{"_id":"56d0a2be376b040b005b304e","parentDoc":null,"version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":37,"createdAt":"2015-09-17T16:58:03.490Z","releaseDate":"2015-09-17T16:58:03.490Z","categories":["55faf11ca62ba1170021a9ab","55faf8f4d0e22017005b8272","55faf91aa62ba1170021a9b5","55faf929a8a7770d00c2c0bd","55faf932a8a7770d00c2c0bf","55faf94b17b9d00d00969f47","55faf958d0e22017005b8274","55faf95fa8a7770d00c2c0c0","55faf96917b9d00d00969f48","55faf970a8a7770d00c2c0c1","55faf98c825d5f19001fa3a6","55faf99aa62ba1170021a9b8","55faf99fa62ba1170021a9b9","55faf9aa17b9d00d00969f49","55faf9b6a8a7770d00c2c0c3","55faf9bda62ba1170021a9ba","5604570090ee490d00440551","5637e8b2fbe1c50d008cb078","5649bb624fa1460d00780add","5671974d1b6b730d008b4823","5671979d60c8e70d006c9760","568e8eef70ca1f0d0035808e","56d0a2081ecc471500f1795e","56d4a0adde40c70b00823ea3","56d96b03dd90610b00270849","56fbb83d8f21c817002af880","573c811bee2b3b2200422be1","576bc92afb62dd20001cda85","5771811e27a5c20e00030dcd","5785191af3a10c0e009b75b0","57bdf84d5d48411900cd8dc0","57ff5c5dc135231700aed806","5804caf792398f0f00e77521","58458b4fba4f1c0f009692bb","586d3c287c6b5b2300c05055","58ef66d88646742f009a0216","58f5d52d7891630f00fe4e77"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"56d0a2081ecc471500f1795e","project":"55faf11ba62ba1170021a9a7","__v":4,"pages":["56d0a2be376b040b005b304e","56d0a2e6376b040b005b3051","56d0ae447c2e100b000af980","56d0b36d40d36e1d00bc145a"],"version":"55faf11ba62ba1170021a9aa","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-02-26T19:05:44.797Z","from_sync":false,"order":9,"slug":"set-metadata-associated-with-a-private-file","title":"SET METADATA ASSOCIATED WITH A PRIVATE FILE"},"__v":47,"user":"554290cd6592e60d00027d17","project":"55faf11ba62ba1170021a9a7","updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-02-26T19:08:46.081Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"Metadata associated with your private files makes them searchable, keeping your file collection manageable as it grows. It also enables them to be properly grouped for analyses. \n[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"body\": \"* [Overview](#section-overview) \\n* [Metadata categories](#section-metadata-categories)\\n   * [File](#section-file)\\n   * [Sample](#section-sample)\\n   * [Aliquot](#section-aliquot)\\n   * [Case](#section-case)\\n   * [General](#section-general)\\n\\n* [Querying with metadata on the CGC](#section-querying-with-metadata-on-the-cgc)\"\n}\n[/block]\n##Overview\nOne of the most common reasons for failed tasks is missing or improper metadata. Lack of proper metadata increases the chances that tools and workflows will fail to run correctly. We recommend that you set the metadata fields for your input files before executing analyses on the CGC.\n\nThere are three ways to enter or change file metadata:\n\n  * [Using the visual interface](doc:set-metadata-using-the-visual-interface)\n  * [Using the command line uploader](doc:set-metadata-using-the-command-line-uploader) \n  * [Using the API](doc:set-metadata-using-the-api)\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"Metadata properties for files from TCGA dataset are **not** editable in a project. See the [metadata categories](#section-metadata-categories) below for properties editable in your private files on the CGC.\"\n}\n[/block]\nWe have 24 metadata fields associated with each file on the CGC. These are subdivided into five categories ([**File**](#section-file), [**Sample**](#section-sample), [**Aliquot**](#section-aliquot), [**Case**](#section-case), and [**General**](#section-general)). The **Case** category is further subdivided by the following properties: **Diagnosis**, **Demographic**, **Status**, and **Prognosis**. The recommended practice is to enter as much metadata as possible when you first upload files to the CGC. For instance, for raw sequencing files, you should enter **Platform** (**sequencing platform**) and **Sample ID**. See the tables below for more details about the metadata fields.