{"_id":"58ecca9b90f3aa0f00b4d526","project":"55faf11ba62ba1170021a9a7","user":"5613e4f8fdd08f2b00437620","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"},"parentDoc":null,"__v":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"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-04-11T12:22:51.764Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"settings":"","results":{"codes":[]},"auth":"required","params":[],"url":""},"isReference":false,"order":13,"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* [Treatment](#section-treatment)\\n* [Exposure](#section-exposure)\\n* [Drug therapy](#section-drug-therapy)\\n* [Radiation therapy](#section-radiation-therapy)\\n* [Follow up](#section-follow-up)\\n* [New tumor event](#section-new-tumor-event)\\n* [Sample](#section-sample)\\n* [Portion](#section-portion)\\n* [Slide](#section-slide)\\n* [Analyte](#section-analyte)\\n* [Aliquot](#section-aliquot)\\n* [Read group](#section-read-group)\\n* [Read group QC](#section-read-group-qc)\\n* [File](#section-file)\\n* [Analysis](#section-analysis)\"\n}\n[/block]\n##Overview\nMetadata is data that describes other data. On this page, we've detailed TCGA metadata that are available for viewing and filtering TCGA data in the Data Browser, Datasets API, and the SPARQL endpoint on the CGC. TCGA metadata on the CGC consists of properties which describe the entities of the TCGA 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 TCGA GRCh38\n\nEntities for TCGA GRCh38\nThe following are entities for TCGA GRCh38. They represent clinical data, biospecimen data, and data about TCGA GRCh38 files. Note that these entities differ from the [entities of legacy TCGA data](doc:tcga-metadata). Learn more about [TCGA GRCh38 data](doc:tcga-grch38-data).\n  * investigation\n  * case\n  * demographic\n  * diagnosis\n  * treatment\n  * exposure\n  * drug_therapy\n  * radiation_therapy\n  * follow_up\n  * new_tumor_event\n  * sample\n  * portion\n  * slide\n  * analyte\n  * aliquot\n  * read_group\n  * read_group_qc\n  * file\n  * analysis\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\": \"dbGaP accession number\",\n    \"0-1\": \"The dbGaP accession number provided for each study. See NCI Thesaurus Code: C25402.\",\n    \"1-0\": \"Disease type\",\n    \"1-1\": \"The type of the disease or condition studied. See NCI Thesaurus Code: C2991.\",\n    \"2-0\": \"Investigation name\",\n    \"3-0\": \"Primary site\",\n    \"3-1\": \"The anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761.\",\n    \"2-1\": \"The full name of the project or study that generated the data. See NCI Thesaurus Code: C41198.\",\n    \"4-0\": \"Submitter ID\",\n    \"4-1\": \"A human-readable identifier, such as a number or a string that may contain metadata information for investigations.\"\n  },\n  \"cols\": 2,\n  \"rows\": 5\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    \"0-0\": \"Batch number\",\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-1\": \"A set of related analytes prepared for further analysis and numbered sequentially from the same disease. Once a Case has been assigned to a batch number, subsequent shipments from that case are assigned the same batch number as the original. Seven Bridges only field.\",\n    \"1-0\": \"Submitter ID\",\n    \"1-1\": \"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    \"2-0\": \"Tissue source site ID\",\n    \"2-1\": \"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    \"3-0\": \"Tissue source site name\",\n    \"4-0\": \"Tissue source site code\",\n    \"5-0\": \"Tissue source site BCR ID\",\n    \"3-1\": \"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    \"4-1\": \"The alphanumeric code for clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.\",\n    \"5-1\": \"The BCR (Biospecimen Core Resource) provided ID for a tissue source site. See NCI Thesaurus Code: C103264.\"\n  },\n  \"cols\": 2,\n  \"rows\": 6\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\": \"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\": \"Ethnicity\",\n    \"1-1\": \"A socially-defined category of people based on common ancestral, cultural, biological, and social factors. See NCI Thesaurus Code: C29933.\",\n    \"2-0\": \"Race\",\n    \"2-1\": \"A classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution. See NCI Thesaurus Code: C17049.\",\n    \"3-0\": \"Gender\",\n    \"4-0\": \"Year of birth\",\n    \"5-0\": \"Year of death\",\n    \"3-1\": \"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    \"4-1\": \"A numeric value to represent the calendar year in which an individual was born. See CDE (Common Data Element) Public ID: 2896954.\",\n    \"5-1\": \"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\": 6\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\": \"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\": \"Age at diagnosis\",\n    \"1-1\": \"The age in years of the Case at the initial pathological diagnosis of the disease or cancer. See NCI Thesaurus Code: C15220.\",\n    \"2-0\": \"Classification of tumor\",\n    \"2-1\": \"Text that describes the kind of disease present in the tumor specimen as related to a specific point in time. See CDE (Common Data Element) Public ID: 3288124.\",\n    \"3-0\": \"Days to birth\",\n    \"3-1\": \"The time interval from a person's date of birth to the date of initial pathologic diagnosis, represented as a calculated negative number of days. See CDE (Common Data Element) Public ID: 3008233.\",\n    \"4-0\": \"Days to death\",\n    \"4-1\": \"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    \"5-0\": \"Days to last follow up\",\n    \"5-1\": \"The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.\",\n    \"6-0\": \"Days to last known disease status\",\n    \"6-1\": \"The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.\",\n    \"7-0\": \"Days to recurrence\",\n    \"7-1\": \"The time interval from the date of new tumor event, including progression, recurrence and new primary malignancies, to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3392464.\",\n    \"8-0\": \"Last known disease status\",\n    \"9-0\": \"Morphology\",\n    \"10-0\": \"Primary diagnosis\",\n    \"11-0\": \"Prior malignancy\",\n    \"12-0\": \"Progression or recurrence\",\n    \"13-0\": \"New tumor event after initial treatment\",\n    \"14-0\": \"Site of resection or biopsy\",\n    \"15-0\": \"Tissue or organ of origin\",\n    \"16-0\": \"Tumor grade\",\n    \"17-0\": \"Tumor stage\",\n    \"18-0\": \"Vital status\",\n    \"19-0\": \"Histological diagnosis\",\n    \"20-0\": \"Histological diagnosis other\",\n    \"21-0\": \"Year of diagnosis\",\n    \"22-0\": \"Clinical T (TNM)\",\n    \"23-0\": \"Clinical M (TNM)\",\n    \"24-0\": \"Clinical N (TNM)\",\n    \"25-0\": \"Clinical stage\",\n    \"26-0\": \"Pathologic T (TNM)\",\n    \"27-0\": \"Pathologic N (TNM)\",\n    \"28-0\": \"Pathologic M (TNM)\",\n    \"29-0\": \"Performance status scale: Timing\",\n    \"30-0\": \"Performance status scale: Karnofsky score\",\n    \"31-0\": \"Performance status scale: ECOG\",\n    \"32-0\": \"Tumor status\",\n    \"33-0\": \"Primary therapy outcome success\",\n    \"8-1\": \"The state or condition of an individual's neoplasm at a particular point in time. See CDE (Common Data Element) Public ID: 3392464.