01_create_metadata_workflow_schema.ipynb

{
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  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Tutorial 1: Create a Metadata Schema & Workflow \n",
    "\n",
    "The metadata schema presented in this demo is specific to metadata downloaded for the raw RNA-seq CCLE samples, obtained from the SRA project & cBioportal. \n",
    "\n",
    "Additionally, we have developed two additional generic NGS metadata schemas for bulk RNA-sequencing and whole exome sequencing to serve as a jumping off point for tailoring to in-house protocols and experiments. For more information on workflows or to check out generic NGS metadata templates, please refer to the Quilt Open package [examples/ngs-metadata-schemas](https://open.quiltdata.com/b/quilt-example/packages/examples/ngs-metadata-schemas)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# config.yml\n",
    "\n",
    "`./demo_data/workflows/config.yml`\n",
    "\n",
    "```yaml\n",
    "version:\n",
    "  base: \"1\"\n",
    "  catalog: \"1\"\n",
    "is_workflow_required: true\n",
    "workflows:\n",
    "  sra-raw-data:\n",
    "    name: Upload raw data obtained from the Sequence Read Archive (SRA)\n",
    "    metadata_schema: sra-raw-data\n",
    "    handle_pattern: ^ccle/20[0-9]{6}_PRJNA[0-9]{6}_SRR[0-9]{7}$\n",
    "    is_message_required: true\n",
    "schemas:\n",
    "  sra-raw-data:\n",
    "    url: s3://quilt-example-bucket/ccle/workflows/sra-raw-data.schema.json\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# sra-raw-data.json\n",
    "\n",
    "`./demo_data/workflows/sra-raw-data.json`\n",
    "\n",
    "```json\n",
    "\n",
    "{\n",
    "    \"$schema\": \"http://json-schema.org/draft-07/schema#\",\n",
    "    \"$id\": \"sra-raw-data\",\n",
    "    \"title\": \"SRA Raw Data\",\n",
    "    \"Description\": \"Metadata required for public data obtained from the Sequence Read Archive (SRA)\",\n",
    "    \"type\": \"object\",\n",
    "    \"additionalProperties\": false,\n",
    "    \"required\": [\n",
    "        \"Run\",\n",
    "        \"AssayType\",\n",
    "        \"AvgSpotLen\",\n",
    "        \"BiomaterialProvider\",\n",
    "        \"BioProject\",\n",
    "        \"BioSample\",\n",
    "        \"BioSampleModel\",\n",
    "        \"CellLine\",\n",
    "        \"CenterName\",\n",
    "        \"Consent\",\n",
    "        \"Disease\",\n",
    "        \"DiseaseStage\",\n",
    "        \"Ethnicity\",\n",
    "        \"Experiment\",\n",
    "        \"FlowCellID\",\n",
    "        \"Instrument\",\n",
    "        \"Isolate\",\n",
    "        \"LibraryName\",\n",
    "        \"LibraryLayout\",\n",
    "        \"LibrarySelection\",\n",
    "        \"LibrarySource\",\n",
    "        \"Organism\",\n",
    "        \"Platform\",\n",
    "        \"ReleaseDate\",\n",
    "        \"SampleName\",\n",
    "        \"SampleType\",\n",
    "        \"Sex\",\n",
    "        \"SRAStudy\",\n",
    "        \"Tissue\",\n",
    "        \"CreateDate\",\n",
    "        \"Version\"\n",
    "    ],\n",
    "    \"properties\": {\n",
    "        \"Run\": {\n",
    "            \"description\": \"SRA run ID for sample\",\n",
    "            \"type\": \"string\",\n",
    "            \"minLength\": 10,\n",
    "            \"maxLength\": 10,\n",
    "            \"pattern\": \"^SRR[0-9]{7}$\"\n",
    "        },\n",
    "        \"Age\": {\n",
    "            \"description\": \"Age of patient sample was collected from in years\",\n",
    "            \"type\": \"number\",\n",
    "            \"exclusiveMinimum\": 0\n",
    "        },\n",
    "        \"AssayType\": {\n",
    "            \"description\": \"NGS assay performed to generate data\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"RNA-Seq\",\n",
    "                \"WES\",\n",
    "                \"WGS\",\n",
    "                \"CRISPR\"\n",
    "            ]\n",
    "        },\n",
    "        \"AssemblyName\": {\n",
    "            \"description\": \"GenBank assembly accession for reference genome\",\n",
    "            \"type\": \"string\",\n",
    "            \"pattern\": \"^GCA\"\n",
    "        },\n",
    "        \"AvgSpotLen\": {\n",
    "            \"description\": \"Average number of base pairs in a single spot (aka read length)\",\n",
    "            \"type\": \"integer\",\n",
    "            \"enum\": [\n",
    "                198,\n",
    "                202\n",
    "            ]\n",
    "        },\n",
    "        \"Bases\": {\n",
    "            \"description\": \"Total number of nucleotide bases in a sequencing dataset for a given sample\",\n",
    "            \"type\": \"integer\",\n",
    "            \"exclusiveMinimum\": 0\n",
    "        },\n",
    "        \"BiomaterialProvider\": {\n",
    "            \"description\": \"Name of provider supplying input sample material\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"BioProject\": {\n",
    "            \"description\": \"SRA term. Research project or study and encompasses various types of data, including sequencing data, associated with that project\",\n",
    "            \"type\": \"string\",\n",
    "            \"minLength\": 11,\n",
    "            \"maxLength\": 11,\n",
    "            \"pattern\": \"^PRJNA[0-9]{6}$\"\n",
    "        },\n",
    "        \"BioSample\": {\n",
    "            \"description\": \"SRA term. Biological sample that has been used in an experiment or study. Each BioSample record contains information about the biological source, such as the organism, tissue, and individual characteristics.\",\n",
    "            \"type\": \"string\",\n",
    "            \"minLength\": 12,\n",
    "            \"maxLength\": 12,\n",
    "            \"pattern\": \"^SAMN[0-9]{8}$\"\n",
    "        },\n",
    "        \"BioSampleModel\": {\n",
    "            \"description\": \"SRA term. Model or schema used to define structure information of a BioSample record. In the case of tissue samples, this often refers to the species.\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"Human\",\n",
    "                \"Mouse\"\n",
    "            ]\n",
    "        },\n",
    "        \"Bytes\": {\n",
    "            \"description\": \"Size of the file in bytes when downloaded from SRA database\",\n",
    "            \"type\": \"integer\",\n",
    "            \"exclusiveMinimum\": 0\n",
    "        },\n",
    "        \"CellLine\": {\n",
    "            \"description\": \"Name of cell line profiled\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"CenterName\": {\n",
    "            \"description\": \"Name of center profiling cell line\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"BROAD INSTITUTE\"\n",
    "            ]\n",
    "        },\n",
    "        \"Consent\": {\n",
    "            \"description\": \"Level of consent to publish cell line data\",\n",
    "            \"const\": \"public\"\n",
    "        },\n",
    "        \"DataStoreFileType\": {\n",
    "            \"description\": \"SRA file format or storage structure used in the SRA data storage system\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"DataStoreProvider\": {\n",
    "            \"description\": \"Provider used to host SRA data\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"DataStoreRegion\": {\n",
    "            \"description\": \"Region SRA data is hosted in\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"Disease\": {\n",
    "            \"description\": \"Name of disease/cancer type cell line sample was generated from\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"DiseaseStage\": {\n",
    "            \"description\": \"Stage of tumor development\",\n",
    "            \"anyOf\": [\n",
    "                {\n",
    "                    \"type\": \"string\",\n",
    "                    \"enum\": [\n",
    "                        \"primary\",\n",
    "                        \"metastasis\",\n",
    "                        \"benign_neoplasia\"\n",
    "                    ]\n",
    "                },\n",
    "                {\n",
    "                    \"type\": \"null\"\n",
    "                }\n",
    "            ]\n",
    "        },\n",
    "        \"Ethnicity\": {\n",
    "            \"description\": \"Descent of patient cell line was derived from\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"Caucasian\",\n",
    "                \"Asian\",\n",
    "                \"African_american\"\n",
    "            ]\n",
    "        },\n",
    "        \"Experiment\": {\n",
