{"_id":"5981d713302822002abfc8b2","project":"55faf11ba62ba1170021a9a7","version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":38,"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","59a555bccdbd85001bfb1442"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"58458b4fba4f1c0f009692bb","project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-12-05T15:44:15.650Z","from_sync":false,"order":6,"slug":"datasets-hub","title":"DATASETS HUB"},"user":"5613e4f8fdd08f2b00437620","__v":0,"parentDoc":null,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-08-02T13:43:47.457Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":15,"body":"[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"body\": \"* [Overview](#section-overview)\\n* [Investigation](#section-investigation)\\n* [Case](#section-case)\\n* [Demographic](#section-demographic)\\n* [Diagnosis](#section-diagnosis)\\n* [Sample](#section-sample)\\n* [Portion](#section-portion)\\n* [File](#section-file)\\n* [Protocol](#section-protocol)\"\n}\n[/block]\n##Overview\nMetadata is data that describes other data. On this page, we've detailed CPTAC metadata that are available for viewing and filtering CPTAC data in the Data Browser, Datasets API, and the SPARQL endpoint on the CGC. CPTAC metadata on the CGC consists of properties which describe the entities of the CPTAC dataset.\n\n**Entities** are particular resources with UUIDs, such as files, cases, samples, and cell lines.\n\n**Properties** can either describe an entity or relate that entity to another entity. For instance, properties include an entity's vital status, gender, data format, or experimental strategy.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Entities for CPTAC\n\nThe following are entities for CPTAC. Learn more about [CPTAC data](doc:cptac-data).\n  * investigation\n  * case\n  * demographic\n  * diagnosis\n  * sample\n  * portion\n  * file\n  * protocol\n\nBelow, each of these entities is followed by a table of their related properties.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Investigation\n\nThe **investigation** entity represents the project or study that generated the data. Members of the **investigation** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **investigation** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Disease type\",\n    \"0-1\": \"The type of the disease or condition studied. See NCI Thesaurus Code: C2991.\",\n    \"1-0\": \"Primary site\",\n    \"1-1\": \"The anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761.\"\n  },\n  \"cols\": 2,\n  \"rows\": 2\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Case\nThe **case** entity represents TCGA cases. Members of the **case** entity are subjects who have taken part in an investigation or program and can be identified by a Universally Unique Identifier (UUID). See the table below for the clinical properties and descriptions of the **case** entity.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"0-1\": \"Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.\",\n    \"1-0\": \"Tissue source site ID\",\n    \"1-1\": \"A clinical site that collects and provides patient samples and clinical metadata for research use. This is identified with UUID. See NCI Thesaurus Code: C103264.\",\n    \"2-0\": \"Tissue source site name\",\n    \"3-0\": \"Tissue source site code\",\n    \"4-0\": \"Tissue source site BCR ID\",\n    \"2-1\": \"The full name of a clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.\",\n    \"3-1\": \"The alphanumeric code for clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.\",\n    \"4-1\": \"The BCR (Biospecimen Core Resource) provided ID for a tissue source site. See NCI Thesaurus Code: C103264.\"\n  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Demographic\nThe **demographic** entity represents the statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income) and can be identified by a Universally Unique Identifier (UUID). Find the properties of the **demographic** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Ethnicity\",\n    \"0-1\": \"A socially-defined category of people based on common ancestral, cultural, biological, and social factors. See NCI Thesaurus Code: C29933.\",\n    \"1-0\": \"Race\",\n    \"1-1\": \"A classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution. See NCI Thesaurus Code: C17049.\",\n    \"2-0\": \"Gender\",\n    \"3-0\": \"Year of birth\",\n    \"4-0\": \"Year of death\",\n    \"2-1\": \"The collection of behaviors and attitudes that distinguish people on the basis of the societal roles expected for the two sexes. See NCI Thesaurus Code: C17357.\",\n    \"3-1\": \"A numeric value to represent the calendar year in which an individual was born. See CDE (Common Data Element) Public ID: 2896954.\",\n    \"4-1\": \"A numeric value to represent the year of the death of an individual. See CDE (Common Data Element) Public ID: 2897030.