\",\n    \"9-1\": \"The morphology code which describes the characteristics of the tumor itself, including its cell type and biologic activity, according to the third edition of the International Classification of Diseases for Oncology (ICD-O). See CDE (Common Data Element) Public ID: 3226275.\",\n    \"10-1\": \"Text term for the structural pattern of cancer cells used to define a microscopic diagnosis. See CDE (Common Data Element) Public ID: 3081934.\",\n    \"11-1\": \"Text term to describe the patient's history of prior cancer diagnosis and the spatial location of any previous cancer occurrence. See CDE (Common Data Element) Public ID: 3081934.\",\n    \"12-1\": \"Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment. See CDE (Common Data Element) Public ID: 3121376.\",\n    \"13-1\": \"A Boolean value denoting whether a neoplasm developed after the initial treatment was finished.\",\n    \"14-1\": \"The topography code which describes the anatomical site of origin of the neoplasm according to the third edition of the International Classification of Diseases for Oncology (ICD-O). See NCI Thesaurus Code: C37978. See CDE (Common Data Element) Public ID: 3226281.\",\n    \"15-1\": \"The text term that describes the anatomic site of the tumor or disease. See CDE (Common Data Element) Public ID: 3226281.\",\n    \"16-1\": \"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    \"17-1\": \"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    \"18-1\": \"The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.\",\n    \"19-1\": \"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    \"20-1\": \"Additional options for histologics diagnosis (see Histologic diagnosis), which have not been pre-determined in the listed values for histologic diagnosis.\",\n    \"21-1\": \"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    \"22-1\": \"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    \"23-1\": \"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    \"24-1\": \"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    \"25-1\": \"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    \"26-1\": \"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    \"27-1\": \"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    \"28-1\": \"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    \"29-1\": \"A time reference for the Karnofsky score and/or the ECOG score using the defined categories.\",\n    \"30-1\": \"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    \"31-1\": \"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    \"33-1\": \"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    \"32-1\": \"The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.\"\n  },\n  \"cols\": 2,\n  \"rows\": 34\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Treatment\n\nThe **treatment** entity represents records of the administration of therapeutic agents to a patient to alter the course of a pathologic process. Members of the **treatment** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **treatment** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"0-0\": \"Submitter ID\",\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\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\": \"Days to treatment\",\n    \"1-1\": \"The number of days from the date of the initial pathologic diagnosis that treatment began.\",\n    \"2-0\": \"Therapeutic agents\",\n    \"2-1\": \"The text identification of the individual agent(s) used as part of a prior treatment regimen. See CDE (Common Data Element) Public ID: 2975232.\",\n    \"3-0\": \"Treatment intent type\",\n    \"3-1\": \"The text term to identify the reason for the administration of a treatment regimen. [Manually-curated]. See CDE (Common Data Element) Public ID: 2793511.\",\n    \"4-0\": \"Treatment or therapy\",\n    \"4-1\": \"A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected. See CDE (Common Data Element) Public ID: 4231463.\",\n    \"5-0\": \"Country of specimen procurement\",\n    \"5-1\": \"Country where specimen/sample has been procured.\",\n    \"6-0\": \"Longest dimension\",\n    \"6-1\": \"The longest dimension of sample/specimen (in centimeters).\",\n    \"7-0\": \"Intermediate dimension\",\n    \"7-1\": \"The intermediate dimension of sample/specimen (in centimeters).\",\n    \"8-0\": \"Shortest dimension\",\n    \"8-1\": \"The shortest dimension of sample/specimen (in centimeters).\",\n    \"9-0\": \"Initial weight\",\n    \"9-1\": \"Initial sample/specimen weight (in grams).\",\n    \"10-0\": \"Current weight\",\n    \"10-1\": \"Current sample/specimen weight (in grams).\",\n    \"11-0\": \"Freezing method\",\n    \"11-1\": \"The freezing method for sample/specimen.\",\n    \"12-0\": \"OCT embedded\",\n    \"12-1\": \"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    \"13-0\": \"Time between clamping and freezing\",\n    \"13-1\": \"Time elapsed (in minutes) between clamping (supplying vessel) and freezing a sample.\",\n    \"14-0\": \"Time between excision and freezing\",\n    \"14-1\": \"Warm ischemia time, elapsed between clamping and freezing a sample, as denoted in minutes.\",\n    \"15-0\": \"Days to collection\",\n    \"15-1\": \"Days to sample collection. Sample can be collected can be prospectively or retrospectively. This can be a negative value for samples taken retrospectively.\",\n    \"16-0\": \"Days to sample procurement\",\n    \"16-1\": \"Number of days from the date the patient was initially diagnosed pathologically with the disease to the date of the procedure that produced the malignant sample for submission.\",\n    \"17-0\": \"Is FFPE\",\n    \"17-1\": \"A boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).\"\n  },\n  \"cols\": 2,\n  \"rows\": 5\n}\n[/block]\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Exposure\nThe **exposure** entity represents clinically relevant patient information which does not immediately result from genetic predispositions. Members of the **exposure** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **exposure** entity below.\n \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\": \"Alcohol history\",\n    \"1-1\": \"A response to the question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime. See CDE (Common Data Element) Public ID: 2201918. Also: A description of an individual's current and past experience with alcoholic beverage consumption. See NCI Thesaurus Code: C81229.