{
  "version": 3,
  "created_at": "2026-07-08T16:47:02.719Z",
  "task_summary": "Build integrated EoE translational flagship: discovery → targets → companion Dx → pMHC → preclinical (supersedes Paper B)",
  "agents": [],
  "phases": [
    {
      "name": "Plan",
      "delegations": [
        {
          "steps": [
            {
              "title": "Audit + assemble source facts",
              "description": "Read the remaining pMHC/preclinical/Dx source docs in full (preclinical_workflow_roadmap.md, t_cell_assay_protocol.md, pmhc_tcr_mechanism_review.md, food_antigen_pmhc_review.md, companion_dx_specs.csv, protein_design_specs.csv, allergen/epitope tables, index-case suite). Consolidate every quantitative claim into handoff/flagship_facts.json (signature, single-cell, endotypes, GWAS, PPI, 3 targets, companion-Dx cutoffs, epitope/HLA burden, index-case blinded result, preclinical gates). Reuse paperB_facts.json where valid. Inventory which existing figures/tables are reusable as-is vs need a refresh."
            },
            {
              "title": "Pipeline overview figure (Figure 1)",
              "description": "Build a new end-to-end pipeline schematic: Discovery (omics→signature) → Validation (single-cell, endotypes, PPI-refractory) → Target selection (3 leads) → Companion Dx → pMHC antigen-directed arm → Preclinical wet-bench roadmap. Publication-grade via figure-style; phase-colored, artifact-grounded counts. Save figure1_pipeline_overview.png."
            },
            {
              "title": "Discovery + validation figures",
              "description": "Reuse/refresh the Paper B discovery figure (volcano + pathways + accessibility) and single-cell figure (UMAP, 14× mast, states, per-sample burden) and validation figure (differentiation arrest, endotype gradient, GWAS, PPI-refractory). Version as flagship figures. Confirm numbers against flagship_facts.json (14× mast, 567-gene signature, etc.)."
            },
            {
              "title": "Target landscape + three design specifications",
              "description": "Reuse the target-prioritization landscape (Fig 4) and the three-lead structure/ESM design figure (Fig 5). Consolidate the Tier-A dossier table and the design-spec table. Ensure SIGLEC6/IL1RL1/CCL26 modality, epitope, KD, selectivity match protein_design_specs.csv."
            },
            {
              "title": "Companion-diagnostic + pMHC/epitope figure(s)",
              "description": "Build a companion-Dx figure from companion_dx_specs.csv (per-lead assay, matrix, addressability by severity) and a pMHC/epitope figure from the allergen×HLA burden matrices + the blinded index-case validation (2/2 triggers top-2; presentation≠pathology). Publication-grade. Save companion_dx + pmhc figures."
            },
            {
              "title": "Preclinical wet-bench roadmap figure",
              "description": "Build a preclinical roadmap figure from preclinical_workflow_roadmap.md: 4 phases (ex-vivo human → reagent+in-vivo → IND-enabling GLP → Phase-1) with go/no-go decision gates, deliverables, success criteria, and the T-cell assay as the ex-vivo efficacy readout. Save figure preclinical_roadmap.png."
            },
            {
              "title": "Draft integrated manuscript prose",
              "description": "Write paperE_flagship_manuscript.md as an end-to-end translational pipeline paper: Abstract, Intro (EoE unmet need + pipeline thesis), Results (Discovery → Validation → Targets → Companion Dx → pMHC antigen-directed arm incl. blinded index-case validation → Preclinical roadmap), Discussion (path to the clinic, IP incl. Hill patent noted as prior art), Methods, refs. Every number from flagship_facts.json; figures embedded via art_ markers; measured-vs-framed respected; all hypothesis-generating/in-silico caveats explicit."
            },
            {
              "title": "Verify citations + render DOCX",
              "description": "Verify all DOIs against CrossRef before entering text (reuse the 17 verified + any new pMHC/preclinical refs). Resolve figure markers to paths, render paperE_flagship_manuscript.docx, verify embedded image count + key strings via zipfile. Save md + docx."
            }
          ]
        }
      ],
      "id": "phase-0"
    }
  ],
  "desired_outputs": [
    "Integrated flagship manuscript (md + DOCX), peer-review-ready",
    "Pipeline overview figure (discovery→target→Dx→pMHC→preclinical)",
    "Reused/updated omics + target + design figures (Figs from Paper B)",
    "pMHC/epitope analysis figure(s) incl. blinded index-case validation",
    "Companion-diagnostic + preclinical-roadmap figure(s)",
    "Consolidated target + design-spec + companion-Dx tables",
    "Verified reference list (CrossRef-checked)"
  ],
  "feasibility": {
    "rationale": "Nearly all analysis exists as artifacts (omics signature, single-cell, endotypes, GWAS, PPI, 3 design specs, full pMHC/epitope suite, companion-Dx specs, preclinical roadmap, T-cell assay protocol, blinded index-case validation). Work is integration, one new pipeline schematic, consolidation of tables, and prose synthesis into an end-to-end narrative. No new wet-lab or GPU compute required. Business layer deferred per user.",
    "confidence": "high"
  }
}