\"\n  },\n  \"cols\": 2,\n  \"rows\": 3\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Diagnosis\nThe **diagnosis** entity represents the investigation, analysis, or recognition of the presence and nature of a disease, condition, or injury from expressed signs and symptoms. A **diagnosis** can be identified by a Universally Unique Identifier (UUID). Find the properties of the **diagnosis** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Age at diagnosis\",\n    \"0-1\": \"The age in years of the Case at the initial pathological diagnosis of the disease or cancer. See NCI Thesaurus Code: C15220.\",\n    \"1-0\": \"Days to death\",\n    \"1-1\": \"The time interval from a person's date of death to the date of initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3165475.\",\n    \"2-0\": \"Vital status\",\n    \"3-0\": \"Tissue or organ of origin\",\n    \"4-0\": \"Tumor grade\",\n    \"5-0\": \"Tumor stage\",\n    \"6-0\": \"Vital status\",\n    \"7-0\": \"Histological diagnosis\",\n    \"8-0\": \"Histological diagnosis other\",\n    \"9-0\": \"Year of diagnosis\",\n    \"10-0\": \"Clinical T (TNM)\",\n    \"11-0\": \"Clinical M (TNM)\",\n    \"12-0\": \"Clinical N (TNM)\",\n    \"13-0\": \"Clinical stage\",\n    \"14-0\": \"Pathologic T (TNM)\",\n    \"15-0\": \"Pathologic N (TNM)\",\n    \"16-0\": \"Pathologic M (TNM)\",\n    \"17-0\": \"Performance status scale: Timing\",\n    \"18-0\": \"Performance status scale: Karnofsky score\",\n    \"19-0\": \"Performance status scale: ECOG\",\n    \"20-0\": \"Tumor status\",\n    \"21-0\": \"Primary therapy outcome success\",\n    \"2-1\": \"The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.\",\n    \"3-1\": \"The text term that describes the anatomic site of the tumor or disease. See CDE (Common Data Element) Public ID: 3226281.\",\n    \"4-1\": \"The numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness. See CDE (Common Data Element) Public ID: 2785839.\",\n    \"5-1\": \"The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether lymph nodes contain cancer, and whether the cancer has spread from the original site to other parts of the body. NCI Thesaurus Code: C16899; also see NCI Thesaurus Code: C28257 for Pathological stage.\",\n    \"6-1\": \"The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.\",\n    \"7-1\": \"The diagnosis of a disease based on the type of tissue as determined based on the microscopic examination of the tissue. See NCI Thesaurus Code: C61478.\",\n    \"8-1\": \"Additional options for histologics diagnosis (see Histologic diagnosis), which have not been pre-determined in the listed values for histologic diagnosis.\",\n    \"9-1\": \"The numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. See CDE (Common Data Element) Public ID: 2896960.\",\n    \"10-1\": \"The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C253840.\",\n    \"11-1\": \"The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The M category tells whether there are distant metastases (spread of cancer to other parts of the body). NCI Thesaurus Code: C48881 and C25385.\",\n    \"12-1\": \"The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C25384.\",\n    \"13-1\": \"The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether lymph nodes contain cancer, and whether the cancer has spread from the original site to other parts of the body. See CDE (Common Data Element) Public ID: 5243162.\",\n    \"14-1\": \"The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C48739.\",\n    \"15-1\": \"The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C48740.\",\n    \"16-1\": \"The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The M category tells whether there are distant metastases (spread of cancer to other parts of the body). NCI Thesaurus Code: C48881 and C48741.\",\n    \"17-1\": \"A time reference for the Karnofsky score and/or the ECOG score using the defined categories.\",\n    \"18-1\": \"An index designed for classifying patients 16 years of age or older by their functional impairment. A standard way of measuring the ability of cancer patients to perform ordinary tasks. NCI Thesaurus Code: C28013.\",\n    \"19-1\": \"A performance status scale designed to assess disease progression and its effect on the daily living abilities of the patient. NCI Thesaurus Code: C105721.\",\n    \"21-1\": \"A value denoting the result of therapy for a given disease or condition in a patient or group of patients. See NCI Thesaurus Code: C18919.\",\n    \"20-1\": \"The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.