    "            \"description\": \"SRA refers to a specific set of conditions under which sequencing data was generated. It includes details such as the sequencing platform used, library preparation methods, and other experimental parameters.\",\n",
    "            \"type\": \"string\",\n",
    "            \"minLength\": 10,\n",
    "            \"maxLength\": 10,\n",
    "            \"pattern\": \"^SRX[0-9]{7}$\"\n",
    "        },\n",
    "        \"FlowCellID\": {\n",
    "            \"description\": \"Flow cell ID for sequencing run sample was profiled on\",\n",
    "            \"type\": \"string\",\n",
    "            \"pattern\": \"20[0-9]{6}_PRJNA[0-9]{6}_SRR[0-9]{7}$\"\n",
    "        },\n",
    "        \"Instrument\": {\n",
    "            \"description\": \"Machine sequencing was performed on\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"Illumina HiSeq 2500\",\n",
    "                \"Illumina NovaSeq 6000\",\n",
    "                \"Illumina NovaSeq X\",\n",
    "                \"Illumina MiSeq\"\n",
    "            ]\n",
    "        },\n",
    "        \"Isolate\": {\n",
    "            \"description\": \"Source of assay input material eg, substrate nucleic acid extraction performed on\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"cell line\",\n",
    "                \"tissue\",\n",
    "                \"whole blood\",\n",
    "                \"buffy coat\",\n",
    "                \"plasma\"\n",
    "            ]\n",
    "        },\n",
    "        \"LibraryName\": {\n",
    "            \"description\": \"Name of sequencing library\",\n",
    "            \"type\": \"string\",\n",
    "            \"pattern\": \"^(RNASeq|WES|WGS|CRISPR)\"\n",
    "        },\n",
    "        \"LibraryLayout\": {\n",
    "            \"description\": \"Whether a library contains single ended or paired reads\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"PAIRED\",\n",
    "                \"SINGLE\"\n",
    "            ]\n",
    "        },\n",
    "        \"LibrarySelection\": {\n",
    "            \"description\": \"Type of nucleic acid fragments (DNA, RNA ...) selected and isolated for sequencing\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"cDNA\"\n",
    "            ]\n",
    "        },\n",
    "        \"LibrarySource\": {\n",
    "            \"description\": \"Original nucleic acid source for library\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"GENOMIC\",\n",
    "                \"TRANSCRIPTOMIC\"\n",
    "            ]\n",
    "        },\n",
    "        \"Organism\": {\n",
    "            \"description\": \"Organism sample was derived from, in latin\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"Homo sapiens\",\n",
    "                \"Mus musculus\"\n",
    "            ]\n",
    "        },\n",
    "        \"Platform\": {\n",
    "            \"description\": \"Platform used for sequencing\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"ILLUMINA\",\n",
    "                \"NANOPORE\",\n",
    "                \"PACBIO\"\n",
    "            ]\n",
    "        },\n",
    "        \"ReleaseDate\": {\n",
    "            \"description\": \"Date data was released on SRA database\",\n",
    "            \"type\": \"string\",\n",
    "            \"format\": \"date-time\"\n",
    "        },\n",
    "        \"SampleName\": {\n",
    "            \"description\": \"Unique name of sample profiles\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"SampleType\": {\n",
    "            \"description\": \"Type of sample profiled\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"buffy coat\",\n",
    "                \"cell culture\",\n",
    "                \"plasma\",\n",
    "                \"tissue\",\n",
    "                \"whole blood\"\n",
    "            ]\n",
    "        },\n",
    "        \"Sex\": {\n",
    "            \"description\": \"Sex of patient sample originated from\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"Unknown\",\n",
    "                \"female\",\n",
    "                \"male\"\n",
    "            ]\n",
    "        },\n",
    "        \"SRAStudy\": {\n",
    "            \"description\": \"Study ID from Sequence Read Archive (SRA) database associated with sample\",\n",
    "            \"type\": \"string\",\n",
    "            \"minLength\": 9,\n",
    "            \"maxLength\": 9,\n",
    "            \"pattern\": \"^SRP[0-9]{6}$\"\n",
    "        },\n",
    "        \"Tissue\": {\n",
    "            \"description\": \"Organ sample was derived from\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"autonomic_ganglia\",\n",
    "                \"biliary_tract\",\n",
    "                \"bone\",\n",
    "                \"breast\",\n",
    "                \"central_nervous_system\",\n",
    "                \"cervix\",\n",
    "                \"endometrium\",\n",
    "                \"haematopoietic_and_lymphoid_tissue\",\n",
    "                \"kidney\",\n",
    "                \"large_intestine\",\n",
    "                \"liver\",\n",
    "                \"lung\",\n",
    "                \"oesophagus\",\n",
    "                \"ovary\",\n",
    "                \"pancreas\",\n",
    "                \"pleura\",\n",
    "                \"prostate\",\n",
    "                \"salivary_gland\",\n",
    "                \"skin\",\n",
    "                \"small_intestine\",\n",
    "                \"soft_tissue\",\n",
    "                \"stomach\",\n",
    "                \"thyroid\",\n",
    "                \"upper_aerodigestive_tract\",\n",
    "                \"urinary_tract\"\n",
    "            ]\n",
    "        },\n",
    "        \"CreateDate\": {\n",
    "            \"description\": \"Date data record was created in SRA\",\n",
    "            \"type\": \"string\",\n",
    "            \"format\": \"date-time\"\n",
    "        },\n",
    "        \"CreateDateBatch\": {\n",
    "            \"description\": \"Simplified create_date field to represent data generation batches, custom field in format YYYY-MM-DD\",\n",
    "            \"type\": \"string\",\n",
    "            \"format\": \"date\"\n",
    "        },\n",
    "        \"Version\": {\n",
    "            \"decription\": \"Version of data on SRA\",\n",
    "            \"type\": \"number\",\n",
    "            \"exclusiveMinimum\": 0\n",
    "        },\n",
    "        \"StudyID\": {\n",
    "            \"description\": \"Non-SRA Study ID for project\",\n",
    "            \"type\": \"string\",\n",
    "            \"const\": \"ccle_broad_2019\"\n",
    "        },\n",
    "        \"PatientID\": {\n",
    "            \"description\": \"ID for patient sample was acquired from. Not required to be unique, may have obtained multiple samples from the same patient\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"AnnotationSource\": {\n",
    "            \"description\": \"Cancer cell line initiative that annotated sample\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"ACHILLES\",\n",
    "                \"CCLE\",\n",
    "                \"collaborator\",\n",
    "                \"COSMIC\"\n",
    "            ]\n",
    "        },\n",
    "        \"CancerType\": {\n",
    "            \"description\": \"High-level cancer type cell line was derived from\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"B-Lymphoblastic Leukemia/Lymphoma\",\n",
    "                \"Bladder Cancer\",\n",
    "                \"Bone Cancer\",\n",
    "                \"Breast Cancer\",\n",
    "                \"CNS Cancer\",\n",
    "                \"Cervical Cancer\",\n",
    "                \"Cervical Cancer, NOS\",\n",
    "                \"Colorectal Cancer\",\n",
    "                \"Embryonal Tumor\",\n",
    "                \"Endometrial Cancer\",\n",
    "                \"Esophagogastric Cancer\",\n",
    "                \"Glioma\",\n",
    "                \"Head and Neck Cancer\",\n",
    "                \"Hepatobiliary Cancer\",\n",
    "                \"Hodgkin Lymphoma\",\n",
    "                \"Kidney Cancer, NOS\",\n",
    "                \"Leukemia\",\n",
    "                \"Lung Cancer, NOS\",\n",
    "                \"Mature B-Cell Neoplasms\",\n",
    "                \"Mature T and NK Neoplasms\",\n",
    "                \"Melanoma\",\n",
    "                \"Mesothelioma\",\n",
    "                \"Myeloproliferative Neoplasms\",\n",
    "                \"Non-Small Cell Lung Cancer\",\n",
    "                \"Ovarian Cancer\",\n",
    "                \"Ovarian/Fallopian Tube Cancer, NOS\",\n",
    "                \"Pancreatic Cancer\",\n",
    "                \"Peripheral Nervous System\",\n",
    "                \"Prostate Cancer\",\n",