\",\n    \"2-0\": \"Alcohol intensity\",\n    \"2-1\": \"A category to describe the patient's current level of alcohol use as self-reported by the patient. See CDE (Common Data Element) Public ID: 3457767.\",\n    \"3-0\": \"BMI\",\n    \"3-1\": \"The body mass divided by the square of the body height expressed in units of kg/m2. See CDE (Common Data Element) Public ID: 4973892.\",\n    \"4-0\": \"Cigarettes per day\",\n    \"5-0\": \"Height\",\n    \"6-0\": \"Weight\",\n    \"7-0\": \"Years smoked\",\n    \"4-1\": \"The average number of cigarettes smoked per day. See CDE (Common Data Element) Public ID: 2001716.\",\n    \"5-1\": \"The height of the patient in centimeters. See CDE (Common Data Element) Public ID: 649.\",\n    \"7-1\": \"The numeric value (or unknown) to represent the number of years a person has been smoking. See CDE (Common Data Element) Public ID: 3137957.\",\n    \"6-1\": \"The weight of the patient measured in kilograms. See CDE (Common Data Element) Public ID: 651.\"\n  },\n  \"cols\": 2,\n  \"rows\": 8\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Drug therapy\nThe **drug therapy** entity represents the use of pharmaceutical products that contains one or more active and/or inactive ingredients to treat, prevent or alleviate the symptoms of disease. A **Case** can have more them one drug treatment. Members of the **drug therapy** entity can be identified by a Universally Unique Identifier (UUID).\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\": \"Drug name\",\n    \"1-1\": \"The most recognizable term associated with a pharmaceutical product used to prevent, diagnose, treat or relieve symptoms of a disease or abnormal condition. NCI Thesaurus Code: C97104.\",\n    \"2-0\": \"Pharmaceutical therapy type\",\n    \"2-1\": \"The type of treatment of the disease through the use of drugs. NCI Thesaurus Code: C15986.\",\n    \"3-0\": \"Percent tumor cells\",\n    \"3-1\": \"The percent of tumor cells based on the tissue image.\",\n    \"4-0\": \"Percent tumor nuclei\",\n    \"4-1\": \"The percent of tumor nuclei based on the tissue image.\",\n    \"5-0\": \"Percent normal cells\",\n    \"5-1\": \"The percent of normal cell based on the tissue image.\",\n    \"6-0\": \"Percent necrosis\",\n    \"6-1\": \"The percent of normal cell based on the tissue image.\",\n    \"7-0\": \"Percent stromal cells\",\n    \"7-1\": \"The ratio of stromal cells present on the tissue slide.\",\n    \"8-0\": \"Percent inflam infiltration\",\n    \"8-1\": \"The ratio of inflammatory cells to the gross cell population seen on a slide.\",\n    \"9-0\": \"Percent lymphocyte infiltration\",\n    \"9-1\": \"The fraction of lymphocyte cells to the gross inflammatory cells seen on a slide.\",\n    \"10-0\": \"Percent monocyte infiltration\",\n    \"10-1\": \"The fraction of monocyte cells to the gross inflammatory cells seen on a slide.\",\n    \"11-0\": \"Percent granulocyte infiltration\",\n    \"11-1\": \"The fraction of the granulocyte component to the gross inflammatory cells seen on a slide.\",\n    \"12-0\": \"Percent neutrophile infiltration\",\n    \"12-1\": \"The fraction of neutrophile cells to the gross granulocyte component of inflammatory cells seen on a slide.\",\n    \"13-0\": \"Percent eosinophil infiltration\",\n    \"13-1\": \"The fraction of eosinophil cells to the gross granulocyte component of inflammatory cells seen on a slide.\"\n  },\n  \"cols\": 2,\n  \"rows\": 3\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Radiation therapy\nThe **radiation therapy** entity represents the treatment of a disease with **radiation therapy**, in which the whole or a portion of the patient's body is exposed to radiation. A Case can have more than one radiation treatment. Members of the **radiation therapy** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **radiation therapy** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"1-0\": \"Radiation type\",\n    \"0-0\": \"Submitter ID\",\n    \"0-1\": \"This refers to the radiation therapy id, a human-readable identifier, such as a number or a string that may contain metadata information, for the radiation treatment of a disease by means of exposure of the target or the whole body to radiation. NCI Thesaurus Code: C15986.\",\n    \"1-1\": \"The value denotes the type of high-energy radiation used to kill cancer cells and shrink tumors. NCI Thesaurus Code: C15986.\",\n    \"2-0\": \"Radiation therapy site\",\n    \"2-1\": \"The location to which radiation therapy was administered.\",\n    \"3-0\": \"Amount\",\n    \"3-1\": \"Amount of a product (in μg) prepared for an analysis.\",\n    \"4-0\": \"Concentration\",\n    \"4-1\": \"Concentration of a product (in μg/μL) prepared for an analysis.\",\n    \"5-0\": \"a260_a280 ratio\",\n    \"5-1\": \"A numerical value denoting purity assessment using the A260/A280 Ratios.\",\n    \"6-0\": \"Well number\",\n    \"6-1\": \"The number of wells on the plate in which an analyte has been stored for shipment and for the analysis.\",\n    \"7-0\": \"Spectrophotometer method\",\n    \"7-1\": \"A method of quantifying the content of nucleic acids in any sample.\"\n  },\n  \"cols\": 2,\n  \"rows\": 3\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Follow up\nThe **follow up** entity refers to follow ups which monitor a person's health over time after treatment. A Case can have multiple follow ups generated at different times. Members of the **follow up** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **follow up** entity below.\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\": \"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\": \"Days to last follow up\",\n    \"2-1\": \"The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.\",\n    \"3-0\": \"New tumor event after initial treatment\",\n    \"4-0\": \"Tumor status\",\n    \"5-0\": \"Vital status\",\n    \"3-1\": \"A Boolean value which denotes whether a neoplasm developed after the initial treatment has finished.\",\n    \"4-1\": \"The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.\",\n    \"5-1\": \"The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.\"\n  },\n  \"cols\": 2,\n  \"rows\": 6\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##New tumor event\nThe **new tumor event** entity represents a newly developed neoplasm after initial treatment has finished. Members of the new tumor event entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **new tumor event** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"New tumor anatomic site\",\n    \"1-0\": \"Other new tumor anatomic site\",\n    \"0-1\": \"Anatomic site of newly developed neoplasm.\",\n    \"1-1\": \"Alternative anatomic site of a newly developed neoplasm which has not been listed under 'New tumor anatomic site'.\",\n    \"2-0\": \"New tumor event type\",\n    \"2-1\": \"Type of newly developed neoplasm after initial treatment has finished.