\"\n  },\n  \"cols\": 2,\n  \"rows\": 3\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Sample\nThe **sample** entity represents samples or specimen material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes. For instance, samples include tissues, body fluids, cells, organs, embryos, and body excretory products. Members of the **sample** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **sample** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"1-0\": \"Sample type\",\n    \"2-0\": \"Sample type ID\",\n    \"3-0\": \"Composition\",\n    \"4-0\": \"Current weight\",\n    \"5-0\": \"Days to collection\",\n    \"6-0\": \"Country of sample procurement\",\n    \"7-0\": \"Days to sample procurement\",\n    \"8-0\": \"Freezing method\",\n    \"9-0\": \"Initial weight\",\n    \"10-0\": \"Intermediate dimension\",\n    \"11-0\": \"Is FFFP\",\n    \"12-0\": \"Longest dimension\",\n    \"13-0\": \"OCT embedded\",\n    \"14-0\": \"Pathology report UUID\",\n    \"15-0\": \"Preservation method\",\n    \"16-0\": \"Shortest dimension\",\n    \"17-0\": \"Time between clamping and freezing\",\n    \"18-0\": \"Time between excision and freezing\",\n    \"19-0\": \"Tissue type\",\n    \"20-0\": \"Tumor code\",\n    \"21-0\": \"Tumor code ID\",\n    \"22-0\": \"Tumor descriptor\",\n    \"0-1\": \"Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.\",\n    \"1-1\": \"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. See NCI Thesaurus Code: C70713.\",\n    \"2-1\": \"A code that determines 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. See NCI Thesaurus Code: C70713.\",\n    \"3-1\": \"The cellular composition of the sample.\",\n    \"4-1\": \"Current sample/specimen weight (in grams).\",\n    \"5-1\": \"The time interval from the date of biospecimen collection to the date of initial pathologic diagnosis, represented as a calculated number of days. Sample can be collected prospectively or retrospectively. This can be a negative value for samples taken retrospectively. See CDE (Common Data Element) Public ID: 3008340.\",\n    \"6-1\": \"Country where the specimen/sample has been procured.\",\n    \"7-1\": \"The time interval from the date of sample collection to the date of sample procurement, expressed in days.\",\n    \"8-1\": \"Method used to freeze the sample/specimen.\",\n    \"9-1\": \"Initial sample/specimen weight (in grams).\",\n    \"10-1\": \"The intermediate dimension of sample/specimen (in millimeters).\",\n    \"11-1\": \"A Boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).\",\n    \"12-1\": \"The longest dimension of the sample/specimen, in millimeters.\",\n    \"13-1\": \"A Boolean value indicating whether the Optimal Cutting Temperature compound (OCT) is used to embed tissue samples prior to frozen sectioning on a microtome-cryostat.\",\n    \"14-1\": \"UUID of the related pathology report.\",\n    \"15-1\": \"The primary preservation method used to store the sample.\",\n    \"16-1\": \"The shortest dimension of the sample/specimen, in millimeters.\",\n    \"17-1\": \"The time elapsed (in minutes) between clamping (supplying vessel) and freezing a sample.\",\n    \"18-1\": \"Warm ischemia time, elapsed between clamping and freezing a sample, as denoted in minutes.\",\n    \"19-1\": \"A description of the tissue type with respect its tumor/normal source.\",\n    \"20-1\": \"The diagnostic tumor code of the tissue sample source.\",\n    \"21-1\": \"A BCR-defined ID code for the tumor sample.\",\n    \"22-1\": \"A description of the tumor from which the sample was derived\"\n  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Portion\nThe **portion** entity represents the sequential 100-120 mg sections derived from samples. Members of the **portion** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **portion** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"1-0\": \"Is FFFP\",\n    \"2-0\": \"Portion weight\",\n    \"3-0\": \"Portion number\",\n    \"4-0\": \"Center ID\",\n    \"5-0\": \"Center type\",\n    \"6-0\": \"Center code\",\n    \"7-0\": \"Center name\",\n    \"8-0\": \"Center namespace\",\n    \"9-0\": \"Center short name\",\n    \"0-1\": \"Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.\",\n    \"1-1\": \"A Boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).\",\n    \"2-1\": \"Weight of a portion prepared for the analysis (in mg).\",\n    \"3-1\": \"The numerical value that represents the order of a portion in the series.\",\n    \"4-1\": \"A professional organization or group which has or is able to submit data. It can be identified by a UUID.\",\n    \"5-1\": \"The type classification of the center (e.g. CGCC).\",\n    \"6-1\": \"The code that determins center that has submitted data.\",\n    \"7-1\": \"The name of the center (e.g. Broad Institute of MIT and Harvard).\",\n    \"8-1\": \"The domain name of the center (e.g. borad.mit.edu).\",\n    \"9-1\": \"A shortened name of the center (e.g. BI).\"\n  },\n  \"cols\": 2,\n  \"rows\": 1\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##File\nThe **file** entity refers to the files in TCGA produced by aliquot analyses. Members of the file entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **file** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"1-0\": \"File type\",\n    \"2-0\": \"Data format\",\n    \"3-0\": \"Access level\",\n    \"0-1\": \"Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.\",\n    \"1-1\": \"The type of file which stores the data.\",\n    \"2-1\": \"The type of format that determines data content.