{
  "report_schema": "oncoref.cta-scope-report.v1",
  "species": "human",
  "taxon_id": 9606,
  "oncoref_version": "1.9.15",
  "taxonomy_id": "oncoref:normal-tissues:v1:sha256:a290d40bfc2e8794e78ed615e32d70d4e630ac18177ce7c1a5fdf8c89f9c82d6",
  "policy_version": "2026-10-19.1",
  "source_receipts": {
    "hpa_rna_consensus": {
      "name": "hpa_rna_consensus",
      "version": "v23",
      "url": "https://v23.proteinatlas.org/download/rna_tissue_consensus.tsv.zip",
      "bytes": 37949495,
      "recorded_bytes": 37949495,
      "sha256": "c49b5b33a076e3b9c1eb4f7d15d063ee936e07045e192ceccfeb9edcf1d90ddb",
      "downloaded_at": "2026-06-12T01:52:16+00:00",
      "exists": true,
      "manifest_recorded": true
    },
    "hpa_normal_tissue": {
      "name": "hpa_normal_tissue",
      "version": "v23",
      "url": "https://v23.proteinatlas.org/download/normal_tissue.tsv.zip",
      "bytes": 82941549,
      "recorded_bytes": 82941549,
      "sha256": "1fa9111070f23290d29a32eaa30695689599b5231e7d0bc935b60a777ad3a1cc",
      "downloaded_at": "2026-06-12T01:52:18+00:00",
      "exists": true,
      "manifest_recorded": true
    }
  },
  "routine_contexts": {
    "bulk_rna": [
      [
        "adipose tissue",
        ""
      ],
      [
        "adrenal gland",
        ""
      ],
      [
        "amygdala",
        ""
      ],
      [
        "appendix",
        ""
      ],
      [
        "basal ganglia",
        ""
      ],
      [
        "bone marrow",
        ""
      ],
      [
        "breast",
        ""
      ],
      [
        "cerebellum",
        ""
      ],
      [
        "cerebral cortex",
        ""
      ],
      [
        "cervix",
        ""
      ],
      [
        "choroid plexus",
        ""
      ],
      [
        "colon",
        ""
      ],
      [
        "duodenum",
        ""
      ],
      [
        "endometrium",
        ""
      ],
      [
        "epididymis",
        ""
      ],
      [
        "esophagus",
        ""
      ],
      [
        "fallopian tube",
        ""
      ],
      [
        "gallbladder",
        ""
      ],
      [
        "heart muscle",
        ""
      ],
      [
        "hippocampal formation",
        ""
      ],
      [
        "hypothalamus",
        ""
      ],
      [
        "kidney",
        ""
      ],
      [
        "liver",
        ""
      ],
      [
        "lung",
        ""
      ],
      [
        "lymph node",
        ""
      ],
      [
        "midbrain",
        ""
      ],
      [
        "ovary",
        ""
      ],
      [
        "pancreas",
        ""
      ],
      [
        "parathyroid gland",
        ""
      ],
      [
        "pituitary gland",
        ""
      ],
      [
        "placenta",
        ""
      ],
      [
        "prostate",
        ""
      ],
      [
        "rectum",
        ""
      ],
      [
        "retina",
        ""
      ],
      [
        "salivary gland",
        ""
      ],
      [
        "seminal vesicle",
        ""
      ],
      [
        "skeletal muscle",
        ""
      ],
      [
        "skin",
        ""
      ],
      [
        "small intestine",
        ""
      ],
      [
        "smooth muscle",
        ""
      ],
      [
        "spinal cord",
        ""
      ],
      [
        "spleen",
        ""
      ],
      [
        "stomach",
        ""
      ],
      [
        "testis",
        ""
      ],
      [
        "thymus",
        ""
      ],
      [
        "thyroid gland",
        ""
      ],
      [
        "tongue",
        ""
      ],
      [
        "tonsil",
        ""
      ],
      [
        "urinary bladder",
        ""
      ],
      [
        "vagina",
        ""
      ]
    ],
    "ihc": [
      [
        "adipose tissue",
        "adipocytes"
      ],
      [
        "adrenal gland",
        "glandular cells"
      ],
      [
        "appendix",
        "glandular cells"
      ],
      [
        "appendix",
        "lymphoid tissue"
      ],
      [
        "bone marrow",
        "hematopoietic cells"
      ],
      [
        "breast",
        "adipocytes"
      ],
      [
        "breast",
        "glandular cells"
      ],
      [
        "breast",
        "myoepithelial cells"
      ],
      [
        "bronchus",
        "respiratory epithelial cells"
      ],
      [
        "caudate",
        "glial cells"
      ],
      [
        "caudate",
