{
  "schema": "oncoref.normal-tissue-taxonomy",
  "schema_version": 1,
  "policy_version": "2026-10-19.2",
  "taxon_ids": [
    9606,
    9615,
    10090
  ],
  "references": {
    "blagosklonny2003": {
      "title": "Tissue-selective therapy of cancer",
      "url": "https://doi.org/10.1038/sj.bjc.6601256",
      "kind": "conceptual_minireview",
      "scope": "Proposed examples: melanocytes, prostate, testis, breast, ovary; not an exhaustive or clinically validated whitelist."
    },
    "openstax_female": {
      "title": "Anatomy and Physiology: Female Reproductive System",
      "url": "https://openstax.org/books/anatomy-and-physiology/pages/27-2-anatomy-and-physiology-of-the-female-reproductive-system",
      "kind": "anatomy",
      "scope": "Reproductive organs, ovarian compartments, and mammary glands as accessory reproductive organs."
    },
    "openstax_male": {
      "title": "Anatomy and Physiology: Male Reproductive System",
      "url": "https://openstax.org/books/anatomy-and-physiology/pages/27-1-anatomy-and-physiology-of-the-male-reproductive-system",
      "kind": "anatomy",
      "scope": "Testis, excurrent ducts, accessory glands and external genitalia."
    },
    "mouse_anatomy": {
      "title": "The Anatomy of the Laboratory Mouse, Margaret J. Cook",
      "url": "https://www.informatics.jax.org/cookbook/chapters/contents2.shtml",
      "kind": "comparative_anatomy",
      "scope": "Mouse reproductive anatomy; anatomical applicability does not establish therapeutic tolerability."
    },
    "dog_anatomy": {
      "title": "Male reproductive pelvic and external genitalia, ICAR-IVRI",
      "url": "https://veterinaryanatomy.com/atlas/hindlimb-pelvis/splanchnology/male-reproductive-pelvic-and-external-genitalia/",
      "kind": "comparative_anatomy",
      "scope": "Dog lacks seminal vesicles and bulbourethral glands; prostate is its principal accessory sex gland."
    },
    "hpa_tissues": {
      "title": "Human Protein Atlas tissue and cell-type definitions",
      "url": "https://www.proteinatlas.org/humanproteome/tissue/data",
      "kind": "source_documentation",
      "scope": "Source tissue and cell-type labels; version-specific mapping rows refer to the v23 files."
    },
    "hpa_skin": {
      "title": "Human Protein Atlas: skin histology",
      "url": "https://www.proteinatlas.org/learn/dictionary/normal/skin",
      "kind": "source_documentation",
      "scope": "Skin melanocytes and hair follicles are separate compartments from other skin cells."
    },
    "hpa_pigment": {
      "title": "Human Protein Atlas: pigment cells",
      "url": "https://www.proteinatlas.org/humanproteome/single%2Bcell/single%2Bcell%2Btype/pigment%2Bcells",
      "kind": "source_documentation",
      "scope": "Skin melanocytes distinct from retinal pigment epithelial cells."
    },
    "johnson2009": {
      "title": "Gene therapy with human and mouse T-cell receptors mediates cancer regression and targets normal tissues expressing cognate antigen",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC2929689/",
      "kind": "clinical_study",
      "scope": "Melanocyte-antigen targeting can affect skin, eye and ear; a cutaneous exception must not include ocular or inner-ear compartments."
    },
    "purba2019": {
      "title": "CDK4/6 inhibition mitigates stem cell damage in a novel model for taxane-induced alopecia",
      "url": "https://pubmed.ncbi.nlm.nih.gov/31512803/",
      "kind": "human_ex_vivo_study",
      "scope": "Follicular matrix and stem-cell injury differ; follicular toxicity can cause persistent alopecia. Supports compartment distinction, not safety of immune ablation."
    },
    "nci_alopecia": {
      "title": "Hair Loss (Alopecia) and Cancer Treatment",
      "url": "https://www.cancer.gov/about-cancer/treatment/side-effects/hair-loss",
      "kind": "clinical_information",
      "scope": "Alopecia is a recognized cancer-treatment toxicity; regrowth and permanence depend on treatment."