    "                \"Prostate Cancer, NOS\",\n",
    "                \"Renal Cell Carcinoma\",\n",
    "                \"Rhabdoid Cancer\",\n",
    "                \"Salivary Gland Cancer\",\n",
    "                \"Sex Cord Stromal Tumor\",\n",
    "                \"Small Bowel Cancer\",\n",
    "                \"Small Cell Lung Cancer\",\n",
    "                \"Soft Tissue Sarcoma\",\n",
    "                \"T-Lymphoblastic Leukemia/Lymphoma\",\n",
    "                \"Thyroid Cancer\",\n",
    "                \"Thyroid Cancer, NOS\",\n",
    "                \"Uterine Sarcoma\"\n",
    "            ]\n",
    "        },\n",
    "        \"CancerTypeDetailed\": {\n",
    "            \"description\": \"Detailed description of cancer type cell line was derived from\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"Acute Myeloid Leukemia\",\n",
    "                \"Adenosquamous Carcinoma of the Stomach\",\n",
    "                \"Adult T-Cell Leukemia/Lymphoma\",\n",
    "                \"Alveolar Rhabdomyosarcoma\",\n",
    "                \"Anaplastic Astrocytoma\",\n",
    "                \"Anaplastic Large Cell Lymphoma\",\n",
    "                \"Anaplastic Thyroid Cancer\",\n",
    "                \"Astrocytoma\",\n",
    "                \"Atypical Teratoid/Rhabdoid Tumor\",\n",
    "                \"B-Lymphoblastic Leukemia/Lymphoma\",\n",
    "                \"Bladder Squamous Cell Carcinoma\",\n",
    "                \"Bladder Urothelial Carcinoma\",\n",
    "                \"Breast Invasive Ductal Carcinoma\",\n",
    "                \"Brenner Tumor\",\n",
    "                \"Burkitt Lymphoma\",\n",
    "                \"Cervical Squamous Cell Carcinoma\",\n",
    "                \"Cervix\",\n",
    "                \"Chondrosarcoma\",\n",
    "                \"Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma\",\n",
    "                \"Chronic Myelogenous Leukemia\",\n",
    "                \"Clear Cell Ovarian Cancer\",\n",
    "                \"Colorectal Adenocarcinoma\",\n",
    "                \"Cutaneous Melanoma\",\n",
    "                \"Diffuse Large B-Cell Lymphoma, NOS\",\n",
    "                \"Diffuse Type Stomach Adenocarcinoma\",\n",
    "                \"Embryonal Rhabdomyosarcoma\",\n",
    "                \"Endometrial Carcinoma\",\n",
    "                \"Endometrial Stromal Sarcoma\",\n",
    "                \"Endometrioid Ovarian Cancer\",\n",
    "                \"Esophageal Adenocarcinoma\",\n",
    "                \"Esophageal Squamous Cell Carcinoma\",\n",
    "                \"Essential Thrombocythemia\",\n",
    "                \"Ewing Sarcoma\",\n",
    "                \"Extrahepatic Cholangiocarcinoma\",\n",
    "                \"Fibroblastic Osteosarcoma\",\n",
    "                \"Fibrosarcoma\",\n",
    "                \"Follicular Thyroid Cancer\",\n",
    "                \"Gallbladder Adenocarcinoma, NOS\",\n",
    "                \"Giant Cell Tumor of Bone\",\n",
    "                \"Glioblastoma\",\n",
    "                \"Glioblastoma Multiforme\",\n",
    "                \"Gliosarcoma\",\n",
    "                \"Granulosa Cell Tumor\",\n",
    "                \"Head and Neck Squamous Cell Carcinoma\",\n",
    "                \"Hepatoblastoma\",\n",
    "                \"Hepatocellular Carcinoma\",\n",
    "                \"High-Grade Glioma, NOS\",\n",
    "                \"High-Grade Serous Ovarian Cancer\",\n",
    "                \"Hodgkin Lymphoma\",\n",
    "                \"Hypopharynx Squamous Cell Carcinoma\",\n",
    "                \"Intestinal Type Stomach Adenocarcinoma\",\n",
    "                \"Intrahepatic Cholangiocarcinoma\",\n",
    "                \"Invasive Breast Carcinoma\",\n",
    "                \"Kidney\",\n",
    "                \"Large Cell Lung Carcinoma\",\n",
    "                \"Larynx Squamous Cell Carcinoma\",\n",
    "                \"Leiomyosarcoma\",\n",
    "                \"Low-Grade Serous Ovarian Cancer\",\n",
    "                \"Lung\",\n",
    "                \"Lung Adenocarcinoma\",\n",
    "                \"Lung Adenosquamous Carcinoma\",\n",
    "                \"Lung Carcinoid\",\n",
    "                \"Lung Squamous Cell Carcinoma\",\n",
    "                \"Mantle Cell Lymphoma\",\n",
    "                \"Mature B-Cell Neoplasms\",\n",
    "                \"Mature T and NK Neoplasms\",\n",
    "                \"Medulloblastoma\",\n",
    "                \"Meningioma\",\n",
    "                \"Metaplastic Breast Cancer\",\n",
    "                \"Mixed Ovarian Carcinoma\",\n",
    "                \"Mucinous Ovarian Cancer\",\n",
    "                \"Mucinous Stomach Adenocarcinoma\",\n",
    "                \"Mucoepidermoid Carcinoma\",\n",
    "                \"Mucoepidermoid Carcinoma of the Lung\",\n",
    "                \"Mycosis Fungoides\",\n",
    "                \"Neuroblastoma\",\n",
    "                \"Non-Small Cell Lung Cancer\",\n",
    "                \"Oligodendroglioma\",\n",
    "                \"Oral Cavity Squamous Cell Carcinoma\",\n",
    "                \"Oropharynx Squamous Cell Carcinoma\",\n",
    "                \"Osteosarcoma\",\n",
    "                \"Ovarian Epithelial Tumor\",\n",
    "                \"Ovary/Fallopian Tube\",\n",
    "                \"Pancreatic Adenocarcinoma\",\n",
    "                \"Papillary Thyroid Cancer\",\n",
    "                \"Peripheral T-Cell lymphoma, NOS\",\n",
    "                \"Plasma Cell Myeloma\",\n",
    "                \"Pleural Mesothelioma\",\n",
    "                \"Prostate\",\n",
    "                \"Prostate Adenocarcinoma\",\n",
    "                \"Prostate Small Cell Carcinoma\",\n",
    "                \"Renal Cell Carcinoma\",\n",
    "                \"Renal Clear Cell Carcinoma\",\n",
    "                \"Rhabdoid Cancer\",\n",
    "                \"Rhabdomyosarcoma\",\n",
    "                \"Serous Ovarian Cancer\",\n",
    "                \"Signet Ring Cell Carcinoma of the Stomach\",\n",
    "                \"Small Cell Carcinoma of the Stomach\",\n",
    "                \"Small Cell Lung Cancer\",\n",
    "                \"Small Intestinal Carcinoma\",\n",
    "                \"Stomach Adenocarcinoma\",\n",
    "                \"T-Lymphoblastic Leukemia/Lymphoma\",\n",
    "                \"Thyroid\",\n",
    "                \"Tubular Stomach Adenocarcinoma\",\n",
    "                \"Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma/High-Grade Spindle Cell Sarcoma\",\n",
    "                \"Undifferentiated Stomach Adenocarcinoma\",\n",
    "                \"Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor\",\n",
    "                \"Uterine Endometrioid Carcinoma\",\n",
    "                \"Uterine Sarcoma/Mesenchymal\"\n",
    "            ]\n",
    "        },\n",
    "        \"CellLineSource\": {\n",
    "            \"description\": \"Origin source of cell line, often name of institution that derived or provided cell line to the study\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"ACADEMIC\",\n",
    "                \"ACDC LAB\",\n",
    "                \"ATCC\",\n",
    "                \"Academic Lab\",\n",
    "                \"Acd Lab\",\n",
    "                \"DSMZ\",\n",
    "                \"EACC\",\n",
    "                \"ECAAC\",\n",
    "                \"ECACC\",\n",
    "                \"GNF\",\n",
    "                \"Garraway Lab\",\n",
    "                \"HPACC\",\n",
    "                \"HSRRB\",\n",
    "                \"HSSRB\",\n",
    "                \"ICLC\",\n",
    "                \"JCRB\",\n",
    "                \"JHSF\",\n",
    "                \"KCLB\",\n",
    "                \"NCI/DCTD\",\n",
    "                \"NIBRI\",\n",
    "                \"NIBRI/ATCC\",\n",
    "                \"PT-6ZZI\",\n",
    "                \"RIKEN\",\n",
    "                \"Riken\",\n",
    "                \"WISTAR\"\n",
    "            ]\n",
    "        },\n",
    "        \"Characteristics\": {\n",
    "            \"description\": \"Free form description of cell line characteristics, especially as they pertain to growth patterns and morphology\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"DepMapID\": {\n",
    "            \"description\": \"Cell line ID on the Dependency Map (DepMap) portal profiling cancer vulnerabilities of cell lines\",\n",
    "            \"type\": \"string\",\n",
    "            \"minLength\": 10,\n",
    "            \"maxLength\": 10,\n",