\",\n    \"3-1\": \"A Boolean value indicating Controlled Data or Open Data. Controlled Data is data from public datasets that has limitations on use and requires approval by dbGaP. Open Data is data from public datasets that doesn't have limitations on its use.\"\n  },\n  \"cols\": 2,\n  \"rows\": 4\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Protocol\nSee below for links to the publications that describe the experimental protocols used to generate each subcollection of data.\n\n  * [TCGA-BRCA](http://www.nature.com/nature/journal/v534/n7605/full/nature18003.html)\n  * [TCGA-OV](https://www.ncbi.nlm.nih.gov/pubmed/27372738)\n  * [TCGA-COAD and TCGA-READ ](http://www.nature.com/nature/journal/v513/n7518/full/nature13438.html)\n\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"<a href=\"about-metadata-for-datasets\" style=\"color:#132c56\">ABOUT METADATA FOR DATASETS</a> > CPTAC metadata","slug":"cptac-metadata","type":"basic","title":"CPTAC metadata"}

CPTAC metadata

<a href="about-metadata-for-datasets" style="color:#132c56">ABOUT METADATA FOR DATASETS</a> > CPTAC metadata

[block:callout] { "type": "warning", "title": "On this page:", "body": "* [Overview](#section-overview)\n* [Investigation](#section-investigation)\n* [Case](#section-case)\n* [Demographic](#section-demographic)\n* [Diagnosis](#section-diagnosis)\n* [Sample](#section-sample)\n* [Portion](#section-portion)\n* [File](#section-file)\n* [Protocol](#section-protocol)" } [/block] ##Overview Metadata is data that describes other data. On this page, we've detailed CPTAC metadata that are available for viewing and filtering CPTAC data in the Data Browser, Datasets API, and the SPARQL endpoint on the CGC. CPTAC metadata on the CGC consists of properties which describe the entities of the CPTAC dataset. **Entities** are particular resources with UUIDs, such as files, cases, samples, and cell lines. **Properties** can either describe an entity or relate that entity to another entity. For instance, properties include an entity's vital status, gender, data format, or experimental strategy. <div align="right"><a href="#top">top</a></div> ##Entities for CPTAC The following are entities for CPTAC. Learn more about [CPTAC data](doc:cptac-data). * investigation * case * demographic * diagnosis * sample * portion * file * protocol Below, each of these entities is followed by a table of their related properties. <div align="right"><a href="#top">top</a></div> ##Investigation The **investigation** entity represents the project or study that generated the data. Members of the **investigation** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **investigation** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Disease type", "0-1": "The type of the disease or condition studied. See NCI Thesaurus Code: C2991.", "1-0": "Primary site", "1-1": "The anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761." }, "cols": 2, "rows": 2 } [/block] <div align="right"><a href="#top">top</a></div> ##Case The **case** entity represents TCGA cases. Members of the **case** entity are subjects who have taken part in an investigation or program and can be identified by a Universally Unique Identifier (UUID). See the table below for the clinical properties and descriptions of the **case** entity. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "0-1": "Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.", "1-0": "Tissue source site ID", "1-1": "A clinical site that collects and provides patient samples and clinical metadata for research use. This is identified with UUID. See NCI Thesaurus Code: C103264.", "2-0": "Tissue source site name", "3-0": "Tissue source site code", "4-0": "Tissue source site BCR ID", "2-1": "The full name of a clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.", "3-1": "The alphanumeric code for clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.", "4-1": "The BCR (Biospecimen Core Resource) provided ID for a tissue source site. See NCI Thesaurus Code: C103264." }, "cols": 2, "rows": 1 } [/block] <div align="right"><a href="#top">top</a></div> ##Demographic The **demographic** entity represents the statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income) and can be identified by a Universally Unique Identifier (UUID). Find the properties of the **demographic** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Ethnicity", "0-1": "A socially-defined category of people based on common ancestral, cultural, biological, and social factors. See NCI Thesaurus Code: C29933.", "1-0": "Race", "1-1": "A classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution. See NCI Thesaurus Code: C17049.", "2-0": "Gender", "3-0": "Year of birth", "4-0": "Year of death", "2-1": "The collection of behaviors and attitudes that distinguish people on the basis of the societal roles expected for the two sexes. See NCI Thesaurus Code: C17357.", "3-1": "A numeric value to represent the calendar year in which an individual was born. See CDE (Common Data Element) Public ID: 2896954.", "4-1": "A numeric value to represent