    },
    "barkbase2019": {
      "title": "BarkBase: Epigenomic Annotation of Canine Genomes",
      "url": "https://doi.org/10.3390/genes10060433",
      "kind": "primary_atlas",
      "scope": "Canine adult and embryonic tissues; retain source developmental-stage terminology."
    },
    "fetal_atlas2020": {
      "title": "A human cell atlas of fetal gene expression",
      "url": "https://pubmed.ncbi.nlm.nih.gov/33184181/",
      "kind": "primary_atlas",
      "scope": "Fetal organ and cell identities are stage-specific and must not stand for adult-organ evidence."
    },
    "project_policy": {
      "title": "oncoref normal-tissue scope policy, version 1",
      "url": "https://github.com/pirl-unc/oncoref/blob/main/docs/normal-tissue-scopes.md",
      "kind": "project_definition",
      "scope": "Reproductive includes reproductive organs, mammary tissue, placenta, extraembryonic, embryonic and fetal contexts. Disposable normal is a conditional research scope, not a clinical safety claim. The expanded permitted scope adds whole skin, salivary gland and thymus by project request. Tiered RNA ceilings are project screening parameters; IHC detections outside the permitted scope remain exclusions."
    },
    "nci_organ_inflammation": {
      "title": "Immunotherapy and Organ-Related Inflammation",
      "url": "https://www.cancer.gov/about-cancer/treatment/side-effects/organ-inflammation",
      "kind": "clinical_information",
      "scope": "Organ-specific immune injury supports conservative review of normal expression. Does not validate this project's tissue tiers or numerical cutoffs."
    },
    "niddk_adrenal": {
      "title": "Definition and Facts of Adrenal Insufficiency and Addison's Disease",
      "url": "https://www.niddk.nih.gov/health-information/endocrine-diseases/adrenal-insufficiency-addisons-disease/definition-facts",
      "kind": "clinical_information",
      "scope": "Adrenal crisis can be life-threatening. Supports including adrenal and pituitary contexts in the conservative vital tier; not an RNA threshold validation."
    },
    "mouse_coagulating": {
      "title": "MGI Adult Mouse Anatomy: coagulating gland (MA:0000402)",
      "url": "https://www.informatics.jax.org/vocab/gxd/ma_ontology/MA%3A0000402",
      "kind": "anatomy_ontology",
      "scope": "Mouse male reproductive gland, synonym prostate gland anterior lobe."
    },
    "mouse_lymphoid": {
      "title": "Janeway Immunobiology: Organization of the mucosal immune system",
      "url": "https://nerd.wwnorton.com/ebooks/epub/janeway10/EPUB/content/12.1-chapter12.xhtml",
      "kind": "comparative_anatomy",
      "scope": "Mouse nasal-associated lymphoid tissue is not anatomically a tonsil."
    }
  },
  "concepts": {
    "testis": {
      "label": "testis",
      "parents": [],
      "aliases": [
        "testes"
      ],
      "references": [
        "openstax_male",
        "mouse_anatomy",
        "dog_anatomy"
      ]
    },
    "spermatogonium": {
      "label": "spermatogonium",
      "parents": [
        "testis"
      ],
      "aliases": [
        "spermatogonia",
        "spermatogonia cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "spermatocyte": {
      "label": "spermatocyte",
      "parents": [
        "testis"
      ],
      "aliases": [
        "spermatocytes",
        "pachytene spermatocytes",
        "preleptotene spermatocytes"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "spermatid": {
      "label": "spermatid",
      "parents": [
        "testis"
      ],
      "aliases": [
        "spermatids",
        "early spermatids",
        "late spermatids",
        "round or early spermatids",
        "elongated or late spermatids"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "spermatozoon": {
      "label": "spermatozoon",
      "parents": [],
      "aliases": [
        "spermatozoa",
        "sperm"
      ],
      "references": [
        "hpa_tissues"
      ],
      "notes": "Male germ cells without an inferred anatomical site; a sperm observation alone does not establish testis restriction."