\",\n    \"3-0\": \"Experimental strategy\",\n    \"3-1\": \"The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.\",\n    \"5-0\": \"Data type\",\n    \"4-0\": \"Platform\",\n    \"4-1\": \"The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.\",\n    \"5-1\": \"The classification of data used in (or produced by) the analysis, based on its form and content. See NCI Thesaurus Code: C42645.\",\n    \"6-0\": \"Data subtype\",\n    \"6-1\": \"A further, more specific classification of the data type, based on the information that it contains.\",\n    \"7-0\": \"Data submitting center\",\n    \"7-1\": \"This field takes a string denoting the name of the center that has submitted data.\",\n    \"8-0\": \"Reference genome\",\n    \"9-0\": \"Access level\",\n    \"8-1\": \"The reference assembly (such as HG19 or GRCh37) to which the nucleotide sequence of a case can be aligned.\",\n    \"9-1\": \"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\": 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\": 23\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\": 10\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Slide\nThe **slide** entity represents slides, thin slices of a snap-frozen OCT embedded block of tissue sent for imaging. This same tissue also provides DNA and RNA for further analyses after they are reviewed by histopathologists. Members of the **slide** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **slide** entity below.\n\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"1-0\": \"Section location\",\n    \"2-0\": \"Number proliferating cells\",\n    \"3-0\": \"Percent eosinophil infiltration\",\n    \"4-0\": \"Percent granulocyte infiltration\",\n    \"5-0\": \"Percent inflam infiltration\",\n    \"6-0\": \"Percent lymphocyte infiltration\",\n    \"7-0\": \"Percent monocyte infiltration\",\n    \"8-0\": \"Percent necrosis\",\n    \"9-0\": \"Percent neutrophil infiltration\",\n    \"10-0\": \"Percent normal cells\",\n    \"11-0\": \"Percent stromal cells\",\n    \"13-0\": \"Percent tumor nuclei\",\n    \"12-0\": \"Percent tumor cells\",\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 section of a tissue that has been imaged. The value denotes top, middle, or bottom.\",\n    \"2-1\": \"The number of proliferating cells identified in the slide sample.\",\n    \"3-1\": \"The fraction of eosinophil cells to the gross granulocyte component of inflammatory cells seen on a slide.\",\n    \"4-1\": \"The fraction of the granulocyte component to the gross inflammatory cells seen on a slide.\",\n    \"5-1\": \"The ratio of inflammatory cells to the gross cell population seen on a slide.\",\n    \"6-1\": \"The fraction of lymphocyte cells to the gross inflammatory cells seen on a slide.\",\n    \"7-1\": \"The fraction of monocyte cells to the gross inflammatory cells seen on a slide.\",\n    \"8-1\": \"The percent of identified tumor cell necrosis based on the tissue image.\",\n    \"9-1\": \"The fraction of neutrophile cells to the gross granulocyte component of inflammatory cells seen on a slide.\",\n    \"10-1\": \"The percent of identified normal cell based on the tissue image.\",\n    \"11-1\": \"The ratio of identified stromal cells present on the tissue slide.\",\n    \"12-1\": \"The percent of identified tumor cells based on the tissue image.\",\n    \"13-1\": \"The percent of identified tumor nuclei based on the tissue image.\"\n  },\n  \"cols\": 2,\n  \"rows\": 14\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Analyte\nThe **analyte** entity represents the analytes or molecules, such as DNA or RNA, used for analyses. An analyte is a molecular specimen extracted for analysis from a portion using a specific extraction protocol. Members of the **analyte** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **analyte** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"1-0\": \"Amount\",\n    \"2-0\": \"A260_A280 ratio\",\n    \"3-0\": \"Analyte type\",\n    \"4-0\": \"Analyte type ID\",\n    \"5-0\": \"Concentration\",\n    \"6-0\": \"Spectrophotometer method\",\n    \"7-0\": \"Well number\",\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 amount of a product (in g or volume in mL) prepared for an analysis.\",\n    \"2-1\": \"A purity measurement that weighs the absorbance at 260nm (DNA concentration) against the absorbance at 280nm (protein concentration/contamination).\",\n    \"3-1\": \"This defines the type of an analyte on molecular bases.\",\n    \"4-1\": \"An ID that determines the type of an analyte on molecular bases. A single letter BCR code for the analyte type.\",\n    \"5-1\": \"The concentration of a product (in molarity) prepared for an analysis.\",\n    \"6-1\": \"A method of quantifying the content of nucleic acids in any sample, used to measure sample purity (e.g. UV spec.)\",\n    \"7-1\": \"The number of wells on the plate in which an analyte has been stored for shipment and for the analysis.\"\n  },\n  \"cols\": 2,\n  \"rows\": 8\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Aliquot\nThe **aliquot** entity represents to aliquots, products or units extracted from a sample or specimen 's portion and prepared for analysis. Members of the **aliquot** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **aliquot** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"1-0\": \"Amount\",\n    \"2-0\": \"Concentration\",\n    \"3-0\": \"Source center\",\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\": \"The amount of a product (in g or volume in mL) prepared for an analysis.\",\n    \"2-1\": \"The concentration of a product (in molarity) prepared for an analysis.\",\n    \"3-1\": \"The name of the center that provided the item.\",\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 determines 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\": \"The shortened name of the center (e.g. BI).\"\n  },\n  \"cols\": 2,\n  \"rows\": 10\n}\n[/block]\n<div align=\"right\"><a href=\"#top>top</a></div>\n\n##Read group\nThe **read group** entity refers to the sequencing reads from one lane of an NGS experiment. Members of the **read group** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **read group** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"1-0\": \"Read group name\",\n    \"2-0\": \"Adapter name\",\n    \"3-0\": \"Adapter sequence\",\n    \"4-0\": \"Base caller name\",\n    \"5-0\": \"Base caller version\",\n    \"6-0\": \"Experiment name\",\n    \"7-0\": \"Flow cell barcode\",\n    \"8-0\": \"Includes spike ins\",\n    \"9-0\": \"Instrument model\",\n    \"10-0\": \"Is paired end\",\n    \"11-0\": \"Library name\",\n    \"12-0\": \"Library preparation kit catalog number\",\n    \"13-0\": \"Library preparation kit name\",\n    \"14-0\": \"Library preparation kit vendor\",\n    \"15-0\": \"Library preparation kit version\",\n    \"16-0\": \"Library selection\",\n    \"17-0\": \"Library strand\",\n    \"18-0\": \"Library strategy\",\n    \"19-0\": \"Platform\",\n    \"20-0\": \"Read length\",\n    \"21-0\": \"RIN\",\n    \"22-0\": \"Sequencing center\",\n    \"23-0\": \"Sequencing date\",\n    \"24-0\": \"Size selection range\",\n    \"25-0\": \"Spike ins concentration\",\n    \"26-0\": \"Spike ins fasta\",\n    \"27-0\": \"Target capture kit catalog number\",\n    \"28-0\": \"Target capture kit name\",\n    \"29-0\": \"Target capture kit target region\",\n    \"30-0\": \"Target capture kit vendor\",\n    \"31-0\": \"Target capture kit version\",\n    \"32-0\": \"To trim adapter sequence\",\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 name of the read group.