the year of the death of an individual. See CDE (Common Data Element) Public ID: 2897030." }, "cols": 2, "rows": 3 } [/block] <div align="right"><a href="#top">top</a></div> ##Diagnosis The **diagnosis** entity represents the investigation, analysis, or recognition of the presence and nature of a disease, condition, or injury from expressed signs and symptoms. A **diagnosis** can be identified by a Universally Unique Identifier (UUID). Find the properties of the **diagnosis** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Age at diagnosis", "0-1": "The age in years of the Case at the initial pathological diagnosis of the disease or cancer. See NCI Thesaurus Code: C15220.", "1-0": "Days to death", "1-1": "The time interval from a person's date of death to the date of initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3165475.", "2-0": "Vital status", "3-0": "Tissue or organ of origin", "4-0": "Tumor grade", "5-0": "Tumor stage", "6-0": "Vital status", "7-0": "Histological diagnosis", "8-0": "Histological diagnosis other", "9-0": "Year of diagnosis", "10-0": "Clinical T (TNM)", "11-0": "Clinical M (TNM)", "12-0": "Clinical N (TNM)", "13-0": "Clinical stage", "14-0": "Pathologic T (TNM)", "15-0": "Pathologic N (TNM)", "16-0": "Pathologic M (TNM)", "17-0": "Performance status scale: Timing", "18-0": "Performance status scale: Karnofsky score", "19-0": "Performance status scale: ECOG", "20-0": "Tumor status", "21-0": "Primary therapy outcome success", "2-1": "The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.", "3-1": "The text term that describes the anatomic site of the tumor or disease. See CDE (Common Data Element) Public ID: 3226281.", "4-1": "The numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness. See CDE (Common Data Element) Public ID: 2785839.", "5-1": "The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether lymph nodes contain cancer, and whether the cancer has spread from the original site to other parts of the body. NCI Thesaurus Code: C16899; also see NCI Thesaurus Code: C28257 for Pathological stage.", "6-1": "The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.", "7-1": "The diagnosis of a disease based on the type of tissue as determined based on the microscopic examination of the tissue. See NCI Thesaurus Code: C61478.", "8-1": "Additional options for histologics diagnosis (see Histologic diagnosis), which have not been pre-determined in the listed values for histologic diagnosis.", "9-1": "The numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. See CDE (Common Data Element) Public ID: 2896960.", "10-1": "The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C253840.", "11-1": "The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The M category tells whether there are distant metastases (spread of cancer to other parts of the body). NCI Thesaurus Code: C48881 and C25385.", "12-1": "The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C25384.", "13-1": "The extent of a cancer in the body. Staging is usually based on the size of the tumor, whether lymph nodes contain cancer, and whether the cancer has spread from the original site to other parts of the body. See CDE (Common Data Element) Public ID: 5243162.", "14-1": "The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C48739.", "15-1": "The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C48740.", "16-1": "The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The M category tells whether there are distant metastases (spread of cancer to other parts of the body). NCI Thesaurus Code: C48881 and C48741.", "17-1": "A time reference for the Karnofsky score and/or the ECOG score using the defined categories.", "18-1": "An index designed for classifying patients 16 years of age or older by their functional impairment. A standard way of measuring the ability of cancer patients to perform ordinary tasks. NCI Thesaurus Code: C28013.", "19-1": "A performance status scale designed to assess disease progression and its effect on the daily living abilities of the patient. NCI Thesaurus Code: C105721.", "21-1": "A value denoting the result of therapy for a given disease or condition in a patient or group of patients. See NCI Thesaurus Code: C18919.", "20-1": "The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643." }, "cols": 2, "rows": 3 } [/block] <div align="right"><a href="#top">top</a></div> ##Sample The **sample** entity represents samples or specimen material taken from a biological entity for testing, diagnosis, propagation, treatment, or research purposes. For instance, samples include tissues, body fluids, cells, organs, embryos, and body excretory products. Members of the **sample** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **sample** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "1-0": "Sample type", "2-0": "Sample type ID", "3-0": "Composition", "4-0": "Current weight", "5-0": "Days to collection", "6-0": "Country of sample procurement", "7-0": "Days to sample procurement", "8-0": "Freezing