    },
    "sertoli_cell": {
      "label": "sertoli cell",
      "parents": [
        "testis"
      ],
      "aliases": [
        "sertoli cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "leydig_cell": {
      "label": "leydig cell",
      "parents": [
        "testis"
      ],
      "aliases": [
        "leydig cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "testicular_peritubular_cell": {
      "label": "testicular peritubular cell",
      "parents": [
        "testis"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "seminiferous_tubule": {
      "label": "seminiferous tubule",
      "parents": [
        "testis"
      ],
      "aliases": [
        "seminiferous tubules",
        "cells in seminiferous ducts"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "ovary": {
      "label": "ovary",
      "parents": [],
      "aliases": [
        "ovaries"
      ],
      "references": [
        "openstax_female",
        "mouse_anatomy"
      ]
    },
    "oocyte": {
      "label": "oocyte",
      "parents": [
        "ovary"
      ],
      "aliases": [
        "oocytes",
        "ovum",
        "ova"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "ovarian_follicle": {
      "label": "ovarian follicle",
      "parents": [
        "ovary"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "granulosa_cell": {
      "label": "granulosa cell",
      "parents": [
        "ovarian_follicle"
      ],
      "aliases": [
        "granulosa cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "ovarian_stromal_cell": {
      "label": "ovarian stromal cell",
      "parents": [
        "ovary"
      ],
      "aliases": [
        "ovarian stromal cells",
        "ovarian stroma cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "theca_cell": {
      "label": "theca cell",
      "parents": [
        "ovary"
      ],
      "aliases": [
        "theca cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "corpus_luteum": {
      "label": "corpus luteum",
      "parents": [
        "ovary"
      ],
      "aliases": [
        "corpora lutea"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "epididymis": {
      "label": "epididymis",
      "parents": [],
      "aliases": [
        "epididymides"
      ],
      "references": [
        "openstax_male",
        "mouse_anatomy",
        "dog_anatomy"
      ]
    },
    "vas_deferens": {
      "label": "vas deferens",
      "parents": [],
      "aliases": [
        "ductus deferens",
        "deferent duct"
      ],
      "references": [
        "openstax_male",
        "mouse_anatomy",
        "dog_anatomy"
      ]
    },
    "prostate": {
      "label": "prostate",
      "parents": [],
      "aliases": [
        "prostate gland"
      ],
      "references": [
        "openstax_male",
        "mouse_anatomy",
        "dog_anatomy"
      ]
    },
    "penis": {
      "label": "penis",
      "parents": [],
      "aliases": [],
      "references": [
        "openstax_male",
        "mouse_anatomy",
        "dog_anatomy"
      ]
    },
    "seminal_vesicle": {
      "label": "seminal vesicle",
      "parents": [],
      "aliases": [
        "seminal vesicles",
        "vesicular gland"
      ],
      "references": [
        "openstax_male",
        "mouse_anatomy",
        "dog_anatomy"
      ],
      "taxon_ids": [
        9606,
        10090
      ]
    },
    "bulbourethral_gland": {
      "label": "bulbourethral gland",
      "parents": [],
      "aliases": [
        "bulbourethral glands",
        "cowper gland"
      ],
      "references": [
        "openstax_male",
        "mouse_anatomy",
        "dog_anatomy"
      ],
      "taxon_ids": [
        9606,
        10090
      ]
    },
    "coagulating_gland": {
      "label": "coagulating gland",
      "parents": [
        "prostate"
      ],
      "aliases": [],
      "references": [
        "mouse_anatomy",
        "mouse_coagulating"
      ],
      "taxon_ids": [
        10090
      ],
      "notes": "Mouse anterior prostate/coagulating gland; no dog counterpart is assigned."
