{
  "version": 3,
  "created_at": "2026-07-08T14:35:11.177Z",
  "task_summary": "Systematic literature review grounding the EoE personalized-pMHC preprint",
  "agents": [],
  "phases": [
    {
      "name": "Plan",
      "delegations": [
        {
          "steps": [
            {
              "title": "Define scope & build the search-query matrix",
              "description": "Fix the review scope to the preprint's thesis: rationale for a personalized pMHC-based food-trigger diagnostic for EoE (plus the therapeutic and prevention extensions). Enumerate 8 themes — (1) EoE epidemiology & disease burden, (2) diagnostic status quo & unmet need (elimination diet + endoscopy), (3) pathophysiology (CD4/Th2, eosinophil biology, IFN axis), (4) antigen-specific T cells in EoE / the Hill-Spergel platform, (5) therapeutic landscape (PPI, topical steroids, dupilumab, diet), (6) pMHC / antigen-specific tolerance & anergy approaches, (7) EoE genetics, HLA & GWAS, (8) atopic march & prevention incl. teplizumab/T1D. Write a query matrix (3-6 OpenAlex queries per theme) to a scope file. No artifact yet; deliverable is the query plan used in step 2."
            },
            {
              "title": "Systematic retrieval → deduplicated reference library",
              "description": "Run the full query matrix against OpenAlex (free keyed API), collecting DOI, title, first author, year, venue, citation count, and theme tag for every hit. Deduplicate by DOI across themes, keep the union, and record which theme(s) each paper serves. Save eoe_preprint_reference_library.csv (expected ~80-150 unique DOI-verified references) with columns: doi, title, first_author, year, venue, cited_by, themes, tier(blank). Print per-theme counts and total unique."
            },
            {
              "title": "Relevance screen & evidence tiering",
              "description": "Tier each reference: Tier-1 landmark/primary (e.g. Alexander 2014, Herold 2019, Du Toit 2015, Dilollo/Hill 2025, Blanchard 2006, Kottyan EoE genetics), Tier-2 supporting primary, Tier-3 review/context. Flag the small set of claims the preprint will lean on hardest and confirm each has ≥1 Tier-1 or Tier-2 anchor. Update the tier column in the reference library CSV (version 2). Print the Tier-1 set with one-line relevance notes."
            },
            {
              "title": "Synthesis A — burden, diagnostic gap, pathophysiology",
              "description": "Write themes 1-3 of the review: EoE epidemiology/burden and the quality-of-life cost of the current diagnostic pathway (empiric elimination + serial endoscopy), then the CD4/Th2 food-antigen-driven pathophysiology (tie to this project's prior-phase findings: IFN-γ program, mast/SIGLEC6, eosinophil effectors). Every claim cited to a retrieved DOI. Draft saved into the working review doc (section drafts accumulate to step 9)."
            },
            {
              "title": "Synthesis B — antigen-specific T cells, therapeutics, pMHC/tolerance",
              "description": "Write themes 4-6: the Hill-Spergel antigen-specific-T-cell platform as the diagnostic prior art (eoeTCR-4 β-casein/DR7, patent) and where our personalized-panel front end adds/does not add; the current therapeutic landscape and its gaps (why food-trigger identification matters); and the pMHC / antigen-specific tolerance/anergy mechanism literature (oral tolerance, tolerogenic approaches). Honest prior-art framing throughout, cited to retrieved DOIs."
            },
            {
              "title": "Synthesis C — genetics/HLA & prevention/teplizumab",
              "description": "Write themes 7-8: EoE genetics/HLA and the GWAS architecture (susceptibility vs effector split; HLA-II presentation), then the prevention/atopic-march arm with the teplizumab/T1D template (Alexander 2014 familial risk, Herold 2019, LEAP/EAT, AIT prevention). Reconcile with the atopic_march_prevention_review.md already drafted, avoiding duplication. Cited to retrieved DOIs."
            },
            {
              "title": "Evidence-map / gap-analysis figure",
              "description": "Render eoe_literature_evidence_map.png (publication-grade via apply_figure_style): a theme × evidence-strength map showing, per theme, how many Tier-1/2/3 references support it and where the evidence is thin (e.g. EoE-specific prevention = no direct trials; DQ prediction less benchmarked). A second panel or annotation flags which preprint claims are well-anchored vs hypothesis-level. Save the figure."
            },
            {
              "title": "Consolidate review document + gap analysis",
              "description": "Assemble the thematic drafts into eoe_preprint_literature_review.md: intro/scope, the 8 thematic syntheses, an explicit gap-analysis section (what the preprint's novelty and commercialization-rationale claims can rest on vs what remains hypothesis), and a full DOI-verified reference list. Cross-reference the evidence-map figure. Include the standing disclaimers (computational predictions, prior-art/patent, no clinical validation)."
            },
            {
              "title": "Bundle the literature-review package",
              "description": "Tar the review doc, reference library CSV, and evidence-map figure into eoe_preprint_litreview_bundle.tar.gz; save all as artifacts. Close with a summary of the reference count, tier breakdown, and the key gaps the preprint must be honest about."
            }
          ]
        }
      ],
      "id": "phase-0"
    }
  ],
  "desired_outputs": [
    "Deduplicated DOI-verified reference library (CSV)",
    "Thematic literature-review document (markdown)",
    "Evidence-map / gap-analysis figure",
    "Bundled review package"
  ],
  "feasibility": {
    "rationale": "All sources are free open-data APIs already demonstrated working this session (OpenAlex keyed, Ensembl, GWAS Catalog, full-text fetch via Crossref/Unpaywall/S2/PMC). No paid API credits or GPU/compute required. Many landmark references already retrieved; this systematizes and fills gaps. Main limitation is closed-access full text for some papers (abstract-level synthesis where full text is paywalled).",
    "confidence": "high"
  }
}