\",\n    \"2-1\": \"The name of the sequencing adapter.\",\n    \"3-1\": \"The base sequence of the sequencing adapter.\",\n    \"4-1\": \"The name of the base caller.\",\n    \"5-1\": \"The version of the base caller.\",\n    \"6-1\": \"A submitter-defined name for the experiment.\",\n    \"7-1\": \"The barcode assigned to flow cell.\",\n    \"8-1\": \"A Boolean value which denotes whether a spike-in is included or not.\",\n    \"9-1\": \"A specific model of sequencing instrument used.\",\n    \"10-1\": \"A Boolean value which denotes whether sequence reads are paired end or not.\",\n    \"11-1\": \"The name of the sequencing library preparation.\",\n    \"12-1\": \"The catalog number of the sequencing library preparation kit.\",\n    \"13-1\": \"The name of the sequencing library preparation kit.\",\n    \"14-1\": \"The vendor of the sequencing library preparation kit.\",\n    \"15-1\": \"The version of the sequencing library preparation kit.\",\n    \"16-1\": \"The method used to select and/or enrich the material being sequenced.\",\n    \"17-1\": \"This determines whether the 'first strand' or 'second strand' of cDNA was used to prepare the library.\",\n    \"18-1\": \"The sequencing technique intended for the library.\",\n    \"19-1\": \"The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.\",\n    \"20-1\": \"The length of the reads.\",\n    \"21-1\": \"The RNA integrity number.\",\n    \"22-1\": \"The name of the center that provided the sequence files.\",\n    \"23-1\": \"The date of sequencing.\",\n    \"24-1\": \"The range of size selection.\",\n    \"25-1\": \"The concentration of a spike-in.\",\n    \"26-1\": \"The name of the FASTA file that contains the spike-in sequences.\",\n    \"27-1\": \"The catalog number of target capture kit.\",\n    \"28-1\": \"The name of the target capture kit.\",\n    \"29-1\": \"The target region for target capture kit.\",\n    \"30-1\": \"The vendor of target capture kit.\",\n    \"31-1\": \"The version of a target capture kit.\",\n    \"32-1\": \"A Boolean value for adapter trimming.\"\n  },\n  \"cols\": 2,\n  \"rows\": 33\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Read group QC\nThe **read group QC** represents read group quality control. Members of the **read group QC** entity can be identified with a Universally Unique Identifier (UUID). Find the properties of the **read group QC** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Descripton\",\n    \"0-0\": \"Submitter ID\",\n    \"1-0\": \"Adapter content\",\n    \"2-0\": \"Basic statistics\",\n    \"3-0\": \"Encoding\",\n    \"4-0\": \"FASTQ name\",\n    \"5-0\": \"Kmer content\",\n    \"6-0\": \"Overrepresented sequences\",\n    \"7-0\": \"Per base N content\",\n    \"8-0\": \"Per base sequence content\",\n    \"9-0\": \"Per base sequence quality\",\n    \"10-0\": \"Per sequence GC content\",\n    \"11-0\": \"Per sequence quality score\",\n    \"12-0\": \"Per tile sequence quality\",\n    \"13-0\": \"Percent GC content\",\n    \"14-0\": \"Sequence duplication levels\",\n    \"15-0\": \"Sequence length distribution\",\n    \"16-0\": \"Total sequences\",\n    \"17-0\": \"Workflow start datetime\",\n    \"18-0\": \"Workflow end datetime\",\n    \"19-0\": \"Workflow link\",\n    \"20-0\": \"Workflow type\",\n    \"21-0\": \"Workflow version\",\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\": \"An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"2-1\": \"An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"3-1\": \"The version of ASCII encoding of quality values found in the file.\",\n    \"4-1\": \"The names of FASTQs.\",\n    \"5-1\": \"The number of times the kmer occurs in the sequence. Analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"6-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"7-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"8-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"9-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"10-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"11-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"12-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"13-1\": \"The overall %GC of all bases in all sequences.\",\n    \"14-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"15-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"16-1\": \"The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.\",\n    \"17-1\": \"The start of the analysis workflow in datetime format.\",\n    \"18-1\": \"The end of the analysis workflow in datatime format.\",\n    \"20-1\": \"A generic name for the workflow used to analyze data.\",\n    \"21-1\": \"The version of the workflow used to analyze data.\",\n    \"19-1\": \"The link to Github hash for the CWL workflow used (*GDC* related).\"\n  },\n  \"cols\": 2,\n  \"rows\": 22\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\": \"Data category\",\n    \"2-0\": \"Data type\",\n    \"3-0\": \"Data format\",\n    \"4-0\": \"Experimental strategy\",\n    \"5-0\": \"File size\",\n    \"6-0\": \"Access level\",\n    \"7-0\": \"Platform\",\n    \"8-0\": \"Genome build\",\n    \"9-0\": \"Genome name\",\n    \"10-0\": \"GDC file UUID\",\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 classification of data used in (or produced by) the analysis, based on its form and content. See NCI Thesaurus Code: C42645.\",\n    \"2-1\": \"A further, more specific classification of the data category, based on the information that it contains.\",\n    \"3-1\": \"The type of format that determines data content.\",\n    \"4-1\": \"The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.\",\n    \"5-1\": \"The size of a file measured in bytes (B), kilobytes (KB), megabytes (MB), gigabytes (GB), terabytes (TB), and larger values.\",\n    \"6-1\": \"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    \"7-1\": \"The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.\",\n    \"8-1\": \"The reference genome or assembly (such as HG19/GRCh37 or GRCh38) to which the nucleotide sequence of a case/subject/sample can be aligned.\",\n    \"9-1\": \"The reference genome or assembly that also contains decoy viral sequence to which the nucleotide sequence of a case/subject/sample can be aligned.