{
  "schemaVersion": "cathedral.malaria-resistance.manifest.v1",
  "retrievedAt": "2026-10-29",
  "execution": "Local Node.js; Supabase and cloud compute not used",
  "status": "Original experiment partially reproduced",
  "inputs": [
    {
      "id": "px1_article_source_data",
      "title": "Source data for Emergence and spread of Plasmodium falciparum PX1 polymorphisms associated with decreased susceptibility to antimalarials in Uganda",
      "citation": "Niaré K et al. Nature Medicine (2026). DOI: 10.1038/s41591-026-04590-5",
      "articleUrl": "https://www.nature.com/articles/s41591-026-04590-5",
      "downloadUrl": "https://media.springernature.com/original/springer-static/esm/art:10.1038%2Fs41591-026-04590-5/MediaObjects/41591_2026_4590_MOESM5_ESM.xlsx",
      "sheetUsed": "Source_dataset1",
      "bytes": 106432,
      "sha256": "7f08b7218fe7c0eb4741a003fd298b6656598030a0165653d9f736ce364b9c31",
      "licenseNote": "Article page states CC BY-NC-ND 4.0; confirm source-dataset-specific permissions before redistribution or commercial reuse. Raw file is excluded from version control.",
      "role": "PX1 haplotype, K13 label, metadata and ex-vivo phenotype records. It does not include numeric read-depth or COI values required for exact replication."
    },
    {
      "id": "who_molecular_marker_compendium",
      "title": "WHO Compendium of molecular markers for antimalarial drug resistance, Version 2.0 (July 2026)",
      "url": "https://www.who.int/tools/compendium-of-molecular-markers-for-antimalarial-drug-resistance",
      "downloadUrl": "https://cdn.who.int/media/docs/default-source/malaria/drug-resistance/compendium-of-molecular-markers-for-antimalarial-drug-resistance.xlsx?download=true&sfvrsn=ef5bc699_8",
      "sheetUsed": "Artemisinins (Pf)",
      "bytes": 266426,
      "sha256": "6e7ac3d7d395920153712f983d9a352b64369b487c14e46bf3a08430cd3cd0f3",
      "licenseNote": "Retained locally for analysis; source file is excluded from version control. Consult WHO terms for reuse.",
      "role": "Classification reference for K13 C469Y and A675V; does not classify PX1/PIN."
    }
  ],
  "excludedInputs": [
    {
      "id": "malariagen_pf8",
      "url": "https://malariagen.github.io/parasite-data/pf8/Data_access.html",
      "reason": "Not accessed for this phenotype reanalysis. Current Pf8 access uses authenticated Google Cloud; no unrelated cohort was downloaded or joined to published phenotype data."
    },
    {
      "id": "target_paper_sra_bioproject",
      "accession": "PRJNA1298911",
      "reason": "The target paper's WGS accession is not itself a sample-matched ex-vivo phenotype dataset; no speculative or unverified sample joins were made."
    }
  ],
  "outputs": [
    "results/summary.json",
    "results/phenotype-comparisons.csv",
    "results/core-phenotype-contrast.svg",
    "results/report.md"
  ],
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  "publicationNote": "Only aggregate derived results and reproducibility materials are published. Source workbooks are not included; obtain them from the cited provider and respect their terms."
}