
      "paper": "kammer-2026-foveal-feedback",
      "layer": "verification",
      "command": "python3 verification/audit_run.py kammer-2026-foveal-feedback"
    },
    {
      "paper": "kammer-2026-foveal-feedback",
      "layer": "replication",
      "command": null
    },
    {
      "paper": "kammer-2026-foveal-feedback",
      "layer": "warrant",
      "command": "cd extract && python3 -m claim_graphs.cli warrant --paper kammer-2026-foveal-feedback"
    },
    {
      "paper": "kammer-2026-foveal-feedback",
      "layer": "verification-check",
      "command": "cd extract && python3 -m claim_graphs.cli verification-check --paper kammer-2026-foveal-feedback"
    },
    {
      "paper": "kammer-2026-foveal-feedback",
      "layer": "modules",
      "command": "python3 scripts/modules.py kammer-2026-foveal-feedback --write"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "results-reader",
      "command": "cd extract && python3 -m claim_graphs.cli results-reader --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "caption-reader",
      "command": "cd extract && python3 -m claim_graphs.cli caption-reader --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "structure-reader",
      "command": "cd extract && python3 -m claim_graphs.cli structure-reader --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "reconcile",
      "command": "cd extract && python3 -m claim_graphs.cli reconcile --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "external-review",
      "command": "cd extract && python3 -m claim_graphs.cli external-review --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "edge-inference",
      "command": "cd extract && python3 -m claim_graphs.cli edge-inference --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "questions",
      "command": "cd extract && python3 -m claim_graphs.cli questions --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "parts",
      "command": "cd extract && python3 -m claim_graphs.cli parts --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "reference-check",
      "command": "cd extract && python3 -m claim_graphs.cli verify-refs --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "gap-claim",
      "command": "python3 scripts/gap_claims.py kolb-2026-igabasnfr2 --answer runs/kolb-2026-igabasnfr2/gap-claim.answer.json"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "edge-review",
      "command": "python3 scripts/edge_review.py kolb-2026-igabasnfr2 --answer runs/kolb-2026-igabasnfr2/edge-review.answer.json"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "replication",
      "command": null
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "warrant",
      "command": "cd extract && python3 -m claim_graphs.cli warrant --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "verification-check",
      "command": "cd extract && python3 -m claim_graphs.cli verification-check --paper kolb-2026-igabasnfr2"
    },
    {
      "paper": "kolb-2026-igabasnfr2",
      "layer": "modules",
      "command": "python3 scripts/modules.py kolb-2026-igabasnfr2 --write"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "results-reader",
      "command": "cd extract && python3 -m claim_graphs.cli results-reader --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "caption-reader",
      "command": "cd extract && python3 -m claim_graphs.cli caption-reader --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "structure-reader",
      "command": "cd extract && python3 -m claim_graphs.cli structure-reader --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "reconcile",
      "command": "cd extract && python3 -m claim_graphs.cli reconcile --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "external-review",
      "command": "cd extract && python3 -m claim_graphs.cli external-review --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "edge-inference",
      "command": "cd extract && python3 -m claim_graphs.cli edge-inference --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "questions",
      "command": "cd extract && python3 -m claim_graphs.cli questions --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "parts",
      "command": "cd extract && python3 -m claim_graphs.cli parts --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "reference-check",
      "command": "cd extract && python3 -m claim_graphs.cli verify-refs --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "verification",
      "command": "python3 verification/audit_run.py rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "gap-claim",
      "command": "python3 scripts/gap_claims.py rozak-2026-neurovascular-dl --answer runs/rozak-2026-neurovascular-dl/gap-claim.answer.json"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "edge-review",
      "command": "python3 scripts/edge_review.py rozak-2026-neurovascular-dl --answer runs/rozak-2026-neurovascular-dl/edge-review.answer.json"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "replication",
      "command": null
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "warrant",
      "command": "cd extract && python3 -m claim_graphs.cli warrant --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "verification-check",
      "command": "cd extract && python3 -m claim_graphs.cli verification-check --paper rozak-2026-neurovascular-dl"
    },
    {
      "paper": "rozak-2026-neurovascular-dl",
      "layer": "modules",
      "command": "python3 scripts/modules.py rozak-2026-neurovascular-dl --write"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "results-reader",
      "command": "cd extract && python3 -m claim_graphs.cli results-reader --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "caption-reader",
      "command": "cd extract && python3 -m claim_graphs.cli caption-reader --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "structure-reader",
      "command": "cd extract && python3 -m claim_graphs.cli structure-reader --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "reconcile",
      "command": "cd extract && python3 -m claim_graphs.cli reconcile --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "external-review",
      "command": "cd extract && python3 -m claim_graphs.cli external-review --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "edge-inference",
      "command": "cd extract && python3 -m claim_graphs.cli edge-inference --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "stance",
      "command": "cd extract && python3 -m claim_graphs.cli stance --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "questions",
      "command": "cd extract && python3 -m claim_graphs.cli questions --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "parts",
      "command": "cd extract && python3 -m claim_graphs.cli parts --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "reference-check",
      "command": "cd extract && python3 -m claim_graphs.cli verify-refs --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "gap-claim",
      "command": "python3 scripts/gap_claims.py scheller-2026-self-prioritization --answer runs/scheller-2026-self-prioritization/gap-claim.answer.json"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "edge-review",
      "command": "python3 scripts/edge_review.py scheller-2026-self-prioritization --answer runs/scheller-2026-self-prioritization/edge-review.answer.json"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "replication",
      "command": null
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "warrant",
      "command": "cd extract && python3 -m claim_graphs.cli warrant --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "verification-check",
      "command": "cd extract && python3 -m claim_graphs.cli verification-check --paper scheller-2026-self-prioritization"
    },
    {
      "paper": "scheller-2026-self-prioritization",
      "layer": "modules",
      "command": "python3 scripts/modules.py scheller-2026-self-prioritization --write"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "results-reader",
      "command": "cd extract && python3 -m claim_graphs.cli results-reader --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "caption-reader",
      "command": "cd extract && python3 -m claim_graphs.cli caption-reader --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "structure-reader",
      "command": "cd extract && python3 -m claim_graphs.cli structure-reader --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "reconcile",
      "command": "cd extract && python3 -m claim_graphs.cli reconcile --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "external-review",
      "command": "cd extract && python3 -m claim_graphs.cli external-review --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "edge-inference",
      "command": "cd extract && python3 -m claim_graphs.cli edge-inference --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "questions",
      "command": "cd extract && python3 -m claim_graphs.cli questions --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "parts",
      "command": "cd extract && python3 -m claim_graphs.cli parts --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "reference-check",
      "command": "cd extract && python3 -m claim_graphs.cli verify-refs --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "gap-claim",
      "command": "python3 scripts/gap_claims.py wengert-2026-kcnc1 --answer runs/wengert-2026-kcnc1/gap-claim.answer.json"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "edge-review",
      "command": "python3 scripts/edge_review.py wengert-2026-kcnc1 --answer runs/wengert-2026-kcnc1/edge-review.answer.json"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "replication",
      "command": null
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "warrant",
      "command": "cd extract && python3 -m claim_graphs.cli warrant --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "verification-check",
      "command": "cd extract && python3 -m claim_graphs.cli verification-check --paper wengert-2026-kcnc1"
    },
    {
      "paper": "wengert-2026-kcnc1",
      "layer": "modules",
      "command": "python3 scripts/modules.py wengert-2026-kcnc1 --write"
    }
  ]
}