    "            \"pattern\": \"^ACH-[0-9]{6}$\"\n",
    "        },\n",
    "        \"DiseaseOntology\": {\n",
    "            \"description\": \"Disease ontology, similar to detailed cancer type, as defined by cbioportal\",\n",
    "            \"enum\": [\n",
    "                \"B-cell non-Hodgkin lymphoma\",\n",
    "                \"B-prolymphocytic_leukemia\",\n",
    "                \"Brain Cancer\",\n",
    "                \"Breast Cancer\",\n",
    "                \"Burkitts lymphoma\",\n",
    "                \"CD30+_anaplastic_large_cell_lymphoma\",\n",
    "                \"Colon Cancer\",\n",
    "                \"Down syndrome; acute megakaryoblastic leukaemia\",\n",
    "                \"Endometrial Cancer\",\n",
    "                \"Esophageal Cancer\",\n",
    "                \"Ewing family tumor\",\n",
    "                \"Ewings_sarcoma\",\n",
    "                \"Kidney Cancer\",\n",
    "                \"Leukemia\",\n",
    "                \"Lung Cancer\",\n",
    "                \"Multiple Myeloma\",\n",
    "                \"Ovarian Cancer\",\n",
    "                \"Pancreatic Cancer\",\n",
    "                \"Skin Cancer\",\n",
    "                \"T-ALL\",\n",
    "                \"TALL\",\n",
    "                \"acute lymphoblastic leukemia\",\n",
    "                \"acute myelogenous leukemia M5a\",\n",
    "                \"acute_monocytic_leukemia\",\n",
    "                \"anaplastic_large_cell_lymphoma\",\n",
    "                \"b_cell_non_hodgkin_lymphoma\",\n",
    "                \"bladder_cancer\",\n",
    "                \"bone_cancer\",\n",
    "                \"brain_cancer\",\n",
    "                \"breast_adenocarcinoma\",\n",
    "                \"breast_cancer\",\n",
    "                \"bronchioalveolar_carcinoma; non-small_cell lung_cancer\",\n",
    "                \"chondrosarcoma\",\n",
    "                \"clear_cell_carcinoma\",\n",
    "                \"colon_cancer\",\n",
    "                \"colon_carcinoma\",\n",
    "                \"colon_carcinoma and melanoma\",\n",
    "                \"colorectal_cancer\",\n",
    "                \"cutaneous T cell lymphoma\",\n",
    "                \"diffuse large cell lymphoma non-cleaved type\",\n",
    "                \"diffuse_histiocytic_lymphoma\",\n",
    "                \"ductal_carcinoma\",\n",
    "                \"endometrioid_carcinoma\",\n",
    "                \"erythroleukemia\",\n",
    "                \"fibrosarcoma_cancer\",\n",
    "                \"gastric_cancer\",\n",
    "                \"germinal center B-cell-like (GCB) DLBCL\",\n",
    "                \"head_neck_cancer\",\n",
    "                \"hepatocellular_cancer\",\n",
    "                \"histiocytic_lymphoma\",\n",
    "                \"intermediately differentiated adenocarcinoma\",\n",
    "                \"invasive_ductal_carcinoma\",\n",
    "                \"kidney_cancer\",\n",
    "                \"large_cell_lung_cancer\",\n",
    "                \"leukaemia\",\n",
    "                \"liver_cancer\",\n",
    "                \"lung_cancer\",\n",
    "                \"lymphoma\",\n",
    "                \"malignant_melanoma\",\n",
    "                \"malignant_papillary_serous_adenocarcinoma\",\n",
    "                \"mantle_cell_lymphoma\",\n",
    "                \"medulla_carcinoma\",\n",
    "                \"medulloblastoma\",\n",
    "                \"melanoma\",\n",
    "                \"metaplastic_breast_carcinoma\",\n",
    "                \"moderately differentiated tubular adenocarcinoma\",\n",
    "                \"multiple_myeloma\",\n",
    "                \"mycosis_fungoides\",\n",
    "                \"myeloma\",\n",
    "                \"neuroblastoma\",\n",
    "                \"neuroepithelioma\",\n",
    "                \"non-Hodgkins lymphoma\",\n",
    "                \"non_small_cell_lung_cancer\",\n",
    "                \"oesophageal squamous cell carcinoma\",\n",
    "                \"osteosarcoma\",\n",
    "                \"ovarian_cancer\",\n",
    "                \"ovarian_carcinoma\",\n",
    "                \"pancreatic_cancer\",\n",
    "                \"papillary_adenocarcinoma\",\n",
    "                \"plasma_cell_leukemia\",\n",
    "                \"pleomorphic hepatocellular carcinoma\",\n",
    "                \"poorly_differentiated_gastric carcinoma\",\n",
    "                \"prostate_cancer\",\n",
    "                \"rectum; adenocarcinoma; well differentiated\",\n",
    "                \"recurrent_endometrial_carcinoma\",\n",
    "                \"renal_cell_carcinoma\",\n",
    "                \"renal_leiomyoblastoma\",\n",
    "                \"rhabdoid_tumour\",\n",
    "                \"rhabdomyosarcoma\",\n",
    "                \"sezary_syndrome\",\n",
    "                \"skin_cancer\",\n",
    "                \"small_cell_carcinoma\",\n",
    "                \"thyroid_squamous_cell_carcinoma\",\n",
    "                \"transitional_cell_carcinoma\",\n",
    "                \"undifferentiated B lymphoma\",\n",
    "                \"well differentiated endometrial adenocarcinoma\",\n",
    "                \"well differentiated invasive eosphageal squamous cell carcinoma\"\n",
    "            ]\n",
    "        },\n",
    "        \"DoublingTimeHrs\": {\n",
    "            \"description\": \"Approximate time, in hours, for cell line population to double\",\n",
    "            \"type\": \"number\",\n",
    "            \"exclusiveMinimum\": 0\n",
    "        },\n",
    "        \"FractionGenomeAltered\": {\n",
    "            \"description\": \"Percentage of genome that has been affected by copy number gains or losses, as calculated by cBioportal\",\n",
    "            \"type\": \"number\"\n",
    "        },\n",
    "        \"FreezingMedium\": {\n",
    "            \"description\": \"Medium used to crysopreserve cell lines, often refers to percentage DMSO added to cell culture medium\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"5% DMSO\",\n",
    "                \"10% DMSO\",\n",
    "                \"5% DMSO-7.5% DMSO\",\n",
    "                \"0.05% DMSO\"\n",
    "            ]\n",
    "        },\n",
    "        \"GenomeDoublings\": {\n",
    "            \"description\": \"Number of duplications of the entire set of chromosomes within a cell for a given cell line\",\n",
    "            \"type\": \"integer\",\n",
    "            \"enum\": [\n",
    "                0.0,\n",
    "                1.0,\n",
    "                2.0\n",
    "            ]\n",
    "        },\n",
    "        \"GeographicDistribution\": {\n",
    "            \"description\": \"Location of cell line derivation\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"japan\",\n",
    "                \"korea\",\n",
    "                \"europe\",\n",
    "                \"canada\",\n",
    "                \"france\",\n",
    "                \"sweden\",\n",
    "                \"chinese\",\n",
    "                \"taiwan\",\n",
    "                \"argentina\"\n",
    "            ]\n",
    "        },\n",
    "        \"GrowthMedium\": {\n",
    "            \"description\": \"Cell culture or growth media, is an umbrella term that encompasses any gel or liquid created to support cellular growth in the lab\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"Histology\": {\n",
    "            \"description\": \"Histology of tumor cell line was derived from, as defined by microscopic examination of excised tissue from biopsy or resection\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"Carcinoid-Endocrine_Tumour\",\n",
    "                \"Carcinoma\",\n",
    "                \"Chondrosarcoma\",\n",
    "                \"Ewings_Sarcoma-Peripheral_Primitive_Neuroectodermal_Tumour\",\n",
    "                \"Fibrosarcoma\",\n",
    "                \"Giant_Cell_Tumour\",\n",
    "                \"Glioma\",\n",
    "                \"Haematopoietic_Neoplasm\",\n",
    "                \"Leiomyosarcoma\",\n",
    "                \"Lymphoid_Neoplasm\",\n",
    "                \"Malignant_Fibrous_Histiocytoma-Pleomorphic_Sarcoma\",\n",
    "                \"Malignant_Melanoma\",\n",
    "                \"Meningioma\",\n",
    "                \"Mesothelioma\",\n",
    "                \"Neuroblastoma\",\n",
    "                \"Osteosarcoma\",\n",
    "                \"Other\",\n",
    "                \"Primitive_Neuroectodermal_Tumour-Medulloblastoma\",\n",
    "                \"Rhabdoid_Tumour\",\n",
    "                \"Rhabdomyosarcoma\",\n",