\",\n    \"10-1\": \"The unique identifier for a file, such as a UUID.\"\n  },\n  \"cols\": 2,\n  \"rows\": 11\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Analysis\nThe **analysis** entity represents analysis workflows used for processing data. Members of the **analysis** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **analysis** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"1-0\": \"Workflow start datetime\",\n    \"2-0\": \"Workflow end datetime\",\n    \"3-0\": \"Workflow link\",\n    \"4-0\": \"Workflow type\",\n    \"5-0\": \"Workflow version\",\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 start of the analysis workflow in date/time format.\",\n    \"3-1\": \"A link to Github hash for the CWL workflow used (GDC related).\",\n    \"2-1\": \"The end of the analysis workflow in date/time format.\",\n    \"4-1\": \"The generic name for the workflow used to analyze data.\",\n    \"5-1\": \"The version of the workflow used to analyze data.\"\n  },\n  \"cols\": 2,\n  \"rows\": 6\n}\n[/block]\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> > TCGA GRCh38 metadata","slug":"tcga-grch38-metadata","type":"basic","title":"TCGA GRCh38 metadata"}

TCGA GRCh38 metadata

<a href="about-metadata-for-datasets" style="color:#132c56">ABOUT METADATA FOR DATASETS</a> > TCGA GRCh38 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* [Treatment](#section-treatment)\n* [Exposure](#section-exposure)\n* [Drug therapy](#section-drug-therapy)\n* [Radiation therapy](#section-radiation-therapy)\n* [Follow up](#section-follow-up)\n* [New tumor event](#section-new-tumor-event)\n* [Sample](#section-sample)\n* [Portion](#section-portion)\n* [Slide](#section-slide)\n* [Analyte](#section-analyte)\n* [Aliquot](#section-aliquot)\n* [Read group](#section-read-group)\n* [Read group QC](#section-read-group-qc)\n* [File](#section-file)\n* [Analysis](#section-analysis)" } [/block] ##Overview Metadata is data that describes other data. On this page, we've detailed TCGA metadata that are available for viewing and filtering TCGA data in the Data Browser, Datasets API, and the SPARQL endpoint on the CGC. TCGA metadata on the CGC consists of properties which describe the entities of the TCGA 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 TCGA GRCh38 Entities for TCGA GRCh38 The following are entities for TCGA GRCh38. They represent clinical data, biospecimen data, and data about TCGA GRCh38 files. Note that these entities differ from the [entities of legacy TCGA data](doc:tcga-metadata). Learn more about [TCGA GRCh38 data](doc:tcga-grch38-data). * investigation * case * demographic * diagnosis * treatment * exposure * drug_therapy * radiation_therapy * follow_up * new_tumor_event * sample * portion * slide * analyte * aliquot * read_group * read_group_qc * file * analysis 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": "dbGaP accession number", "0-1": "The dbGaP accession number provided for each study. See NCI Thesaurus Code: C25402.", "1-0": "Disease type", "1-1": "The type of the disease or condition studied. See NCI Thesaurus Code: C2991.", "2-0": "Investigation name", "3-0": "Primary site", "3-1": "The anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761.", "2-1": "The full name of the project or study that generated the data. See NCI Thesaurus Code: C41198.", "4-0": "Submitter ID", "4-1": "A human-readable identifier, such as a number or a string that may contain metadata information for investigations." }, "cols": 2, "rows": 5 } [/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": { "0-0": "Batch number", "h-0": "Property", "h-1": "Description", "0-1": "A set of related analytes prepared for further analysis and numbered sequentially from the same disease. Once a Case has been assigned to a batch number, subsequent shipments from that case are assigned the same batch number as the original. Seven Bridges only field.", "1-0": "Submitter ID", "1-1": "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.", "2-0": "Tissue source site ID", "2-1": "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.", "3-0": "Tissue source site name", "4-0": "Tissue source site code", "5-0": "Tissue source site BCR ID", "3-1": "The full name of a clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.", "4-1": "The alphanumeric code for clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.", "5-1": "The BCR (Biospecimen Core Resource) provided ID for a tissue source site. See NCI Thesaurus Code: C103264." }, "cols": 2, "rows": 6 } [/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": "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": "Ethnicity", "1-1": "A socially-defined category of people based on common ancestral, cultural, biological, and social factors. See NCI Thesaurus Code: C29933.", "2-0": "Race", "2-1": "A classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution. See NCI Thesaurus Code: C17049.", "3-0": "Gender", "4-0": "Year of birth", "5-0": "Year of death", "3-1": "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.", "4-1": "A numeric value to represent the calendar year in which an individual was born. See CDE (Common Data Element) Public ID: 2896954.", "5-1": "A numeric value to represent the year of the death of an individual. See CDE (Common Data Element) Public ID: 2897030." }, "cols": 2, "rows": 6 } [/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": "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": "Age at diagnosis", "1-1": "The age in years of the Case at the initial pathological diagnosis of the disease or cancer. See NCI Thesaurus Code: C15220.", "2-0": "Classification of tumor", "2-1": "Text that describes the kind of disease present in the tumor specimen as related to a specific point in time. See CDE (Common Data Element) Public ID: 3288124.", "3-0": "Days to birth", "3-1": "The time interval from a person's date of birth to the date of initial pathologic diagnosis, represented as a calculated negative number of days. See CDE (Common Data Element) Public ID: 3008233.", "4-0": "Days to death", "4-1": "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.", "5-0": "Days to last follow up", "5-1": "The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.", "6-0": "Days to last known disease status", "6-1": "The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.", "7-0": "Days to recurrence", "7-1": "The time interval from the date of new tumor event, including progression, recurrence and new primary malignancies, to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3392464.", "8-0": "Last known disease status", "9-0": "Morphology", "10-0": "Primary diagnosis", "11-0": "Prior malignancy", "12-0": "Progression or recurrence", "13-0": "New tumor event after initial treatment", "14-0": "Site of resection or biopsy", "15-0": "Tissue or organ of