    },
    "fallopian_tube": {
      "label": "fallopian tube",
      "parents": [],
      "aliases": [
        "fallopian tubes",
        "oviduct",
        "oviducts",
        "uterine tube"
      ],
      "references": [
        "openstax_female",
        "mouse_anatomy"
      ]
    },
    "uterus": {
      "label": "uterus",
      "parents": [],
      "aliases": [
        "uterine corpus"
      ],
      "references": [
        "openstax_female",
        "mouse_anatomy"
      ]
    },
    "vagina": {
      "label": "vagina",
      "parents": [],
      "aliases": [],
      "references": [
        "openstax_female",
        "mouse_anatomy"
      ]
    },
    "vulva": {
      "label": "vulva",
      "parents": [],
      "aliases": [],
      "references": [
        "openstax_female",
        "mouse_anatomy"
      ]
    },
    "clitoris": {
      "label": "clitoris",
      "parents": [],
      "aliases": [],
      "references": [
        "openstax_female",
        "mouse_anatomy"
      ]
    },
    "endometrium": {
      "label": "endometrium",
      "parents": [
        "uterus"
      ],
      "aliases": [
        "endometrium 1",
        "endometrium 2",
        "uterine endometrium"
      ],
      "references": [
        "openstax_female",
        "mouse_anatomy"
      ]
    },
    "myometrium": {
      "label": "myometrium",
      "parents": [
        "uterus"
      ],
      "aliases": [],
      "references": [
        "openstax_female",
        "mouse_anatomy"
      ]
    },
    "cervix": {
      "label": "cervix",
      "parents": [
        "uterus"
      ],
      "aliases": [
        "cervix uteri",
        "uterine cervix"
      ],
      "references": [
        "openstax_female",
        "mouse_anatomy"
      ]
    },
    "uterine_horn": {
      "label": "uterine horn",
      "parents": [
        "uterus"
      ],
      "aliases": [
        "uterine horns"
      ],
      "references": [
        "mouse_anatomy",
        "barkbase2019"
      ],
      "taxon_ids": [
        9615,
        10090
      ]
    },
    "mammary_tissue": {
      "label": "Mammary tissue (whole breast or mammary gland)",
      "parents": [],
      "aliases": [
        "breast",
        "mammary gland",
        "mammary glands",
        "mammary tissue",
        "lactating breast"
      ],
      "references": [
        "openstax_female",
        "blagosklonny2003",
        "mouse_anatomy"
      ],
      "notes": "Whole-organ observation includes stroma; it does not establish glandular-cell restriction. Source sex and lactation state remain separate metadata."
    },
    "mammary_glandular": {
      "label": "Mammary glandular epithelium",
      "parents": [
        "mammary_tissue"
      ],
      "aliases": [
        "mammary glandular tissue",
        "breast glandular cells",
        "breast myoepithelial cells"
      ],
      "references": [
        "openstax_female",
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "placenta": {
      "label": "placenta",
      "parents": [],
      "aliases": [
        "placental tissue"
      ],
      "references": [
        "hpa_tissues",
        "project_policy"
      ],
      "notes": "Placenta-specific evidence qualifies directly; maternal/fetal compartment resolution is not required."
    },
    "trophoblast": {
      "label": "trophoblast",
      "parents": [
        "placenta"
      ],
      "aliases": [
        "trophoblasts",
        "trophoblastic cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "cytotrophoblast": {
      "label": "cytotrophoblast",
      "parents": [
        "placenta"
      ],
      "aliases": [
        "cytotrophoblasts"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "syncytiotrophoblast": {
      "label": "syncytiotrophoblast",
      "parents": [
        "placenta"
      ],
      "aliases": [
        "syncytiotrophoblasts"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "extravillous_trophoblast": {
      "label": "extravillous trophoblast",
      "parents": [
        "placenta"
      ],
      "aliases": [
        "extravillous trophoblasts"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "placental_decidua": {
      "label": "placental decidua",
      "parents": [
        "placenta"
      ],
      "aliases": [
        "placental decidual cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "hofbauer_cell": {
      "label": "hofbauer cell",
      "parents": [
        "placenta"
      ],
      "aliases": [
        "hofbauer cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "amnion": {
      "label": "amnion",
      "parents": [],
      "aliases": [
        "amniotic membrane"
      ],
      "references": [
        "project_policy",
        "fetal_atlas2020"
      ]
    },
    "chorion": {
      "label": "chorion",
      "parents": [],
      "aliases": [
        "chorionic membrane"
      ],
      "references": [
        "project_policy",
        "fetal_atlas2020"
      ]
    },
    "yolk_sac": {
      "label": "yolk sac",
      "parents": [],
      "aliases": [],
      "references": [
        "project_policy",
        "fetal_atlas2020"
      ]
    },
    "allantois": {
      "label": "allantois",
      "parents": [],
      "aliases": [],
      "references": [
        "project_policy",
        "fetal_atlas2020"
      ]
    },
    "umbilical_cord": {
      "label": "umbilical cord",
      "parents": [],
      "aliases": [],
      "references": [
        "project_policy",
        "fetal_atlas2020"
      ]
    },
    "embryo": {
      "label": "embryo",
      "parents": [],
      "aliases": [
        "whole embryo",
        "embryonic tissue"
      ],
      "references": [
        "barkbase2019",
        "project_policy"
      ]
    },
    "fetus": {
      "label": "fetus",
      "parents": [],
      "aliases": [
        "foetus",
        "whole fetus",
        "fetal tissue",
        "foetal tissue"
      ],
      "references": [
        "fetal_atlas2020",
        "project_policy"
      ]
    },
    "skin": {
      "label": "skin",
      "parents": [],
      "aliases": [
        "skin 1",
        "skin 2",
        "zone of skin"
      ],
      "references": [
        "hpa_skin"
      ]
    },
    "cutaneous_melanocyte": {
      "label": "Cutaneous melanocytes",
      "parents": [
        "skin"
      ],
      "aliases": [
        "skin melanocytes",
        "cutaneous melanocytes",
        "epidermal melanocytes"
      ],
      "references": [
        "blagosklonny2003",
        "johnson2009",
        "hpa_skin"
      ],
      "notes": "Only cutaneous melanocytes; an unsited melanocyte label, eye, retina and inner ear do not qualify."