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Metadata categories\n\n###File\n\nIn the following table, you will find the name, description, and values of metadata fields for **File**. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files).\n[block:parameters]\n{\n  \"data\": {\n    \"0-0\": \"**Library ID**\",\n    \"h-0\": \"Name\",\n    \"h-1\": \"API key\",\n    \"h-2\": \"Description\",\n    \"h-3\": \"Values\",\n    \"0-3\": \"This takes a string.\",\n    \"1-3\": \"This takes a string.\\nSuggested values:\\n  * Affymetrix SNP Array 6.0\\n  * Illumina HiSeq\\n  * Illumina Human Methylation 450\\n  * Illumina GA\\n  * MDA_RPPA_Core\\n  * BCR Record\\n  * Hospital Record\\n  * llumina Human Methylation 27\\n  * ABI capillary sequencer\\n  * AgilentG4502A_07_3\\n  * HG-CGH-244A\\n  * HG-CGH-415K_G4124A\\n  * CGH-1x1M_G4447A\\n  * Illumina MiSeq\\n  * HT_HG-U133A\\n  * Illumina Human 1M Duo\\n  * H-miRNA_8x15Kv2\\n  * Illumina HumanHap550\\n  * H-miRNA_8x15K\\n  * AgilentG4502A_07_2\\n  * HuEx-1_0-st-v2\\n  * ABI SOLiD\\n  * Complete Genomics\\n  * HG-U133_Plus_2\\n  * Illumina DNA Methylation OMA003 CPI\\n  * Illumina DNA Methylation OMA002 CPI\\n  * AgilentG4502A_07_1\\n  * Ion Torrent PGM\\n  * Affymetrix U133 Plus 2\\n  * LS 454\\n  * HiSeq X Ten\\n  * Mixed platforms\\n  * Illumina\\n  * Helicos\\n  * PacBio\\n  * Not available\",\n    \"2-3\": \"This takes a string.\",\n    \"3-3\": \"This takes a value of 1 or 2.\\n\\n**Note**: For single-end sequencing no value is needed.\",\n    \"4-3\": \"This takes an integer.\",\n    \"5-3\": \"Choose from one of the following options:\\n  * sanger\\n  * llumina13\\n  * illumina15\\n  * illumina18\\n  * solexa\\nOr, enter no value.\",\n    \"6-3\": \"This takes a string.\\nSuggested values:\\n  * DNA-Seq\\n  * WXS\\n  * WGS\\n  * Amplicon\\n  * Bisulfite-Seq\\n  * VALIDATION\\n  * RNA-Seq\\n  * miRNA-Seq\\n  * Total RNA-Seq\\n  * Genotyping Array\\n  * Exon Array\\n  * CGH Array\\n  * Methylation Array\\n  * Gene Expression Array\\n  * miRNA Array\\n  * Protein Expression Array\\n  * MSI- Mono- Dinucleotide Array\\n  * Not available\",\n    \"7-3\": \"This takes a string.\\n\\nSuggested values:\\n\\n  * NCBI36_BCCAGSC_variant\\n  * NCBI36_BCM_variant\\n  * NCBI36_WUGSC_variant\\n  * HG18\\n  * HG18_Broad_variant\\n  * GRCh37\\n  * GRCh37-lite\\n  * GRCh37_BI_Variant\\n  * GRCh37-lite-+-HPV_Redux-build\\n  * GRCh37-lite_WUGSC_variant_1\\n  * GRCh37-lite_WUGSC_variant_2\\n  * HG19\\n  * HG19_Broad_variant\\n  * HS37D5\\n  * GRCh38\",\n    \"1-0\": \"**Platform**\",\n    \"2-0\": \"**Platform unit ID**\",\n    \"3-0\": \"**Paired end**\",\n    \"4-0\": \"**File segment number**\",\n    \"5-0\": \"**Quality scale**\",\n    \"6-0\": \"**Experimental strategy**\",\n    \"7-0\": \"**Reference genome**\",\n    \"0-1\": \"**library_id**\",\n    \"1-1\": \"**platform**\",\n    \"2-1\": \"**platform_unit_id**\",\n    \"3-1\": \"**paired_end**\",\n    \"4-1\": \"**file_segment_number**\",\n    \"5-1\": \"**quality_scale**\",\n    \"6-1\": \"**experimental_strategy**\",\n    \"7-1\": \"**reference_genome**\",\n    \"0-2\": \"This is an identifier for the sequencing library preparation.\",\n    \"1-2\": \"This is the version (manufacturer, model, etc.) of the technology that was used sequencing or assaying.\",\n    \"2-2\": \"This is an identifier for lanes (Illumina), or for slides (SOLiD) in the case that a library was split and ran over multiple lanes on the flow cell or slides. The platform unit ID refers to the lane ID or the slide ID.\",\n    \"3-2\": \"For paired-end sequencing, this value determines the end of the fragment sequenced.\",\n    \"4-2\": \"If the sequencing reads for a single library, sample and lane are divided into multiple (smaller) files, the File segment number is used to enumerate these. Otherwise, this field can be left blank.\",\n    \"5-2\": \"For raw reads, this value denotes the sequencing technology and quality format. For BAM and SAM files, this value should always be ‘Sanger’.\",\n    \"6-2\": \"This is the method or protocol used to perform the laboratory analysis.\",\n    \"7-2\": \"The reference assembly (such as HG19 or GRCh37) to which the nucleotide sequence of a case can be aligned.