origin", "16-0": "Tumor grade", "17-0": "Tumor stage", "18-0": "Vital status", "19-0": "Histological diagnosis", "20-0": "Histological diagnosis other", "21-0": "Year of diagnosis", "22-0": "Clinical T (TNM)", "23-0": "Clinical M (TNM)", "24-0": "Clinical N (TNM)", "25-0": "Clinical stage", "26-0": "Pathologic T (TNM)", "27-0": "Pathologic N (TNM)", "28-0": "Pathologic M (TNM)", "29-0": "Performance status scale: Timing", "30-0": "Performance status scale: Karnofsky score", "31-0": "Performance status scale: ECOG", "32-0": "Tumor status", "33-0": "Primary therapy outcome success", "8-1": "The state or condition of an individual's neoplasm at a particular point in time. See CDE (Common Data Element) Public ID: 3392464.", "9-1": "The morphology code which describes the characteristics of the tumor itself, including its cell type and biologic activity, according to the third edition of the International Classification of Diseases for Oncology (ICD-O). See CDE (Common Data Element) Public ID: 3226275.", "10-1": "Text term for the structural pattern of cancer cells used to define a microscopic diagnosis. See CDE (Common Data Element) Public ID: 3081934.", "11-1": "Text term to describe the patient's history of prior cancer diagnosis and the spatial location of any previous cancer occurrence. See CDE (Common Data Element) Public ID: 3081934.", "12-1": "Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment. See CDE (Common Data Element) Public ID: 3121376.", "13-1": "A Boolean value denoting whether a neoplasm developed after the initial treatment was finished.", "14-1": "The topography code which describes the anatomical site of origin of the neoplasm according to the third edition of the International Classification of Diseases for Oncology (ICD-O). See NCI Thesaurus Code: C37978. See CDE (Common Data Element) Public ID: 3226281.", "15-1": "The text term that describes the anatomic site of the tumor or disease. See CDE (Common Data Element) Public ID: 3226281.", "16-1": "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.", "17-1": "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.", "18-1": "The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.", "19-1": "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.", "20-1": "Additional options for histologics diagnosis (see Histologic diagnosis), which have not been pre-determined in the listed values for histologic diagnosis.", "21-1": "The numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. See CDE (Common Data Element) Public ID: 2896960.", "22-1": "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.", "23-1": "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.", "24-1": "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.", "25-1": "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.", "26-1": "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.", "27-1": "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.", "28-1": "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.", "29-1": "A time reference for the Karnofsky score and/or the ECOG score using the defined categories.", "30-1": "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.", "31-1": "A performance status scale designed to assess disease progression and its effect on the daily living abilities of the patient. NCI Thesaurus Code: C105721.", "33-1": "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.", "32-1": "The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643." }, "cols": 2, "rows": 34 } [/block] <div align="right"><a href="#top">top</a></div> ##Treatment The **treatment** entity represents records of the administration of therapeutic agents to a patient to alter the course of a pathologic process. Members of the **treatment** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **treatment** entity below. [block:parameters] { "data": { "0-0": "Submitter ID", "h-0": "Property", "h-1": "Description", "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": "Days to treatment", "1-1": "The number of days from the date of the initial pathologic diagnosis that treatment began.", "2-0": "Therapeutic agents", "2-1": "The text identification of the individual agent(s) used as part of a prior treatment regimen. See CDE (Common Data Element) Public ID: 2975232.", "3-0": "Treatment intent type", "3-1": "The text term to identify the reason for the administration of a treatment regimen. [Manually-curated]. See CDE (Common Data Element) Public ID: 2793511.", "4-0": "Treatment or therapy", "4-1": "A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected. See CDE (Common Data Element) Public ID: 4231463.", "5-0": "Country of specimen procurement", "5-1": "Country where specimen/sample has been procured.", "6-0": "Longest dimension", "6-1": "The longest dimension of sample/specimen (in centimeters).", "7-0": "Intermediate dimension", "7-1": "The intermediate dimension of sample/specimen (in centimeters).", "8-0": "Shortest dimension", "8-1": "The shortest dimension of sample/specimen (in centimeters).", "9-0": "Initial weight", "9-1": "Initial sample/specimen weight (in grams).", "10-0": "Current weight", "10-1": "Current sample/specimen weight (in grams).", "11-0": "Freezing method", "11-1": "The freezing method for sample/specimen.", "12-0": "OCT embedded", "12-1": "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.", "13-0": "Time between clamping and freezing", "13-1": "Time elapsed (in minutes) between clamping (supplying vessel) and freezing a sample.", "14-0": "Time between excision and freezing", "14-1": "Warm ischemia time, elapsed between clamping and freezing a sample, as denoted in minutes.", "15-0": "Days to collection", "15-1": "Days to sample collection. Sample can be collected can be prospectively or retrospectively. This can be a negative value for samples taken retrospectively.", "16-0": "Days to sample procurement", "16-1": "Number of days from the date the patient was initially diagnosed pathologically with the disease to the date of the procedure that produced the malignant sample for submission.", "17-0": "Is FFPE", "17-1": "A boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE)." }, "cols": 2, "rows": 5 } [/block] <div align="right"><a href="#top">top</a></div> ##Exposure The **exposure** entity represents clinically relevant patient information which does not immediately result from genetic predispositions. Members of the **exposure** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **exposure** entity below. [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": "Alcohol history", "1-1": "A response to the question that asks whether the participant has consumed at least 12 drinks of any kind of alcoholic beverage in their lifetime. See CDE (Common Data Element) Public ID: 2201918. Also: A description of an individual's current and past experience with alcoholic beverage consumption. See NCI