    },
    "hair_follicle": {
      "label": "Hair follicle compartment",
      "parents": [
        "skin"
      ],
      "aliases": [
        "hair follicles",
        "hair follicle epithelium",
        "follicular keratinocytes"
      ],
      "references": [
        "nci_alopecia",
        "purba2019",
        "hpa_skin"
      ],
      "notes": "Conditional acceptance of alopecia; includes follicular epithelial compartments. A bulk follicle does not resolve matrix versus bulge/stem-cell involvement or reversibility."
    },
    "adipose_tissue": {
      "label": "adipose tissue",
      "parents": [],
      "aliases": [
        "adipose"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "adrenal_gland": {
      "label": "adrenal gland",
      "parents": [],
      "aliases": [
        "adrenal"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "brain": {
      "label": "brain",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "amygdala": {
      "label": "amygdala",
      "parents": [
        "brain"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "basal_ganglia": {
      "label": "basal ganglia",
      "parents": [
        "brain"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "cerebellum": {
      "label": "cerebellum",
      "parents": [
        "brain"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "cerebral_cortex": {
      "label": "cerebral cortex",
      "parents": [
        "cerebrum"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "choroid_plexus": {
      "label": "choroid plexus",
      "parents": [
        "brain"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "hippocampus": {
      "label": "hippocampus",
      "parents": [
        "hippocampal_formation"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "hypothalamus": {
      "label": "hypothalamus",
      "parents": [
        "brain"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "midbrain": {
      "label": "midbrain",
      "parents": [
        "brain"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "dorsal_raphe": {
      "label": "dorsal raphe",
      "parents": [
        "brain"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "substantia_nigra": {
      "label": "substantia nigra",
      "parents": [
        "brain"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "spinal_cord": {
      "label": "spinal cord",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "retina": {
      "label": "retina",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "eye": {
      "label": "eye",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "inner_ear": {
      "label": "inner ear",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "heart": {
      "label": "heart",
      "parents": [],
      "aliases": [
        "heart muscle"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "kidney": {
      "label": "kidney",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "liver": {
      "label": "liver",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "lung": {
      "label": "lung",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "pancreas": {
      "label": "pancreas",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "thyroid_gland": {
      "label": "thyroid gland",
      "parents": [],
      "aliases": [
        "thyroid"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "parathyroid_gland": {
      "label": "parathyroid gland",
      "parents": [],
      "aliases": [
        "parathyroid"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "pituitary_gland": {
      "label": "pituitary gland",
      "parents": [],
      "aliases": [
        "pituitary"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "salivary_gland": {
      "label": "salivary gland",
      "parents": [],
      "aliases": [
        "salivary"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "bone_marrow": {
      "label": "bone marrow",
      "parents": [],
      "aliases": [
        "bonemarrow"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "blood": {
      "label": "blood",
      "parents": [],
      "aliases": [
        "white blood cells",
        "peripheral blood mononuclear cells"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "lymph_node": {
      "label": "lymph node",
      "parents": [],
      "aliases": [
        "lymphnode"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "spleen": {
      "label": "spleen",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "thymus": {
      "label": "thymus",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "tonsil": {
      "label": "tonsil",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues",
        "mouse_lymphoid"
      ],
      "taxon_ids": [
        9606,
        9615
      ]
    },
    "appendix": {
      "label": "appendix",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ],
      "taxon_ids": [
        9606
      ],
      "notes": "Human appendix label only; animal caecal lymphoid tissue is not mapped to vermiform appendix."