\"\n  },\n  \"cols\": 4,\n  \"rows\": 8\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Sample\n\nIn the following table, you will find the name, description, and values of metadata fields for **Sample**. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files).\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"API key\",\n    \"h-2\": \"Description\",\n    \"h-3\": \"Value\",\n    \"0-3\": \"This takes a string.\",\n    \"1-3\": \"This takes a string.\\n\\nSuggested values:\\n\\n  * Blood Derived Normal\\n  * Buccal Cell Normal\\n  * Primary Blood Derived Cancer - Peripheral Blood\\n  * Recurrent Blood Derived Cancer - Peripheral Blood\\n  * Primary Tumor\\n  * Recurrent Blood Derived Cancer - Bone Marrow\\n  * Recurrent Tumor\\n  * Solid Tissue Normal\\n  * Metastatic\\n  * Additional - New Primary\\n  * Additional Metastatic\\n  * Human Tumor Original Cells\\n  * Primary Blood Derived Cancer - Bone Marrow\\n  * Cell Lines\\n  * Xenograft Tissue\\n  * Bone Marrow Normal\\n  * Fibroblasts from Bone Marrow Normal\\n  * Not available\",\n    \"2-3\": \"This takes a string.\",\n    \"2-0\": \"**Sample UUID**\",\n    \"2-1\": \"**sample_uuid**\",\n    \"1-0\": \"**Sample type**\",\n    \"1-1\": \"**sample_type**\",\n    \"0-0\": \"**Sample ID**\",\n    \"0-1\": \"**sample_id**\",\n    \"0-2\": \"A human readable identifier for a sample or specimen, which could contain some metadata information. A sample or specimen is material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes, including but not limited to tissues, body fluids, cells, organs, embryos, body excretory products, etc.\",\n    \"1-2\": \"The type of material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes. This includes tissues, body fluids, cells, organs, embryos, body excretory products, etc.\",\n    \"2-2\": \"A unique identifier for the sample or specimen used in the investigation, such as a Universally Unique Identifier (UUID). A sample or specimen is material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes, including but not limited to tissues, body fluids, cells, organs, embryos, body excretory products, etc.\"\n  },\n  \"cols\": 4,\n  \"rows\": 3\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Aliquot\n\nIn the following table, you will find the name, description, and values of metadata fields for **Aliquot**. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files).\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"API key\",\n    \"h-2\": \"Description\",\n    \"h-3\": \"Value\",\n    \"0-0\": \"**Aliquot ID**\",\n    \"0-1\": \"**aliquot_id**\",\n    \"0-2\": \"A human readable identifier for an aliquot, which may contain metadata information. The aliquot is a product or unit extracted from a sample of a specimen and prepared for the analysis.\",\n    \"0-3\": \"This takes a string.\",\n    \"1-0\": \"**Aliquot UUID**\",\n    \"1-1\": \"**aliquot_uuid**\",\n    \"1-2\": \"The unique identifier for an aliquot, such as a Universally Unique Identifier (UUID). The aliquot is a product or unit extracted from a sample of a specimen and prepared for the analysis.\",\n    \"1-3\": \"This takes a string.\"\n  },\n  \"cols\": 4,\n  \"rows\": 2\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Case\n\nIn the following table, you will find the name, description, and values of metadata fields for **Case**. The **Case** category is further subdivided by the following properties: **Diagnosis**, **Demographic**, **Status**, and **Prognosis**. These properties are included in italics below the metadata field's name in the first column. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files).\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"API key\",\n    \"h-2\": \"Description\",\n    \"h-3\": \"Value\",\n    \"0-0\": \"**Case ID**\",\n    \"0-1\": \"**case_id**\",\n    \"0-2\": \"An identifier, such as a number or a string that may contain metadata information, for a subject who has taken part in the investigation of study.\",\n    \"0-3\": \"This takes a string.