    "                \"Sarcoma\",\n",
    "                \"Sex_Cord-Stromal_Tumour\"\n",
    "            ]\n",
    "        },\n",
    "        \"HistologySubtype1\": {\n",
    "            \"description\": \"More detailed histological information on tumor cell line was derived from. NS=not specified\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"B_cell_lymphoma_unspecified\",\n",
    "                \"Brenner_tumour\",\n",
    "                \"Burkitt_lymphoma\",\n",
    "                \"Hodgkin_lymphoma\",\n",
    "                \"NS\",\n",
    "                \"acute_lymphoblastic_B_cell_leukaemia\",\n",
    "                \"acute_lymphoblastic_T_cell_leukaemia\",\n",
    "                \"acute_myeloid_leukaemia\",\n",
    "                \"adenocarcinoma\",\n",
    "                \"adult_T_cell_lymphoma-leukaemia\",\n",
    "                \"alveolar\",\n",
    "                \"anaplastic_carcinoma\",\n",
    "                \"anaplastic_large_cell_lymphoma\",\n",
    "                \"astrocytoma\",\n",
    "                \"astrocytoma_Grade_III\",\n",
    "                \"astrocytoma_Grade_III-IV\",\n",
    "                \"astrocytoma_Grade_IV\",\n",
    "                \"barrett_associated_adenocarcinoma\",\n",
    "                \"blast_phase_chronic_myeloid_leukaemia\",\n",
    "                \"bronchioloalveolar_adenocarcinoma\",\n",
    "                \"carcinosarcoma-malignant_mesodermal_mixed_tumour\",\n",
    "                \"chronic_lymphocytic_leukaemia-small_lymphocytic_lymphoma\",\n",
    "                \"chronic_myeloid_leukaemia\",\n",
    "                \"clear_cell_carcinoma\",\n",
    "                \"clear_cell_renal_cell_carcinoma\",\n",
    "                \"dedifferentiated\",\n",
    "                \"diffuse_adenocarcinoma\",\n",
    "                \"diffuse_large_B_cell_lymphoma\",\n",
    "                \"ductal_carcinoma\",\n",
    "                \"embryonal\",\n",
    "                \"endometrioid_carcinoma\",\n",
    "                \"essential_thrombocythaemia\",\n",
    "                \"follicular_carcinoma\",\n",
    "                \"gliosarcoma\",\n",
    "                \"granulosa_cell_tumour\",\n",
    "                \"hepatoblastoma\",\n",
    "                \"hepatocellular_carcinoma\",\n",
    "                \"immortalized_embryonic_fibroblast\",\n",
    "                \"immortalized_epithelial\",\n",
    "                \"intestinal_adenocarcinoma\",\n",
    "                \"large_cell_carcinoma\",\n",
    "                \"mantle_cell_lymphoma\",\n",
    "                \"medullary_carcinoma\",\n",
    "                \"metaplasia\",\n",
    "                \"metaplastic_carcinoma\",\n",
    "                \"mixed_adenosquamous_carcinoma\",\n",
    "                \"mixed_carcinoma\",\n",
    "                \"mucinous_carcinoma\",\n",
    "                \"mucoepidermoid_carcinoma\",\n",
    "                \"mycosis_fungoides-Sezary_syndrome\",\n",
    "                \"non_small_cell_carcinoma\",\n",
    "                \"oligodendroglioma\",\n",
    "                \"papillary_carcinoma\",\n",
    "                \"papilloma\",\n",
    "                \"peripheral_T_cell_lymphoma_unspecified\",\n",
    "                \"plasma_cell_myeloma\",\n",
    "                \"renal_cell_carcinoma\",\n",
    "                \"serous_carcinoma\",\n",
    "                \"signet_ring_adenocarcinoma\",\n",
    "                \"small_cell_adenocarcinoma\",\n",
    "                \"small_cell_carcinoma\",\n",
    "                \"squamous_cell_carcinoma\",\n",
    "                \"transitional_cell_carcinoma\",\n",
    "                \"tubular_adenocarcinoma\",\n",
    "                \"undifferentiated_adenocarcinoma\",\n",
    "                \"undifferentiated_carcinoma\"\n",
    "            ]\n",
    "        },\n",
    "        \"HistologySubtype2\": {\n",
    "            \"description\": \"Even more detailed histological information on tumor cell line was derived from. NS=not specified\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"L2\",\n",
    "                \"M0\",\n",
    "                \"M2\",\n",
    "                \"M3\",\n",
    "                \"M4\",\n",
    "                \"M5\",\n",
    "                \"M5a\",\n",
    "                \"M6\",\n",
    "                \"M7\",\n",
    "                \"NS\",\n",
    "                \"Ph_positive\",\n",
    "                \"anaplastic\",\n",
    "                \"glioblastoma_multiforme\",\n",
    "                \"medullary\",\n",
    "                \"papillary\",\n",
    "                \"papillary_transitional_cell_carcinoma\",\n",
    "                \"squamous_cell_carcinoma\"\n",
    "            ]\n",
    "        },\n",
    "        \"LifeStage\": {\n",
    "            \"description\": \"Whether cell line was dervied from an adult or pediatric tumor\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"pediatric\",\n",
    "                \"adult\"\n",
    "            ]\n",
    "        },\n",
    "        \"Lineage\": {\n",
    "            \"description\": \"High-level description of cancer lineage corresponding to cel line\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"bile_duct\",\n",
    "                \"blood\",\n",
    "                \"bone\",\n",
    "                \"breast\",\n",
    "                \"central_nervous_system\",\n",
    "                \"cervix\",\n",
    "                \"colorectal\",\n",
    "                \"engineered_breast\",\n",
    "                \"engineered_central_nervous_system\",\n",
    "                \"engineered_kidney\",\n",
    "                \"engineered_lung\",\n",
    "                \"engineered_ovary\",\n",
    "                \"engineered_prostate\",\n",
    "                \"esophagus\",\n",
    "                \"fibroblast\",\n",
    "                \"gastric\",\n",
    "                \"kidney\",\n",
    "                \"liver\",\n",
    "                \"lung\",\n",
    "                \"lymphocyte\",\n",
    "                \"ovary\",\n",
    "                \"pancreas\",\n",
    "                \"peripheral_nervous_system\",\n",
    "                \"plasma_cell\",\n",
    "                \"prostate\",\n",
    "                \"skin\",\n",
    "                \"soft_tissue\",\n",
    "                \"thyroid\",\n",
    "                \"upper_aerodigestive\",\n",
    "                \"urinary_tract\",\n",
    "                \"uterus\"\n",
    "            ]\n",
    "        },\n",
    "        \"LineageMolecularSubtype\": {\n",
    "            \"description\": \"Molecular subtype of tumor cell line was derived from\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"EWS_ERG\",\n",
    "                \"EWS_FLI\",\n",
    "                \"HER2_amp\",\n",
    "                \"MSI\",\n",
    "                \"MYCN_amp\",\n",
    "                \"MYC_amp\",\n",
    "                \"MYC_exp\",\n",
    "                \"basal_A\",\n",
    "                \"basal_B\",\n",
    "                \"luminal\",\n",
    "                \"luminal_HER2_amp\",\n",
    "                \"non_MYC\"\n",
    "            ]\n",
    "        },\n",
    "        \"LineageSubtype\": {\n",
    "            \"description\": \"Lineage subtype of tumor cell line was derived from, more detailed than Lineage\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"ALL\",\n",
    "                \"AML\",\n",
    "                \"ATL\",\n",
    "                \"ATRT\",\n",
    "                \"CLL\",\n",
    "                \"CML\",\n",
    "                \"Ewing_sarcoma\",\n",
    "                \"MMMT\",\n",
    "                \"NSCLC\",\n",
    "                \"SCLC\",\n",
    "                \"bladder_carcinoma\",\n",
    "                \"breast_adenocarcinoma\",\n",
    "                \"breast_carcinoma\",\n",
    "                \"breast_ductal_carcinoma\",\n",
    "                \"brenner_tumor\",\n",
    "                \"caecum_adenocarcinoma\",\n",
    "                \"cervical_carcinoma\",\n",
    "                \"cholangiocarcinoma\",\n",
    "                \"chondrosarcoma\",\n",
    "                \"clear_cell_carcinoma\",\n",
    "                \"colorectal_adenocarcinoma\",\n",
    "                \"duodenal_adenocarcinoma\",\n",
    "                \"endocrine\",\n",
    "                \"endometrial_adenocarcinoma\",\n",
    "                \"endometrial_adenosquamous\",\n",
    "                \"endometrial_stromal_sarcoma\",\n",