        "neuronal cells"
      ],
      [
        "cerebellum",
        "Purkinje cells"
      ],
      [
        "cerebellum",
        "cells in granular layer"
      ],
      [
        "cerebellum",
        "cells in molecular layer"
      ],
      [
        "cerebral cortex",
        "endothelial cells"
      ],
      [
        "cerebral cortex",
        "glial cells"
      ],
      [
        "cerebral cortex",
        "neuronal cells"
      ],
      [
        "cerebral cortex",
        "neuropil"
      ],
      [
        "cervix",
        "glandular cells"
      ],
      [
        "cervix",
        "squamous epithelial cells"
      ],
      [
        "colon",
        "endothelial cells"
      ],
      [
        "colon",
        "glandular cells"
      ],
      [
        "colon",
        "peripheral nerve/ganglion"
      ],
      [
        "duodenum",
        "glandular cells"
      ],
      [
        "endometrium 1",
        "cells in endometrial stroma"
      ],
      [
        "endometrium 1",
        "glandular cells"
      ],
      [
        "endometrium 2",
        "cells in endometrial stroma"
      ],
      [
        "endometrium 2",
        "glandular cells"
      ],
      [
        "epididymis",
        "glandular cells"
      ],
      [
        "esophagus",
        "squamous epithelial cells"
      ],
      [
        "fallopian tube",
        "glandular cells"
      ],
      [
        "gallbladder",
        "glandular cells"
      ],
      [
        "heart muscle",
        "cardiomyocytes"
      ],
      [
        "hippocampus",
        "glial cells"
      ],
      [
        "hippocampus",
        "neuronal cells"
      ],
      [
        "kidney",
        "cells in glomeruli"
      ],
      [
        "kidney",
        "cells in tubules"
      ],
      [
        "liver",
        "cholangiocytes"
      ],
      [
        "liver",
        "hepatocytes"
      ],
      [
        "lung",
        "alveolar cells"
      ],
      [
        "lung",
        "macrophages"
      ],
      [
        "lymph node",
        "germinal center cells"
      ],
      [
        "lymph node",
        "non-germinal center cells"
      ],
      [
        "nasopharynx",
        "respiratory epithelial cells"
      ],
      [
        "oral mucosa",
        "squamous epithelial cells"
      ],
      [
        "ovary",
        "follicle cells"
      ],
      [
        "ovary",
        "ovarian stroma cells"
      ],
      [
        "pancreas",
        "exocrine glandular cells"
      ],
      [
        "pancreas",
        "pancreatic endocrine cells"
      ],
      [
        "parathyroid gland",
        "glandular cells"
      ],
      [
        "placenta",
        "decidual cells"
      ],
      [
        "placenta",
        "trophoblastic cells"
      ],
      [
        "prostate",
        "glandular cells"
      ],
      [
        "rectum",
        "glandular cells"
      ],
      [
        "salivary gland",
        "glandular cells"
      ],
      [
        "seminal vesicle",
        "glandular cells"
      ],
      [
        "skeletal muscle",
        "myocytes"
      ],
      [
        "skin 1",
        "Langerhans"
      ],
      [
        "skin 1",
        "fibroblasts"
      ],
      [
        "skin 1",
        "keratinocytes"
      ],
      [
        "skin 1",
        "melanocytes"
      ],
      [
        "skin 2",
        "epidermal cells"
      ],
      [
        "small intestine",
        "glandular cells"
      ],
      [
        "smooth muscle",
        "smooth muscle cells"
      ],
      [
        "soft tissue 1",
        "fibroblasts"
      ],
      [
        "soft tissue 1",
        "peripheral nerve"
      ],
      [
        "soft tissue 2",
        "fibroblasts"
      ],
      [
        "soft tissue 2",
        "peripheral nerve"
      ],
      [
        "spleen",
        "cells in red pulp"
      ],
      [
        "spleen",
        "cells in white pulp"
      ],
      [
        "stomach 1",
        "glandular cells"
      ],
      [
        "stomach 2",
        "glandular cells"
      ],
      [
        "testis",
        "Leydig cells"
      ],
      [
        "testis",
        "cells in seminiferous ducts"
      ],
      [
        "thyroid gland",
        "glandular cells"
      ],
      [
        "tonsil",
        "germinal center cells"
      ],
      [
        "tonsil",