\",\n    \"1-0\": \"**Case UUID**\",\n    \"1-1\": \"**case_uuid**\",\n    \"1-2\": \"An unique identifier, such as a Universally Unique Identifier (UUID), for a subject who has taken part in the investigation of study.\",\n    \"1-3\": \"This takes a string.\",\n    \"2-0\": \"**Primary site** \\n(*Diagnosis*)\",\n    \"2-1\": \"**primary_site**\",\n    \"2-2\": \"The anatomical site where the primary tumor is located in the organism.\",\n    \"2-3\": \"This takes a string.\\n\\nSuggested values:\\n  * Adrenal Gland\\n  * Bile Duct\\n  * Bladder\\n  * Blood\\n  * Brain\\n  * Breast\\n  * Cervix\\n  * Colorectal\\n  * Esophagus\\n  * Eye\\n  * Head And Neck\\n  * Liver\\n  * Lung\\n  * Lymph Nodes\\n  * Kidney\\n  * Mesenchymal\\n  * Mesothelium\\n  * Nervous System\\n  * Ovary\\n  * Pancreas\\n  * Prostate\\n  * Skin\\n  * Stomach\\n  * Uterus\\n  * Testis\\n  * Thymus\\n  * Thyroid\\n  * Not available\",\n    \"3-0\": \"**Disease type**\\n(*Diagnosis*)\",\n    \"3-1\": \"**disease_type**\",\n    \"3-2\": \"The type of the disease or condition studied.\",\n    \"3-3\": \"This takes a string.\\n\\nSuggested values:\\n  * Acute Myeloid Leukemia\\n  * Adrenocortical Carcinoma\\n  * Bladder Urothelial Carcinoma\\n  * Brain Lower Grade Glioma\\n  * Breast Invasive Carcinoma\\n  * Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma\\n  * Cholangiocarcinoma\\n  * Chronic Myelogenous Leukemia\\n  * Colon Adenocarcinoma\\n  * Esophageal Carcinoma\\n  * Glioblastoma Multiforme\\n  * Head and Neck Squamous Cell Carcinoma\\n  * Kidney Chromophobe\\n  * Kidney Renal Clear Cell Carcinoma\\n  *  Kidney Renal Papillary Cell Carcinoma\\n  * Liver Hepatocellular Carcinoma\\n  * Lung Adenocarcinoma\\n  * Lung Squamous Cell Carcinoma\\n  * Lymphoid Neoplasm Diffuse Large B-cell Lymphoma\\n  * Mesothelioma\\n  * Ovarian Serous Cystadenocarcinoma\\n  * Pancreatic Adenocarcinoma\\n  * Pheochromocytoma and Paraganglioma\\n  * Prostate Adenocarcinoma\\n  * Rectum Adenocarcinoma\\n  * Sarcoma\\n  * Skin Cutaneous Melanoma\\n  * Stomach Adenocarcinoma\\n  * Testicular Germ Cell Tumors\\n  * Thymoma\\n  * Thyroid Carcinoma\\n  * Uterine Carcinosarcoma\\n  * Uterine Corpus Endometrial Carcinoma\\n  * Uveal Melanoma\\n  * Not available\",\n    \"4-0\": \"**Gender**\\n(*Demographic*)\",\n    \"4-1\": \"**gender**\",\n    \"4-2\": \"The collection of behaviors and attitudes that distinguish people on the basis of societal roles expected for the two sexes.\",\n    \"4-3\": \"Choose from the following:\\n  * Female\\n  * Male\",\n    \"5-0\": \"**Age at diagnosis** \\n(*Diagnosis* )\",\n    \"5-1\": \"**age_at_diagnosis**\",\n    \"5-2\": \"The age in years of the case at the initial pathological diagnosis of disease or cancer.\",\n    \"5-3\": \"This takes a non-negative integer.\",\n    \"6-0\": \"**Vital status**\\n(*Status*)\",\n    \"6-1\": \"**vital_status**\",\n    \"6-2\": \"The state of being living or deceased for cases that are part of the investigation.\",\n    \"6-3\": \"Choose from the following:\\n  * Alive\\n  * Dead\\n  * Lost to follow-up\\n  * Unknown\\n  * Not available\",\n    \"7-0\": \"**Days to death**\\n(*Prognosis*)\",\n    \"7-1\": \"**days_to_death**\",\n    \"7-2\": \"The number of days from the date of the initial pathological diagnosis to the date of death for the case in investigation.\",\n    \"7-3\": \"This takes a non-negative integer.\",\n    \"8-0\": \"**Race**\\n(*Demographic*)\",\n    \"8-1\": \"**race**\",\n    \"8-2\": \"A classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution.\",\n    \"8-3\": \"This takes a string.\\n\\nSuggested values:\\n  * White\\n  * American Indian or Alaska Native\\n  * Black or African American\\n  * Asian\\n  * Native Hawaiian or other Pacific Islander\\n  * Not reported\\n  * Not available\",\n    \"9-0\": \"**Ethnicity**\\n(*Demographic*)\",\n    \"9-1\": \"**ethnicity**\",\n    \"9-2\": \"A socially defined category of people based on common ancestral, cultural, biological, and social factors.\",\n    \"9-3\": \"This takes a string.