    "                \"esophagus_adenocarcinoma\",\n",
    "                \"esophagus_squamous\",\n",
    "                \"exocrine\",\n",
    "                \"fibroblast_bone\",\n",
    "                \"fibroblast_breast\",\n",
    "                \"fibroblast_colorectal\",\n",
    "                \"fibroblast_lung\",\n",
    "                \"fibroblast_lymphocyte\",\n",
    "                \"fibroblast_skin\",\n",
    "                \"fibroblast_soft_tissue\",\n",
    "                \"fibroblast_upper_aerodigestive\",\n",
    "                \"fibroblast_urinary_tract\",\n",
    "                \"fibrosarcoma\",\n",
    "                \"gallbladder_adenocarcinoma\",\n",
    "                \"gastric_adenocarcinoma\",\n",
    "                \"gastric_small_cell\",\n",
    "                \"glioma\",\n",
    "                \"hepatoblastoma\",\n",
    "                \"hepatocellular_carcinoma\",\n",
    "                \"hodgkin_lymphoma\",\n",
    "                \"leiomyosarcoma\",\n",
    "                \"lung_carcinoid\",\n",
    "                \"lymphoma_unspecified\",\n",
    "                \"malignant_rhabdoid_tumor\",\n",
    "                \"medulloblastoma\",\n",
    "                \"melanoma\",\n",
    "                \"meningioma\",\n",
    "                \"mesothelioma\",\n",
    "                \"mullerian_carcinoma\",\n",
    "                \"multiple_myeloma\",\n",
    "                \"neuroblastoma\",\n",
    "                \"non_hodgkin_lymphoma\",\n",
    "                \"osteosarcoma\",\n",
    "                \"ovary_adenocarcinoma\",\n",
    "                \"ovary_carcinoma\",\n",
    "                \"pleomorphic_sarcoma\",\n",
    "                \"prostate_adenocarcinoma\",\n",
    "                \"prostate_small_cell\",\n",
    "                \"renal_cell_carcinoma\",\n",
    "                \"rhabdomyosarcoma\",\n",
    "                \"thyroid_carcinoma\",\n",
    "                \"thyroid_sarcoma\",\n",
    "                \"thyroid_squamous\",\n",
    "                \"upper_aerodigestive_squamous\",\n",
    "                \"uterine_sarcoma\"\n",
    "            ]\n",
    "        },\n",
    "        \"LineageSubSubtype\": {\n",
    "            \"decription\": \"Lineage sub-subtype of tumor cell line was derived from, more detailed than bath Lineage SubType & Lineage\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"DLBCL\",\n",
    "                \"ERneg_HER2neg\",\n",
    "                \"ERneg_HER2pos\",\n",
    "                \"ERpos_HER2neg\",\n",
    "                \"ERpos_HER2pos\",\n",
    "                \"M2\",\n",
    "                \"M3\",\n",
    "                \"M4\",\n",
    "                \"M5\",\n",
    "                \"M6\",\n",
    "                \"M7\",\n",
    "                \"NSCLC_adenocarcinoma\",\n",
    "                \"NSCLC_adenosquamous\",\n",
    "                \"NSCLC_large_cell\",\n",
    "                \"NSCLC_mucoepidermoid\",\n",
    "                \"NSCLC_squamous\",\n",
    "                \"alveolar\",\n",
    "                \"amelanotic\",\n",
    "                \"anaplastic\",\n",
    "                \"astrocytoma\",\n",
    "                \"b_cell\",\n",
    "                \"b_cell_burkitt\",\n",
    "                \"b_cell_mantle_cell\",\n",
    "                \"basaloid\",\n",
    "                \"bladder_squamous\",\n",
    "                \"bladder_transitional_cell\",\n",
    "                \"blast_crisis\",\n",
    "                \"clear_cell\",\n",
    "                \"diffuse_gastric\",\n",
    "                \"embryonal\",\n",
    "                \"endometrioid\",\n",
    "                \"exocrine_adenocarcinoma\",\n",
    "                \"exocrine_adenosquamous\",\n",
    "                \"extrahepatic\",\n",
    "                \"follicular\",\n",
    "                \"glioblastoma\",\n",
    "                \"hbs_antigen_carrier\",\n",
    "                \"high_grade_serous\",\n",
    "                \"hypopharyngeal\",\n",
    "                \"intrahepatic\",\n",
    "                \"laryngeal\",\n",
    "                \"low_grade_serous\",\n",
    "                \"med_group_3\",\n",
    "                \"mixed_endometrioid_clear_cell\",\n",
    "                \"mixed_serous_clear_cell\",\n",
    "                \"mucinous\",\n",
    "                \"oligodendroglioma\",\n",
    "                \"oral\",\n",
    "                \"papillary\",\n",
    "                \"pharynx\",\n",
    "                \"plasmacytoma\",\n",
    "                \"renal_leiomyoblastoma\",\n",
    "                \"salivary_gland\",\n",
    "                \"serous\",\n",
    "                \"signet_ring_cell\",\n",
    "                \"somatostatinoma\",\n",
    "                \"t_cell\",\n",
    "                \"t_cell_ALCL\",\n",
    "                \"t_cell_cutaneous\",\n",
    "                \"tongue\",\n",
    "                \"transitional_cell\",\n",
    "                \"tubular\"\n",
    "            ]\n",
    "        },\n",
    "        \"MutationCount\": {\n",
    "            \"description\": \"Total  number of non-synonymous mutations in cell line as reported by cBioportal\",\n",
    "            \"type\": \"integer\"\n",
    "        },\n",
    "        \"MutationRate\": {\n",
    "            \"description\": \"Mutations per megabase of the genome\",\n",
    "            \"type\": \"number\"\n",
    "        },\n",
    "        \"CellLineNickName\": {\n",
    "            \"description\": \"Shortened name for cell line\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"OncotreeCode\": {\n",
    "            \"description\": \"OncoTree is an open-source ontology that was developed at Memorial Sloan Kettering Cancer Center (MSK) for standardizing cancer type diagnosis from a clinical perspective by assigning each diagnosis a unique OncoTree code.\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"AASTR\",\n",
    "                \"ALCL\",\n",
    "                \"AML\",\n",
    "                \"ARMS\",\n",
    "                \"ASTR\",\n",
    "                \"ATLL\",\n",
    "                \"ATRT\",\n",
    "                \"BL\",\n",
    "                \"BLCA\",\n",
    "                \"BLL\",\n",
    "                \"BLSC\",\n",
    "                \"BRCA\",\n",
    "                \"BTOV\",\n",
    "                \"CCOV\",\n",
    "                \"CCRCC\",\n",
    "                \"CERVIX\",\n",
    "                \"CESC\",\n",
    "                \"CHS\",\n",
    "                \"CLLSLL\",\n",
    "                \"CML\",\n",
    "                \"COADREAD\",\n",
    "                \"DLBCLNOS\",\n",
    "                \"DSTAD\",\n",
    "                \"EHCH\",\n",
    "                \"EOV\",\n",
    "                \"ERMS\",\n",
    "                \"ES\",\n",
    "                \"ESCA\",\n",
    "                \"ESCC\",\n",
    "                \"ESS\",\n",
    "                \"ET\",\n",
    "                \"FIBS\",\n",
    "                \"FIOS\",\n",
    "                \"GB\",\n",
    "                \"GBAD\",\n",
    "                \"GBM\",\n",
    "                \"GCTB\",\n",
    "                \"GRCT\",\n",
    "                \"GSARC\",\n",
    "                \"HCC\",\n",
    "                \"HGGNOS\",\n",
    "                \"HGSOC\",\n",
    "                \"HL\",\n",
    "                \"HNSC\",\n",
    "                \"HPHSC\",\n",
    "                \"IDC\",\n",
    "                \"IHCH\",\n",
    "                \"ISTAD\",\n",
    "                \"KIDNEY\",\n",
    "                \"LCLC\",\n",
    "                \"LGSOC\",\n",
    "                \"LIHB\",\n",
    "                \"LMS\",\n",
    "                \"LUAD\",\n",
    "                \"LUAS\",\n",
    "                \"LUCA\",\n",
    "                \"LUMEC\",\n",
    "                \"LUNG\",\n",
    "                \"LUSC\",\n",
    "                \"LXSC\",\n",
    "                \"MBC\",\n",
    "                \"MBL\",\n",
    "                \"MBN\",\n",
    "                \"MCL\",\n",
    "                \"MFH\",\n",
    "                \"MNG\",\n",
    "                \"MOV\",\n",
    "                \"MRT\",\n",
    "                \"MSTAD\",\n",
    "                \"MTNN\",\n",
    "                \"MUCC\",\n",
    "                \"MXOV\",\n",
    "                \"MYCF\",\n",
    "                \"NBL\",\n",
    "                \"NSCLC\",\n",
    "                \"OCSC\",\n",