    },
    "esophagus": {
      "label": "esophagus",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "stomach": {
      "label": "stomach",
      "parents": [],
      "aliases": [
        "stomach 1",
        "stomach 2"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "colon": {
      "label": "colon",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "rectum": {
      "label": "rectum",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "small_intestine": {
      "label": "small intestine",
      "parents": [],
      "aliases": [
        "smallintestine"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "gallbladder": {
      "label": "gallbladder",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "urinary_bladder": {
      "label": "urinary bladder",
      "parents": [],
      "aliases": [
        "bladder"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "ureter": {
      "label": "ureter",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "skeletal_muscle": {
      "label": "skeletal muscle",
      "parents": [],
      "aliases": [
        "skeletalmuscle",
        "muscle tissue"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "smooth_muscle": {
      "label": "smooth muscle",
      "parents": [],
      "aliases": [
        "smooth muscle tissue"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "cartilage": {
      "label": "cartilage",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "soft_tissue": {
      "label": "soft tissue",
      "parents": [],
      "aliases": [
        "soft tissue 1",
        "soft tissue 2"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "peripheral_nerve": {
      "label": "peripheral nerve",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "endothelium": {
      "label": "endothelium",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "oral_mucosa": {
      "label": "oral mucosa",
      "parents": [],
      "aliases": [
        "buccal oral mucosa"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "nasopharynx": {
      "label": "nasopharynx",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "tongue": {
      "label": "tongue",
      "parents": [],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "head": {
      "label": "head",
      "parents": [],
      "aliases": [
        "heads"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "nail_bed": {
      "label": "nail bed",
      "parents": [
        "skin"
      ],
      "aliases": [],
      "references": [
        "hpa_tissues"
      ]
    },
    "foot": {
      "label": "foot",
      "parents": [],
      "aliases": [
        "sole of foot"
      ],
      "references": [
        "hpa_tissues"
      ]
    },
    "cerebrum": {
      "label": "cerebrum",
      "parents": [
        "brain"
      ],
      "aliases": [
        "cerebrum"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "caudate": {
      "label": "caudate",
      "parents": [
        "basal_ganglia"
      ],
      "aliases": [
        "caudate"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "hippocampal_formation": {
      "label": "hippocampal formation",
      "parents": [
        "brain"
      ],
      "aliases": [
        "hippocampal formation"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "frontal_cortex": {
      "label": "frontal cortex",
      "parents": [
        "cerebral_cortex"
      ],
      "aliases": [
        "frontalcortex"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "occipital_cortex": {
      "label": "occipital cortex",
      "parents": [
        "cerebral_cortex"
      ],
      "aliases": [
        "occipitalcortex"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "renal_cortex": {
      "label": "renal cortex",
      "parents": [
        "kidney"
      ],
      "aliases": [
        "kidneycortex"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "renal_medulla": {
      "label": "renal medulla",
      "parents": [
        "kidney"
      ],
      "aliases": [
        "kidneymedulla"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "left_atrium": {
      "label": "left atrium",
      "parents": [
        "heart"
      ],
      "aliases": [
        "leftatrium"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "right_atrium": {
      "label": "right atrium",
      "parents": [
        "heart"
      ],
      "aliases": [
        "rightatrium"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "left_ventricle": {
      "label": "left ventricle",
      "parents": [
        "heart"
      ],
      "aliases": [
        "leftventricle"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "right_ventricle": {
      "label": "right ventricle",
      "parents": [
        "heart"
      ],
      "aliases": [
        "rightventricle"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "duodenum": {
      "label": "duodenum",
      "parents": [
        "small_intestine"
      ],
      "aliases": [
        "duodenum"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "ileum": {
      "label": "ileum",
      "parents": [
        "small_intestine"
      ],
      "aliases": [
        "ileum"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "jejunum": {
      "label": "jejunum",
      "parents": [
        "small_intestine"
      ],
      "aliases": [
        "jejunum"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "bronchus": {
      "label": "bronchus",
      "parents": [],
      "aliases": [
        "bronchus"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "parotid_gland": {
      "label": "parotid gland",
      "parents": [
        "salivary_gland"
      ],
      "aliases": [
        "parotid gland"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    },
    "retinal_pigment_epithelium": {
      "label": "retinal pigment epithelium",
      "parents": [
        "retina"
      ],
      "aliases": [
        "retinal pigment epithelium"
      ],
      "references": [
        "hpa_tissues",
        "mouse_anatomy"
      ]
    }
  },
  "scopes": {
    "testis": {
      "roots": [
        "testis"
      ],
      "union": [],
      "aliases": [
        "male_strict"
      ],
      "description": "Testis and its explicitly mapped subcompartments."