\\n\\nSuggested values:\\n  * Hispanic or Latino\\n  * Not Hispanic or Latino\\n  * Not reported\\n  * Not Available\"\n  },\n  \"cols\": 4,\n  \"rows\": 10\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###General\n\nIn the following table, you will find the name, description, and values of metadata fields for **General**. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files).\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Name\",\n    \"h-1\": \"API key\",\n    \"h-2\": \"Description\",\n    \"h-3\": \"Value\",\n    \"0-0\": \"**Investigation**\",\n    \"0-1\": \"**investigation**\",\n    \"0-2\": \"A value denoting the project or study that generated the data.\",\n    \"0-3\": \"This takes a string.\"\n  },\n  \"cols\": 4,\n  \"rows\": 1\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n[block:callout]\n{\n  \"type\": \"info\",\n  \"body\": \"Apart from the standard set of metadata fields that can be seen through the visual interface, custom metadata fields can be added via the [command line uploader](doc:set-metadata-using-the-command-line-uploader) or via the [API](doc:set-metadata-using-the-api).\"\n}\n[/block]\n##Querying with metadata on the CGC\nWhile you are in the Data Browser, you can query files using over 100 [TCGA metadata fields](tcga-metadata-on-the-cgc). After you filter your files and [copy them to a project](the-data-browser#section-copy-files-to-a-project), you will only be able to see the [metadata fields described on this page](#metadata-categories). The Seven Bridges team has selected these fields so you can use them to further filter and analyze your data.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"<a name=\"top\"></a>","slug":"metadata-for-private-data","type":"basic","title":"Metadata for your private data"}

Metadata for your private data

<a name="top"></a>

Metadata associated with your private files makes them searchable, keeping your file collection manageable as it grows. It also enables them to be properly grouped for analyses. [block:callout] { "type": "warning", "title": "On this page:", "body": "* [Overview](#section-overview) \n* [Metadata categories](#section-metadata-categories)\n * [File](#section-file)\n * [Sample](#section-sample)\n * [Aliquot](#section-aliquot)\n * [Case](#section-case)\n * [General](#section-general)\n\n* [Querying with metadata on the CGC](#section-querying-with-metadata-on-the-cgc)" } [/block] ##Overview One of the most common reasons for failed tasks is missing or improper metadata. Lack of proper metadata increases the chances that tools and workflows will fail to run correctly. We recommend that you set the metadata fields for your input files before executing analyses on the CGC. There are three ways to enter or change file metadata: * [Using the visual interface](doc:set-metadata-using-the-visual-interface) * [Using the command line uploader](doc:set-metadata-using-the-command-line-uploader) * [Using the API](doc:set-metadata-using-the-api) [block:callout] { "type": "info", "body": "Metadata properties for files from TCGA dataset are **not** editable in a project. See the [metadata categories](#section-metadata-categories) below for properties editable in your private files on the CGC." } [/block] We have 24 metadata fields associated with each file on the CGC. These are subdivided into five categories ([**File**](#section-file), [**Sample**](#section-sample), [**Aliquot**](#section-aliquot), [**Case**](#section-case), and [**General**](#section-general)). The **Case** category is further subdivided by the following properties: **Diagnosis**, **Demographic**, **Status**, and **Prognosis**. The recommended practice is to enter as much metadata as possible when you first upload files to the CGC. For instance, for raw sequencing files, you should enter **Platform** (**sequencing platform**) and **Sample ID**. See the tables below for more details about the metadata fields. <div align="right"><a href="#top">top</a></div> ##Metadata categories ###File In the following table, you will find the name, description, and values of metadata fields for **File**. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files). [block:parameters] { "data": { "0-0": "**Library ID**", "h-0": "Name", "h-1": "API key", "h-2": "Description", "h-3": "Values", "0-3": "This takes a string.", "1-3": "This takes a string.\nSuggested values:\n * Affymetrix SNP Array 6.0\n * Illumina HiSeq\n * Illumina Human Methylation 450\n * Illumina GA\n * MDA_RPPA_Core\n * BCR Record\n * Hospital Record\n * llumina Human Methylation 27\n * ABI capillary sequencer\n * AgilentG4502A_07_3\n * HG-CGH-244A\n * HG-CGH-415K_G4124A\n * CGH-1x1M_G4447A\n * Illumina MiSeq\n * HT_HG-U133A\n * Illumina Human 1M Duo\n * H-miRNA_8x15Kv2\n * Illumina HumanHap550\n * H-miRNA_8x15K\n * AgilentG4502A_07_2\n * HuEx-1_0-st-v2\n * ABI SOLiD\n * Complete Genomics\n * HG-U133_Plus_2\n * Illumina DNA Methylation OMA003 CPI\n * Illumina DNA Methylation OMA002 CPI\n * AgilentG4502A_07_1\n * Ion Torrent PGM\n * Affymetrix U133 Plus 2\n * LS 454\n * HiSeq X Ten\n * Mixed platforms\n * Illumina\n * Helicos\n * PacBio\n * Not available", "2-3": "This takes a string.", "3-3": "This takes a value of 1 or 2.\n\n**Note**: For single-end sequencing no value is needed.", "4-3": "This takes an integer.", "5-3": "Choose from one of the following options:\n * sanger\n * llumina13\n * illumina15\n * illumina18\n * solexa\nOr, enter no value.", "6-3": "This takes a string.\nSuggested values:\n * DNA-Seq\n * WXS\n * WGS\n * Amplicon\n * Bisulfite-Seq\n * VALIDATION\n * RNA-Seq\n * miRNA-Seq\n * Total RNA-Seq\n * Genotyping Array\n * Exon Array\n * CGH Array\n * Methylation Array\n * Gene Expression Array\n * miRNA Array\n * Protein Expression Array\n * MSI- Mono- Dinucleotide Array\n * Not available", "7-3": "This takes a string.\n\nSuggested values:\n\n * NCBI36_BCCAGSC_variant\n * NCBI36_BCM_variant\n * NCBI36_WUGSC_variant\n * HG18\n * HG18_Broad_variant\n * GRCh37\n * GRCh37-lite\n * GRCh37_BI_Variant\n * GRCh37-lite-+-HPV_Redux-build\n * GRCh37-lite_WUGSC_variant_1\n * GRCh37-lite_WUGSC_variant_2\n * HG19\n * HG19_Broad_variant\n * HS37D5\n * GRCh38", "1-0": "**Platform**", "2-0": "**Platform unit ID**", "3-0": "**Paired end**", "4-0": "**File segment number**", "5-0": "**Quality scale**", "6-0": "**Experimental strategy**", "7-0": "**Reference genome**", "0-1": "**library_id**", "1-1": "**platform**", "2-1": "**platform_unit_id**", "3-1": "**paired_end**", "4-1": "**file_segment_number**", "5-1": "**quality_scale**", "6-1": "**experimental_strategy**", "7-1": "**reference_genome**", "0-2": "This is an identifier for the sequencing library preparation.", "1-2": "This is the version (manufacturer, model, etc.) of the technology that was used sequencing or assaying.", "2-2": "This is an identifier for lanes (Illumina), or for slides (SOLiD) in the case that a library was split and ran over multiple lanes on the flow cell or slides. The platform unit ID refers to the lane ID or the slide ID.", "3-2": "For paired-end sequencing, this value determines the end of the fragment sequenced.", "4-2": "If the sequencing reads for a single library, sample and lane are divided into multiple (smaller) files, the File segment number is used to enumerate these. Otherwise, this field can be left blank.", "5-2": "For raw reads, this value denotes the sequencing technology and quality format. For BAM and SAM files, this value should always be ‘Sanger’.", "6-2": "This is the method or protocol used to perform the laboratory analysis.", "7-2": "The reference assembly (such as HG19 or GRCh37) to which the nucleotide sequence of a case can be aligned." }, "cols": 4, "rows": 8 } [/block] <div align="right"><a href="#top">top</a></div> ###Sample In the following table, you will find the name, description, and values of metadata fields for **Sample**. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files). [block:parameters] { "data": { "h-0": "Name", "h-1": "API key", "h-2": "Description", "h-3": "Value", "0-3": "This takes a string.", "1-3": "This takes a string.