    "                \"ODG\",\n",
    "                \"OPHSC\",\n",
    "                \"OS\",\n",
    "                \"OVARY\",\n",
    "                \"OVT\",\n",
    "                \"PAAD\",\n",
    "                \"PCM\",\n",
    "                \"PLMESO\",\n",
    "                \"PRAD\",\n",
    "                \"PROSTATE\",\n",
    "                \"PRSCC\",\n",
    "                \"PTCL\",\n",
    "                \"RCC\",\n",
    "                \"RMS\",\n",
    "                \"SCLC\",\n",
    "                \"SIC\",\n",
    "                \"SKCM\",\n",
    "                \"SOC\",\n",
    "                \"SSRCC\",\n",
    "                \"STAD\",\n",
    "                \"STAS\",\n",
    "                \"STSC\",\n",
    "                \"THAP\",\n",
    "                \"THFO\",\n",
    "                \"THPA\",\n",
    "                \"THYROID\",\n",
    "                \"TLL\",\n",
    "                \"TSTAD\",\n",
    "                \"UCEC\",\n",
    "                \"UCS\",\n",
    "                \"UEC\",\n",
    "                \"USARC\",\n",
    "                \"USTAD\"\n",
    "            ]\n",
    "        },\n",
    "        \"PathologistAnnotation\": {\n",
    "            \"description\": \"Cancer type of tumor cell line was derived from according to pathologist\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"Biliary_Tract:Carcinoma\",\n",
    "                \"Bladder:Carcinoma\",\n",
    "                \"Bone:Sarcoma_Chondro\",\n",
    "                \"Bone:Sarcoma_Ewing\",\n",
    "                \"Bone:Sarcoma_Osteo\",\n",
    "                \"Breast:Carcinoma\",\n",
    "                \"CNS:Glioma\",\n",
    "                \"CNS:Glioma_HighGrade\",\n",
    "                \"CNS:Medulloblastoma\",\n",
    "                \"Colorectal:Carcinoma\",\n",
    "                \"Endocrine\",\n",
    "                \"Endometrium:Carcinoma\",\n",
    "                \"Endometrium:Others\",\n",
    "                \"Gastric:Carcinoma\",\n",
    "                \"Kidney:Carcinoma\",\n",
    "                \"Leukemia:ALL\",\n",
    "                \"Leukemia:AML\",\n",
    "                \"Leukemia:CLL\",\n",
    "                \"Leukemia:CML\",\n",
    "                \"Leukemia:MPD\",\n",
    "                \"Liver:Carcinoma_Adeno\",\n",
    "                \"Liver:HCC\",\n",
    "                \"Liver:Hepatoblastoma\",\n",
    "                \"Lung:Mesothelioma\",\n",
    "                \"Lung:NSCLC_Adeno\",\n",
    "                \"Lung:NSCLC_Large_Cell\",\n",
    "                \"Lung:NSCLC_Others\",\n",
    "                \"Lung:NSCLC_Squamous\",\n",
    "                \"Lung:Others\",\n",
    "                \"Lung:SCLC\",\n",
    "                \"Lymphoma:Hodgkin\",\n",
    "                \"Lymphoma:Multiple_Myeloma\",\n",
    "                \"Lymphoma:NH_B_cell\",\n",
    "                \"Lymphoma:NH_T_cell\",\n",
    "                \"Oesophagus:Benign\",\n",
    "                \"Oesophagus:Carcinoma\",\n",
    "                \"Ovary:Carcinoma\",\n",
    "                \"Ovary:Germline\",\n",
    "                \"PNET:Neuroblastoma\",\n",
    "                \"Pancreas:Carcinoma\",\n",
    "                \"Prostate:Carcinoma\",\n",
    "                \"Salivary_Gland:Carcinoma\",\n",
    "                \"Skin:Melanoma\",\n",
    "                \"Soft_Tissue:Sarcoma_Fibro\",\n",
    "                \"Soft_Tissue:Sarcoma_FibrousHistiocytoma\",\n",
    "                \"Soft_Tissue:Sarcoma_Leiomyo\",\n",
    "                \"Soft_Tissue:Sarcoma_Others\",\n",
    "                \"Soft_Tissue:Sarcoma_Rhabdoid\",\n",
    "                \"Thyroid:Carcinoma\",\n",
    "                \"Upper_Aerodigestive_Tract:Carcinoma\"\n",
    "            ]\n",
    "        },\n",
    "        \"Ploidy\": {\n",
    "            \"description\": \"Ploidy is the number of complete sets of chromosomes in a cell, baseline unaltered ploisy in humans is 2\",\n",
    "            \"type\": \"number\"\n",
    "        },\n",
    "        \"PrimaryTumorSite\": {\n",
    "            \"description\": \"Location of primary tumor in patient cell line was derived from. If the cell line is derived from a metastasis, the primary tumor location may differ from the anatomical location the cell line source material was collected from.\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"Autonomic_Ganglia\",\n",
    "                \"Biliary_Tract\",\n",
    "                \"Bone\",\n",
    "                \"Breast\",\n",
    "                \"Central_Nervous_System\",\n",
    "                \"Endometrium\",\n",
    "                \"Haematopoietic_And_Lymphoid_Tissue\",\n",
    "                \"Kidney\",\n",
    "                \"Large_Intestine\",\n",
    "                \"Liver\",\n",
    "                \"Lung\",\n",
    "                \"Oesophagus\",\n",
    "                \"Ovary\",\n",
    "                \"Pancreas\",\n",
    "                \"Pleura\",\n",
    "                \"Prostate\",\n",
    "                \"Salivary_Gland\",\n",
    "                \"Skin\",\n",
    "                \"Small_Intestine\",\n",
    "                \"Soft_Tissue\",\n",
    "                \"Stomach\",\n",
    "                \"Thyroid\",\n",
    "                \"Upper_Aerodigestive_Tract\",\n",
    "                \"Urinary_Tract\"\n",
    "            ]\n",
    "        },\n",
    "        \"Proteomics10PlexID\": {\n",
    "            \"description\": \"Cell line ID for Proteomics 10-Plex assay to align datasets by sample\",\n",
    "            \"type\": \"number\"\n",
    "        },\n",
    "        \"ProteomicsTMTLabel\": {\n",
    "            \"description\": \"Tandem Mass Tag (TMT) used in proteomics of cell line in paired dataset\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"Purity\": {\n",
    "            \"description\": \"Proportion of cells in sample of malignant origin, a value of 1 denotes 100% tumor cells in sample\",\n",
    "            \"type\": \"number\"\n",
    "        },\n",
    "        \"SiteOfFinding\": {\n",
    "            \"description\": \"Location of tumor cell line was derived from\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"abdomen\",\n",
    "                \"abdominal_wall\",\n",
    "                \"acetabulum\",\n",
    "                \"adrenal\",\n",
    "                \"ascites\",\n",
    "                \"axillary_node\",\n",
    "                \"bone\",\n",
    "                \"bone_marrow\",\n",
    "                \"brain\",\n",
    "                \"breast\",\n",
    "                \"central_nervous_system\",\n",
    "                \"cerebrospinal_fluid\",\n",
    "                \"cervix\",\n",
    "                \"connective_tissue_trunk\",\n",
    "                \"liver\",\n",
    "                \"lung\",\n",
    "                \"lymph_node\",\n",
    "                \"muscle\",\n",
    "                \"omentum\",\n",
    "                \"pelvic_wall\",\n",
    "                \"pericardial_effusion\",\n",
    "                \"peritoneum\",\n",
    "                \"pleura\",\n",
    "                \"skin\",\n",
    "                \"soft_tissue\",\n",
    "                \"spleen\",\n",
    "                \"subcutaneous_tissue\",\n",
    "                \"supra_orbital_area\",\n",
    "                \"vertebra\"\n",
    "            ]\n",
    "        },\n",
    "        \"SiteSubtype1\": {\n",
    "            \"description\": \"Detailed site location of tumor cell line was derived from\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"NS\",\n",
    "                \"bile_duct\",\n",
    "                \"bladder\",\n",
    "                \"brain\",\n",
    "                \"bronchus\",\n",
    "                \"caecum\",\n",
    "                \"cerebellum\",\n",
    "                \"colon\",\n",
    "                \"duodenum\",\n",
    "                \"femur\",\n",
    "                \"fibrous_tissue_and_uncertain_origin\",\n",
    "                \"frontal_lobe\",\n",
    "                \"head_neck\",\n",
    "                \"humerus\",\n",
    "                \"larynx\",\n",
    "                \"left_upper_lobe\",\n",
    "                \"lower_third\",\n",
    "                \"lymph_node\",\n",
    "                \"meninges\",\n",
    "                \"middle_third\",\n",
    "                \"mouth\",\n",
    "                \"nan\",\n",
    "                \"parietal_lobe\",\n",
    "                \"pelvis\",\n",
    "                \"pharynx\",\n",