method", "9-0": "Initial weight", "10-0": "Intermediate dimension", "11-0": "Is FFFP", "12-0": "Longest dimension", "13-0": "OCT embedded", "14-0": "Pathology report UUID", "15-0": "Preservation method", "16-0": "Shortest dimension", "17-0": "Time between clamping and freezing", "18-0": "Time between excision and freezing", "19-0": "Tissue type", "20-0": "Tumor code", "21-0": "Tumor code ID", "22-0": "Tumor descriptor", "0-1": "Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.", "1-1": "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. See NCI Thesaurus Code: C70713.", "2-1": "A code that determines 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. See NCI Thesaurus Code: C70713.", "3-1": "The cellular composition of the sample.", "4-1": "Current sample/specimen weight (in grams).", "5-1": "The time interval from the date of biospecimen collection to the date of initial pathologic diagnosis, represented as a calculated number of days. Sample can be collected prospectively or retrospectively. This can be a negative value for samples taken retrospectively. See CDE (Common Data Element) Public ID: 3008340.", "6-1": "Country where the specimen/sample has been procured.", "7-1": "The time interval from the date of sample collection to the date of sample procurement, expressed in days.", "8-1": "Method used to freeze the sample/specimen.", "9-1": "Initial sample/specimen weight (in grams).", "10-1": "The intermediate dimension of sample/specimen (in millimeters).", "11-1": "A Boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).", "12-1": "The longest dimension of the sample/specimen, in millimeters.", "13-1": "A Boolean value indicating whether the Optimal Cutting Temperature compound (OCT) is used to embed tissue samples prior to frozen sectioning on a microtome-cryostat.", "14-1": "UUID of the related pathology report.", "15-1": "The primary preservation method used to store the sample.", "16-1": "The shortest dimension of the sample/specimen, in millimeters.", "17-1": "The time elapsed (in minutes) between clamping (supplying vessel) and freezing a sample.", "18-1": "Warm ischemia time, elapsed between clamping and freezing a sample, as denoted in minutes.", "19-1": "A description of the tissue type with respect its tumor/normal source.", "20-1": "The diagnostic tumor code of the tissue sample source.", "21-1": "A BCR-defined ID code for the tumor sample.", "22-1": "A description of the tumor from which the sample was derived" }, "cols": 2, "rows": 1 } [/block] <div align="right"><a href="#top">top</a></div> ##Portion The **portion** entity represents the sequential 100-120 mg sections derived from samples. Members of the **portion** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **portion** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "1-0": "Is FFFP", "2-0": "Portion weight", "3-0": "Portion number", "4-0": "Center ID", "5-0": "Center type", "6-0": "Center code", "7-0": "Center name", "8-0": "Center namespace", "9-0": "Center short name", "0-1": "Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.", "1-1": "A Boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).", "2-1": "Weight of a portion prepared for the analysis (in mg).", "3-1": "The numerical value that represents the order of a portion in the series.", "4-1": "A professional organization or group which has or is able to submit data. It can be identified by a UUID.", "5-1": "The type classification of the center (e.g. CGCC).", "6-1": "The code that determins center that has submitted data.", "7-1": "The name of the center (e.g. Broad Institute of MIT and Harvard).", "8-1": "The domain name of the center (e.g. borad.mit.edu).", "9-1": "A shortened name of the center (e.g. BI)." }, "cols": 2, "rows": 1 } [/block] <div align="right"><a href="#top">top</a></div> ##File The **file** entity refers to the files in TCGA produced by aliquot analyses. Members of the file entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **file** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "1-0": "File type", "2-0": "Data format", "3-0": "Access level", "0-1": "Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.", "1-1": "The type of file which stores the data.", "2-1": "The type of format that determines data content.", "3-1": "A Boolean value indicating Controlled Data or Open Data. Controlled Data is data from public datasets that has limitations on use and requires approval by dbGaP. Open Data is data from public datasets that doesn't have limitations on its use." }, "cols": 2, "rows": 4 } [/block] <div align="right"><a href="#top">top</a></div> ##Protocol See below for links to the publications that describe the experimental protocols used to generate each subcollection of data. * [TCGA-BRCA](http://www.nature.com/nature/journal/v534/n7605/full/nature18003.html) * [TCGA-OV](https://www.ncbi.nlm.nih.gov/pubmed/27372738) * [TCGA-COAD and TCGA-READ ](http://www.nature.com/nature/journal/v513/n7518/full/nature13438.html) <div align="right"><a href="#top">top</a></div>