\n\nSuggested values:\n\n * Blood Derived Normal\n * Buccal Cell Normal\n * Primary Blood Derived Cancer - Peripheral Blood\n * Recurrent Blood Derived Cancer - Peripheral Blood\n * Primary Tumor\n * Recurrent Blood Derived Cancer - Bone Marrow\n * Recurrent Tumor\n * Solid Tissue Normal\n * Metastatic\n * Additional - New Primary\n * Additional Metastatic\n * Human Tumor Original Cells\n * Primary Blood Derived Cancer - Bone Marrow\n * Cell Lines\n * Xenograft Tissue\n * Bone Marrow Normal\n * Fibroblasts from Bone Marrow Normal\n * Not available", "2-3": "This takes a string.", "2-0": "**Sample UUID**", "2-1": "**sample_uuid**", "1-0": "**Sample type**", "1-1": "**sample_type**", "0-0": "**Sample ID**", "0-1": "**sample_id**", "0-2": "A human readable identifier for a sample or specimen, which could contain some metadata information. A sample or specimen is material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes, including but not limited to tissues, body fluids, cells, organs, embryos, body excretory products, etc.", "1-2": "The type of material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes. This includes tissues, body fluids, cells, organs, embryos, body excretory products, etc.", "2-2": "A unique identifier for the sample or specimen used in the investigation, such as a Universally Unique Identifier (UUID). A sample or specimen is material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes, including but not limited to tissues, body fluids, cells, organs, embryos, body excretory products, etc." }, "cols": 4, "rows": 3 } [/block] <div align="right"><a href="#top">top</a></div> ###Aliquot In the following table, you will find the name, description, and values of metadata fields for **Aliquot**. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files). [block:parameters] { "data": { "h-0": "Name", "h-1": "API key", "h-2": "Description", "h-3": "Value", "0-0": "**Aliquot ID**", "0-1": "**aliquot_id**", "0-2": "A human readable identifier for an aliquot, which may contain metadata information. The aliquot is a product or unit extracted from a sample of a specimen and prepared for the analysis.", "0-3": "This takes a string.", "1-0": "**Aliquot UUID**", "1-1": "**aliquot_uuid**", "1-2": "The unique identifier for an aliquot, such as a Universally Unique Identifier (UUID). The aliquot is a product or unit extracted from a sample of a specimen and prepared for the analysis.", "1-3": "This takes a string." }, "cols": 4, "rows": 2 } [/block] <div align="right"><a href="#top">top</a></div> ###Case In the following table, you will find the name, description, and values of metadata fields for **Case**. The **Case** category is further subdivided by the following properties: **Diagnosis**, **Demographic**, **Status**, and **Prognosis**. These properties are included in italics below the metadata field's name in the first column. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files). [block:parameters] { "data": { "h-0": "Name", "h-1": "API key", "h-2": "Description", "h-3": "Value", "0-0": "**Case ID**", "0-1": "**case_id**", "0-2": "An identifier, such as a number or a string that may contain metadata information, for a subject who has taken part in the investigation of study.", "0-3": "This takes a string.", "1-0": "**Case UUID**", "1-1": "**case_uuid**", "1-2": "An unique identifier, such as a Universally Unique Identifier (UUID), for a subject who has taken part in the investigation of study.", "1-3": "This takes a string.", "2-0": "**Primary site** \n(*Diagnosis*)", "2-1": "**primary_site**", "2-2": "The anatomical site where the primary tumor is located in the organism.", "2-3": "This takes a string.\n\nSuggested values:\n * Adrenal Gland\n * Bile Duct\n * Bladder\n * Blood\n * Brain\n * Breast\n * Cervix\n * Colorectal\n * Esophagus\n * Eye\n * Head And Neck\n * Liver\n * Lung\n * Lymph Nodes\n * Kidney\n * Mesenchymal\n * Mesothelium\n * Nervous System\n * Ovary\n * Pancreas\n * Prostate\n * Skin\n * Stomach\n * Uterus\n * Testis\n * Thymus\n * Thyroid\n * Not available", "3-0": "**Disease type**\n(*Diagnosis*)", "3-1": "**disease_type**", "3-2": "The type of the disease or condition studied.", "3-3": "This takes a string.