    },
    "oocyte": {
      "roots": [
        "oocyte"
      ],
      "union": [],
      "aliases": [
        "female_strict"
      ],
      "description": "Oocytes only; bulk ovary and follicle cells do not imply oocyte expression."
    },
    "ovary": {
      "roots": [
        "ovary"
      ],
      "union": [],
      "aliases": [],
      "description": "Whole ovary and ovarian subcompartments, including oocytes."
    },
    "mammary_glandular": {
      "roots": [
        "mammary_glandular"
      ],
      "union": [],
      "aliases": [],
      "description": "Explicit mammary glandular epithelium; bulk breast/mammary samples are broader."
    },
    "mammary": {
      "roots": [
        "mammary_tissue"
      ],
      "union": [],
      "aliases": [],
      "description": "Mammary organ and its mapped subcompartments; lactation and sex retained separately."
    },
    "male_reproductive": {
      "roots": [
        "epididymis",
        "vas_deferens",
        "prostate",
        "seminal_vesicle",
        "bulbourethral_gland",
        "penis",
        "spermatozoon"
      ],
      "union": [
        "testis"
      ],
      "aliases": [
        "male_extended"
      ],
      "description": "Testis, spermatozoa, and species-applicable male reproductive ducts, accessory glands and penis."
    },
    "female_reproductive": {
      "roots": [
        "fallopian_tube",
        "uterus",
        "vagina",
        "vulva",
        "clitoris"
      ],
      "union": [
        "ovary",
        "mammary"
      ],
      "aliases": [
        "female_extended"
      ],
      "description": "Ovary, reproductive tract and mammary tissue; this anatomical grouping does not infer sample sex."
    },
    "placental": {
      "roots": [
        "placenta"
      ],
      "union": [],
      "aliases": [],
      "description": "Placenta, with or without further compartment annotation."
    },
    "extraembryonic": {
      "roots": [
        "amnion",
        "chorion",
        "yolk_sac",
        "allantois",
        "umbilical_cord"
      ],
      "union": [
        "placental"
      ],
      "aliases": [],
      "description": "Placenta and other extraembryonic tissues."
    },
    "embryonic": {
      "roots": [
        "embryo"
      ],
      "union": [],
      "aliases": [],
      "description": "Whole embryo or tissue explicitly sampled at an embryonic stage; source organ is retained."
    },
    "fetal": {
      "roots": [
        "fetus"
      ],
      "union": [],
      "aliases": [],
      "description": "Whole fetus or tissue explicitly sampled at a fetal stage; source organ is retained."
    },
    "reproductive_core": {
      "roots": [],
      "union": [
        "testis",
        "ovary",
        "placental"
      ],
      "aliases": [
        "core"
      ],
      "description": "Historical core anatomical union: testis, ovary and placenta."
    },
    "reproductive": {
      "roots": [],
      "union": [
        "male_reproductive",
        "female_reproductive",
        "extraembryonic",
        "embryonic",
        "fetal"
      ],
      "aliases": [
        "extended",
        "permissive"
      ],
      "description": "Project union across all reproductive-organ and developmental contexts."
    },
    "disposable_normal": {
      "roots": [
        "cutaneous_melanocyte",
        "hair_follicle"
      ],
      "union": [],
      "aliases": [],
      "description": "Conditional research exception for cutaneous melanocytes and hair follicles. Not all skin, pigment cells or normal tissues. Human rationale; animal tolerability is unvalidated."
    },
    "reproductive_or_disposable": {
      "roots": [],
      "union": [
        "reproductive",
        "disposable_normal"
      ],
      "aliases": [],
      "description": "Union of reproductive and conditionally disposable normal tissue contexts."