    "                \"rectum\",\n",
    "                \"skin\",\n",
    "                \"smooth_muscle\",\n",
    "                \"spleen\",\n",
    "                \"striated_muscle\",\n",
    "                \"submaxillary\",\n",
    "                \"temporal_lobe\",\n",
    "                \"tongue\",\n",
    "                \"upper_leg\",\n",
    "                \"upper_third\",\n",
    "                \"ureter\"\n",
    "            ]\n",
    "        },\n",
    "        \"SiteSubtype2\": {\n",
    "            \"description\": \"Detailed site location of tumor cell line was derived from, more detailed than Site Subtype 1\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"NS\",\n",
    "                \"abdomen\",\n",
    "                \"gingiva\",\n",
    "                \"glottis\",\n",
    "                \"hypopharynx\",\n",
    "                \"kidney\",\n",
    "                \"nan\",\n",
    "                \"ovary\",\n",
    "                \"right\",\n",
    "                \"sigmoid\",\n",
    "                \"subglottis\",\n",
    "                \"supraglottis\",\n",
    "                \"thyroid\",\n",
    "                \"tongue\",\n",
    "                \"uterus\",\n",
    "                \"vulva\"\n",
    "            ]\n",
    "        },\n",
    "        \"Subtype\": {\n",
    "            \"description\": \"Tumor subtype cell line was derived from\",\n",
    "            \"type\": \"string\",\n",
    "            \"enum\": [\n",
    "                \"ATL\",\n",
    "                \"Acute Lymphoblastic Leukemia (ALL), B-cell\",\n",
    "                \"Acute Lymphoblastic Leukemia (ALL), T-cell\",\n",
    "                \"Acute Myelogenous Leukemia (AML)\",\n",
    "                \"Acute Myelogenous Leukemia (AML), M2 (Myeloblastic)\",\n",
    "                \"Acute Myelogenous Leukemia (AML), M3 (Promyelocytic)\",\n",
    "                \"Acute Myelogenous Leukemia (AML), M4 (Myelomonocytic)\",\n",
    "                \"Acute Myelogenous Leukemia (AML), M5 (Eosinophilic/Monocytic)\",\n",
    "                \"Acute Myelogenous Leukemia (AML), M6 (Erythroleukemia)\",\n",
    "                \"Acute Myelogenous Leukemia (AML), M7 (Megakaryoblastic)\",\n",
    "                \"Adenocarcinoma\",\n",
    "                \"Adenocarcinoma, clear cell\",\n",
    "                \"Adenocarcinoma, endometrioid\",\n",
    "                \"Adenocarcinoma, high grade serous\",\n",
    "                \"Adenocarcinoma, low grade serous\",\n",
    "                \"Adenocarcinoma, mixed\",\n",
    "                \"Adenocarcinoma, mucinous\",\n",
    "                \"Adenocarcinoma, serous\",\n",
    "                \"Adenocarcinoma, signet ring cell\",\n",
    "                \"Adenocarcinoma, tubular\",\n",
    "                \"Astrocytoma\",\n",
    "                \"Atypical Teratoid Rhabdoid Tumor (ATRT)\",\n",
    "                \"B-cell\",\n",
    "                \"B-cell, Hodgkins\",\n",
    "                \"B-cell, Non-Hodgkins\",\n",
    "                \"B-cell, Non-Hodgkins, Burkitts\",\n",
    "                \"B-cell, Non-Hodgkins, Mantle Cell\",\n",
    "                \"Bladder\",\n",
    "                \"Bone\",\n",
    "                \"Breast\",\n",
    "                \"Breast Ductal Carcinoma\",\n",
    "                \"Caecum Adenocarcinoma\",\n",
    "                \"Carcinoid\",\n",
    "                \"Carcinoma\",\n",
    "                \"Carcinoma, anaplastic\",\n",
    "                \"Carcinoma, brenner\",\n",
    "                \"Carcinoma, follicular\",\n",
    "                \"Carcinoma, papillary\",\n",
    "                \"Cholangiocarcinoma, extrahepatic\",\n",
    "                \"Cholangiocarcinoma, intrahepatic\",\n",
    "                \"Chondrosarcoma\",\n",
    "                \"Chronic Lymphoblastic Leukemia (CLL), B-cell\",\n",
    "                \"Chronic Myelogenous Leukemia (CML)\",\n",
    "                \"Chronic Myelogenous Leukemia (CML), blast crisis\",\n",
    "                \"Clear Cell Carcinoma\",\n",
    "                \"Colorectal\",\n",
    "                \"Cystadenocarcinoma, clear cell\",\n",
    "                \"Cystadenocarcinoma, endometrioid\",\n",
    "                \"Cystadenocarcinoma, high grade serous\",\n",
    "                \"Cystadenocarcinoma, mucinous\",\n",
    "                \"Diffuse Large B-cell Lymphoma (DLBCL)\",\n",
    "                \"Ductal Adenocarcinoma, exocrine\",\n",
    "                \"Ductal Adenosquamous Carcinoma\",\n",
    "                \"Ductal Adenosquamous Carcinoma, exocrine\",\n",
    "                \"Duodenal Adenocarcinoma\",\n",
    "                \"Endometrial Adenocarcinoma\",\n",
    "                \"Endometrial Adenosquamous Carcinoma\",\n",
    "                \"Endometrial Stromal Sarcoma\",\n",
    "                \"Ewings Sarcoma\",\n",
    "                \"Fibrosarcoma\",\n",
    "                \"Glioblastoma\",\n",
    "                \"Glioma\",\n",
    "                \"Hepatoblastoma\",\n",
    "                \"Hepatocellular Carcinoma\",\n",
    "                \"Hepatocellular Carcinoma, HBs-antigen carrier\",\n",
    "                \"Leiomyosarcoma\",\n",
    "                \"Lung\",\n",
    "                \"Lymphoma\",\n",
    "                \"Malignant Mixed Mullerian Tumor (MMMT)\",\n",
    "                \"Malignant Rhabdoid Tumor\",\n",
    "                \"Medulloblastoma\",\n",
    "                \"Melanoma\",\n",
    "                \"Melanoma, amelanotic\",\n",
    "                \"Meningioma\",\n",
    "                \"Mesothelioma\",\n",
    "                \"Mullerian Carcinoma\",\n",
    "                \"Multiple Myeloma\",\n",
    "                \"Multiple Myeloma, plasmacytoma\",\n",
    "                \"Myeloma\",\n",
    "                \"Non-Small Cell Lung Cancer (NSCLC), Adenocarcinoma\",\n",
    "                \"Non-Small Cell Lung Cancer (NSCLC), Adenosquamous Carcinoma\",\n",
    "                \"Non-Small Cell Lung Cancer (NSCLC), Large Cell Carcinoma\",\n",
    "                \"Non-Small Cell Lung Cancer (NSCLC), Mucoepidermoid Carcinoma\",\n",
    "                \"Non-Small Cell Lung Cancer (NSCLC), Squamous Cell Carcinoma\",\n",
    "                \"Non-Small Cell Lung Cancer (NSCLC), unspecified\",\n",
    "                \"Oligodendroglioma\",\n",
    "                \"Osteosarcoma\",\n",
    "                \"Pleomorphic Sarcoma\",\n",
    "                \"Renal Carcinoma, clear cell\",\n",
    "                \"Renal Carcinoma, transitional cell\",\n",
    "                \"Renal Cell Carcinoma\",\n",
    "                \"Renal Leiomyoblastoma\",\n",
    "                \"Rhabdomyosarcoma\",\n",
    "                \"Rhabdomyosarcoma, alveolar\",\n",
    "                \"Rhabdomyosarcoma, embryonal\",\n",
    "                \"Skin\",\n",
    "                \"Small Cell Carcinoma\",\n",
    "                \"Small Cell Lung Cancer (SCLC)\",\n",
    "                \"Soft tissue\",\n",
    "                \"Somatostatinoma\",\n",
    "                \"Squamous Cell Carcinoma\",\n",
    "                \"Squamous Cell Carcinoma, basaloid\",\n",
    "                \"Squamous Cell Carcinoma, hypopharyngeal\",\n",
    "                \"Squamous Cell Carcinoma, laryngeal\",\n",
    "                \"Squamous Cell Carcinoma, oral\",\n",
    "                \"Squamous Cell Carcinoma, pharynx\",\n",
    "                \"Squamous Cell Carcinoma, salivary gland\",\n",
    "                \"Squamous Cell Carcinoma, tongue\",\n",
    "                \"T-cell\",\n",
    "                \"T-cell, Non-Hodgkins, Anaplastic Large Cell (ALCL)\",\n",
    "                \"T-cell, Non-Hodgkins, Cutaneous\",\n",
    "                \"Thyroid Sarcoma\",\n",
    "                \"Transitional Cell Carcinoma\",\n",
    "                \"Upper aerodigestive\",\n",
    "                \"Uterine Sarcoma\"\n",
    "            ]\n",
    "        },\n",
    "        \"Supplements\": {\n",
    "            \"description\": \"Additivies to cell line growth medium\",\n",
    "            \"type\": \"string\"\n",
    "        },\n",
    "        \"TMBNonSynonymous\": {\n",
    "            \"description\": \"Tumor Mutation Burden (TMB), number of nonsyn mutations per MB of DNA, as calculated by cBioportal\",\n",
    "            \"type\": \"number\"\n",
    "        }\n",
    "    }\n",
    "}\n",
    "\n",
    "```"
   ]
  }
 ],
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