\n\nSuggested values:\n * Acute Myeloid Leukemia\n * Adrenocortical Carcinoma\n * Bladder Urothelial Carcinoma\n * Brain Lower Grade Glioma\n * Breast Invasive Carcinoma\n * Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma\n * Cholangiocarcinoma\n * Chronic Myelogenous Leukemia\n * Colon Adenocarcinoma\n * Esophageal Carcinoma\n * Glioblastoma Multiforme\n * Head and Neck Squamous Cell Carcinoma\n * Kidney Chromophobe\n * Kidney Renal Clear Cell Carcinoma\n * Kidney Renal Papillary Cell Carcinoma\n * Liver Hepatocellular Carcinoma\n * Lung Adenocarcinoma\n * Lung Squamous Cell Carcinoma\n * Lymphoid Neoplasm Diffuse Large B-cell Lymphoma\n * Mesothelioma\n * Ovarian Serous Cystadenocarcinoma\n * Pancreatic Adenocarcinoma\n * Pheochromocytoma and Paraganglioma\n * Prostate Adenocarcinoma\n * Rectum Adenocarcinoma\n * Sarcoma\n * Skin Cutaneous Melanoma\n * Stomach Adenocarcinoma\n * Testicular Germ Cell Tumors\n * Thymoma\n * Thyroid Carcinoma\n * Uterine Carcinosarcoma\n * Uterine Corpus Endometrial Carcinoma\n * Uveal Melanoma\n * Not available", "4-0": "**Gender**\n(*Demographic*)", "4-1": "**gender**", "4-2": "The collection of behaviors and attitudes that distinguish people on the basis of societal roles expected for the two sexes.", "4-3": "Choose from the following:\n * Female\n * Male", "5-0": "**Age at diagnosis** \n(*Diagnosis* )", "5-1": "**age_at_diagnosis**", "5-2": "The age in years of the case at the initial pathological diagnosis of disease or cancer.", "5-3": "This takes a non-negative integer.", "6-0": "**Vital status**\n(*Status*)", "6-1": "**vital_status**", "6-2": "The state of being living or deceased for cases that are part of the investigation.", "6-3": "Choose from the following:\n * Alive\n * Dead\n * Lost to follow-up\n * Unknown\n * Not available", "7-0": "**Days to death**\n(*Prognosis*)", "7-1": "**days_to_death**", "7-2": "The number of days from the date of the initial pathological diagnosis to the date of death for the case in investigation.", "7-3": "This takes a non-negative integer.", "8-0": "**Race**\n(*Demographic*)", "8-1": "**race**", "8-2": "A classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution.", "8-3": "This takes a string.\n\nSuggested values:\n * White\n * American Indian or Alaska Native\n * Black or African American\n * Asian\n * Native Hawaiian or other Pacific Islander\n * Not reported\n * Not available", "9-0": "**Ethnicity**\n(*Demographic*)", "9-1": "**ethnicity**", "9-2": "A socially defined category of people based on common ancestral, cultural, biological, and social factors.", "9-3": "This takes a string.\n\nSuggested values:\n * Hispanic or Latino\n * Not Hispanic or Latino\n * Not reported\n * Not Available" }, "cols": 4, "rows": 10 } [/block] <div align="right"><a href="#top">top</a></div> ###General In the following table, you will find the name, description, and values of metadata fields for **General**. The second column, **API key**, allows you to access the specified metadata field through the API. Learn more about [accessing metadata via the API](files). [block:parameters] { "data": { "h-0": "Name", "h-1": "API key", "h-2": "Description", "h-3": "Value", "0-0": "**Investigation**", "0-1": "**investigation**", "0-2": "A value denoting the project or study that generated the data.", "0-3": "This takes a string." }, "cols": 4, "rows": 1 } [/block] <div align="right"><a href="#top">top</a></div> [block:callout] { "type": "info", "body": "Apart from the standard set of metadata fields that can be seen through the visual interface, custom metadata fields can be added via the [command line uploader](doc:set-metadata-using-the-command-line-uploader) or via the [API](doc:set-metadata-using-the-api)." } [/block] ##Querying with metadata on the CGC While you are in the Data Browser, you can query files using over 100 [TCGA metadata fields](tcga-metadata-on-the-cgc). After you filter your files and [copy them to a project](the-data-browser#section-copy-files-to-a-project), you will only be able to see the [metadata fields described on this page](#metadata-categories). The Seven Bridges team has selected these fields so you can use them to further filter and analyze your data. <div align="right"><a href="#top">top</a></div>