    },
    "permitted_normal": {
      "roots": [
        "skin",
        "salivary_gland",
        "thymus"
      ],
      "union": [
        "disposable_normal"
      ],
      "aliases": [],
      "description": "Project-requested normal-tissue allowance comprising whole skin and mapped skin compartments, salivary glands and thymus, plus the narrower disposable scope. Anatomical permission is not evidence of tolerable injury."
    },
    "reproductive_or_permitted_normal": {
      "roots": [],
      "union": [
        "reproductive",
        "permitted_normal"
      ],
      "aliases": [],
      "description": "Expanded project union of reproductive contexts and permitted normal tissues. Heart, lung, CNS, liver, pancreas, retina and muscle are outside."
    }
  },
  "screening_policies": {
    "tiered_cta": {
      "policy_id": "oncoref.cta-permitted-screen.2026-10-19.1",
      "permitted_scope": "reproductive_or_permitted_normal",
      "rna_source": "hpa_rna_consensus",
      "rna_source_version": "v23",
      "rna_species": "human",
      "rna_unit": "nTPM",
      "minimum_permitted_rna": 1.0,
      "positive_ihc_levels": [
        "Low",
        "Medium",
        "High",
        "Ascending",
        "Descending"
      ],
      "vital": {
        "maximum_rna": 1.0,
        "roots": [
          "heart",
          "lung",
          "bronchus",
          "brain",
          "spinal_cord",
          "liver",
          "kidney",
          "bone_marrow",
          "blood",
          "adrenal_gland",
          "pituitary_gland",
          "pancreas",
          "small_intestine",
          "skeletal_muscle",
          "smooth_muscle",
          "peripheral_nerve",
          "endothelium"
        ],
        "description": "Conservative project tier for critical organs and broadly sampled systems whose extensive injury can threaten life. Includes all mapped descendants."
      },
      "protected": {
        "maximum_rna": 5.0,
        "roots": [
          "adipose_tissue",
          "retina",
          "eye",
          "inner_ear",
          "thyroid_gland",
          "parathyroid_gland",
          "lymph_node",
          "spleen",
          "tonsil",
          "appendix",
          "esophagus",
          "stomach",
          "colon",
          "rectum",
          "gallbladder",
          "urinary_bladder",
          "ureter",
          "cartilage",
          "oral_mucosa",
          "nasopharynx",
          "tongue"
        ],
        "description": "Protected normal tissues outside the permitted scope, with a higher RNA ceiling but the same exclusion for any positive IHC. This tier does not assert that loss is harmless or that severe injury cannot be fatal."
      },
      "unresolved_roots": [
        "head",
        "foot",
        "soft_tissue"
      ],
      "references": [
        "project_policy",
        "hpa_tissues",
        "nci_organ_inflammation",
        "niddk_adrenal"
      ],
      "coverage": "Complete routine bulk RNA is required. Missing or partial IHC is reported explicitly and cannot establish protein absence. Unresolved positive anatomy, unusable measurements and reviewed unreliable IHC block retention.",
      "species_note": "Anatomical tiers apply to human, dog and mouse. The numerical policy is calibrated only as a project screen for human HPA v23 nTPM; numerical thresholds and clinical tolerability do not transfer to other species."
    }
  },
  "source_artifacts": [
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      "source_id": "hpa_single_cell",
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      "taxon_id": 9615,
      "source_id": "pfizer-dog-protein",
      "source_version": "MSV000099744-update-2026-03-23",
      "path": "species/dog/pfizer-dog-protein-samples.json",
      "sha256": "c009998a3525758c31295b881b900d78461b99ddeda1af649d9161155218b5b2",
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      "source_version": "2025-05-06-publisher-version",
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      "sha256": "825450315ad1433b7c98d49a2e8c715f3e3760ca2889c5bb1a1041c2bfcdc391",
      "hashed_content": "source document in the CTA evidence receipt"
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    {
      "taxon_id": 9615,
      "source_id": "nemec2019",
      "source_version": "2019-article-abstract-europepmc-2026-10-13",
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      "sha256": "6f27557f46c3607dde7bb32c158e7cc0a26adc6a75a230dbdf9dfc748bd11b73",
      "hashed_content": "source document in the CTA evidence receipt"
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  ],
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}