        "non-germinal center cells"
      ],
      [
        "tonsil",
        "squamous epithelial cells"
      ],
      [
        "urinary bladder",
        "urothelial cells"
      ],
      [
        "vagina",
        "squamous epithelial cells"
      ]
    ]
  },
  "candidate_universe": "All registered published nomination sets; source scopes and targeted selections are preserved. No minimum-cover preselection.",
  "strict_rna_rule": "Every positive estimate (>0 nTPM), complete routine bulk RNA, no positive outside scope; raw IHC Low/Medium/High/Ascending/Descending considered.",
  "unreliable_ihc_rule": "Existing adaptive policy ignores reviewed cross-reactive IHC; strict sensitivity retains raw outside detections and otherwise marks unreliable IHC unresolved.",
  "single_cell_rna": "Not part of these two historical RNA/IHC filtering policies; unsited cell labels cannot establish complete anatomical coverage.",
  "baseline_parity": "Exact adaptive reproductive gene-set equality to cta_extended_gene_ids verified",
  "python": "3.12.6",
  "packages": {
    "pandas": "3.0.5",
    "numpy": "2.5.2",
    "matplotlib": "3.11.1",
    "reportlab": "5.0.1",
    "pypdf": "6.19.0"
  },
  "implementation_sha256": {
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    "scripts/cta_scope_report_render.py": "989c9b9e235856d5690c3395d9d090fcaa6e014179cacef22440bf7bd21ac615",
    "oncoref/cta.py": "aefd16716e7a6dbe97991c398432ce85c978049066aa89ce47e501fc49a00c56",
    "oncoref/cta_regen.py": "6c8dec187ee9c99862f48060b9a35d6e9da1437d1afac5a05fa8d714453341cb",
    "oncoref/normal_tissues.py": "219875c6d9790e2207946955abc3442a0963bd5fe22a36a2ba47a794fd6f6cb4"
  },
  "packaged_input_sha256": {
    "cancer-testis-antigens-extended.csv": "9640d314b6ac6748f6ac3fbe394969cd6734033e049bce68e6960a5a0700508a",
    "cta-specificity-audit.csv": "ddfd7e6097beadf6593397b9364c8a3f57a76ee7c1f201c2d0f1602f37b3fd98",
    "cta-ihc-unreliable.csv": "57ec0ec264c68eed9b7d3c22090e9df252a53fed5850fe79caf5bc1607a0ecb2",
    "cta-publication-sources.csv": "31d01d31a607054910b89edb5121e779761d1b1c22d6a09b698f66c0919abd70",
    "cta-publication-membership.csv": "0c233c84e7dd49f1f305f18f06f54e65d28d881e492c4e40777fddedf08e9578",
    "normal-tissue-taxonomy.yaml": "d3d4abf10a1b69c1d94ac2bdcc660e587d228b20621a4dfb0856b2e5fc3db394",
    "normal-tissue-mappings.csv": "9e852c13dfea2638e804f855fef8d7a19c7fe5902ae55c9aee1b094e43eca4f5"
  },
  "outputs": {
    "candidate-decisions.csv": "33a20f18d17559c7034c8c4eccddb35169c0f4fc1e7e8971b2de64fc28efa9ce",
    "cta-tissue-scope-report.pdf": "95b266928b6c4cf92f7694d03ac06ebe7d6816682be074a6f6feab4b7f8471dc",
    "disposable-gains.csv": "8960c5f01319d0cb28fd57bb0c17ea8b07c508c171ba596f30519249ae0144f3",
    "evidence-coverage.pdf": "341d92e3d7d8e715e896d35fcb06011295ff42d7b0262510b0ab1ec6a61f07dc",
    "evidence-coverage.png": "a8ca71ba531616b31fa9b6238eb5f917de3e1da7f0baf194d7a1844623b0caec",
    "evidence-status-counts.csv": "cab771d1e1edf83359ffab4be525e5f4bb340357a6692d77b494ff5f1f032696",
    "filtering-stages.pdf": "15c499f5cbe4da8ea2d2a380a3dfe73ab5995d1cafdf8cd6d69d9eed774ddd8a",
    "filtering-stages.png": "adc12f4a999800791aae3cc71bf36f4343e35d6d9d597bee9201e67124bc6ec2",
    "historical-only-candidates.csv": "07293bcff12ee5867bc8c67f7495ac8e2e1d93813f7836887c25bb5a53aa2e91",
    "index.md": "4977bdb47a3e1fc107b7ac41e7c8ffb0aadbb51b548db2f57a7f5f6cb8efb91a",
    "normal-observations.csv.gz": "f1fbcb17b583d6f5fa27630271a29bfde13792ee6158dcf71f65961ed07a67e9",
    "publication-sources.csv": "9b344e1167e31ff4d39953c4b712fa25c1abfc7fda37de3607e50ef1e4e2b4cb",
    "scope-summary.csv": "77f89043f59ec1d25458045bcc81f782efb74462deb508c84f48289d531dddd1",
    "source-counts.csv": "1c58d94159bd04339716fec1810c87782d847d920229e133e8ee132879a8c861",
    "source-intake.pdf": "f255eefd932d502b41092df8ebca2a6db45537b2ed756b3833db0bc36cc540e3",
    "source-intake.png": "b07d3854109dfac1ab22120eae691777354e540d5f6218e31a75a7e1cd8bc89f",
    "source-membership.csv.gz": "a506dee098bf48cb73375c6c5f85cae63dbf8cf3900c82b08f3dcb7461b82c28",
    "source-retention.pdf": "5932d81368f7cbf5bbfadb4f869deac4277db2d46533d3af95a2c0bd1e9fd1c8",
    "source-retention.png": "289a327f428df10992d3245d14b7a2a82384ecfee27065cf898a507b84f303a8",
    "tissue-taxonomy.json": "731aa32338c65cb9cc2e93b13fe8bf3253f7ac9d5fee8a3fa7b46cf7400ef88c"
  }
}