Thesaurus Code: C81229.", "2-0": "Alcohol intensity", "2-1": "A category to describe the patient's current level of alcohol use as self-reported by the patient. See CDE (Common Data Element) Public ID: 3457767.", "3-0": "BMI", "3-1": "The body mass divided by the square of the body height expressed in units of kg/m2. See CDE (Common Data Element) Public ID: 4973892.", "4-0": "Cigarettes per day", "5-0": "Height", "6-0": "Weight", "7-0": "Years smoked", "4-1": "The average number of cigarettes smoked per day. See CDE (Common Data Element) Public ID: 2001716.", "5-1": "The height of the patient in centimeters. See CDE (Common Data Element) Public ID: 649.", "7-1": "The numeric value (or unknown) to represent the number of years a person has been smoking. See CDE (Common Data Element) Public ID: 3137957.", "6-1": "The weight of the patient measured in kilograms. See CDE (Common Data Element) Public ID: 651." }, "cols": 2, "rows": 8 } [/block] <div align="right"><a href="#top">top</a></div> ###Drug therapy The **drug therapy** entity represents the use of pharmaceutical products that contains one or more active and/or inactive ingredients to treat, prevent or alleviate the symptoms of disease. A **Case** can have more them one drug treatment. Members of the **drug therapy** entity can be identified by a Universally Unique Identifier (UUID). [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": "Drug name", "1-1": "The most recognizable term associated with a pharmaceutical product used to prevent, diagnose, treat or relieve symptoms of a disease or abnormal condition. NCI Thesaurus Code: C97104.", "2-0": "Pharmaceutical therapy type", "2-1": "The type of treatment of the disease through the use of drugs. NCI Thesaurus Code: C15986.", "3-0": "Percent tumor cells", "3-1": "The percent of tumor cells based on the tissue image.", "4-0": "Percent tumor nuclei", "4-1": "The percent of tumor nuclei based on the tissue image.", "5-0": "Percent normal cells", "5-1": "The percent of normal cell based on the tissue image.", "6-0": "Percent necrosis", "6-1": "The percent of normal cell based on the tissue image.", "7-0": "Percent stromal cells", "7-1": "The ratio of stromal cells present on the tissue slide.", "8-0": "Percent inflam infiltration", "8-1": "The ratio of inflammatory cells to the gross cell population seen on a slide.", "9-0": "Percent lymphocyte infiltration", "9-1": "The fraction of lymphocyte cells to the gross inflammatory cells seen on a slide.", "10-0": "Percent monocyte infiltration", "10-1": "The fraction of monocyte cells to the gross inflammatory cells seen on a slide.", "11-0": "Percent granulocyte infiltration", "11-1": "The fraction of the granulocyte component to the gross inflammatory cells seen on a slide.", "12-0": "Percent neutrophile infiltration", "12-1": "The fraction of neutrophile cells to the gross granulocyte component of inflammatory cells seen on a slide.", "13-0": "Percent eosinophil infiltration", "13-1": "The fraction of eosinophil cells to the gross granulocyte component of inflammatory cells seen on a slide." }, "cols": 2, "rows": 3 } [/block] <div align="right"><a href="#top">top</a></div> ###Radiation therapy The **radiation therapy** entity represents the treatment of a disease with **radiation therapy**, in which the whole or a portion of the patient's body is exposed to radiation. A Case can have more than one radiation treatment. Members of the **radiation therapy** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **radiation therapy** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "1-0": "Radiation type", "0-0": "Submitter ID", "0-1": "This refers to the radiation therapy id, a human-readable identifier, such as a number or a string that may contain metadata information, for the radiation treatment of a disease by means of exposure of the target or the whole body to radiation. NCI Thesaurus Code: C15986.", "1-1": "The value denotes the type of high-energy radiation used to kill cancer cells and shrink tumors. NCI Thesaurus Code: C15986.", "2-0": "Radiation therapy site", "2-1": "The location to which radiation therapy was administered.", "3-0": "Amount", "3-1": "Amount of a product (in μg) prepared for an analysis.", "4-0": "Concentration", "4-1": "Concentration of a product (in μg/μL) prepared for an analysis.", "5-0": "a260_a280 ratio", "5-1": "A numerical value denoting purity assessment using the A260/A280 Ratios.", "6-0": "Well number", "6-1": "The number of wells on the plate in which an analyte has been stored for shipment and for the analysis.", "7-0": "Spectrophotometer method", "7-1": "A method of quantifying the content of nucleic acids in any sample." }, "cols": 2, "rows": 3 } [/block] <div align="right"><a href="#top">top</a></div> ###Follow up The **follow up** entity refers to follow ups which monitor a person's health over time after treatment. A Case can have multiple follow ups generated at different times. Members of the **follow up** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **follow up** entity below. [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": "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": "Days to last follow up", "2-1": "The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.", "3-0": "New tumor event after initial treatment", "4-0": "Tumor status", "5-0": "Vital status", "3-1": "A Boolean value which denotes whether a neoplasm developed after the initial treatment has finished.", "4-1": "The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.", "5-1": "The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717." }, "cols": 2, "rows": 6 } [/block] <div align="right"><a href="#top">top</a></div> ##New tumor event The **new tumor event** entity represents a newly developed neoplasm after initial treatment has finished. Members of the new tumor event entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **new tumor event** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "New tumor anatomic site", "1-0": "Other new tumor anatomic site", "0-1": "Anatomic site of newly developed neoplasm.", "1-1": "Alternative anatomic site of a newly developed neoplasm which has not been listed under 'New tumor anatomic site'.", "2-0": "New tumor event type", "2-1": "Type of newly developed neoplasm after initial treatment has finished.", "3-0": "Experimental strategy", "3-1": "The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.", "5-0": "Data type", "4-0": "Platform", "4-1": "The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.", "5-1": "The classification of data used in (or produced by) the analysis, based on its form and content. See NCI Thesaurus Code: C42645.", "6-0": "Data subtype", "6-1": "A further, more specific classification of the data type, based on the information that it contains.", "7-0": "Data submitting center", "7-1": "This field takes a string denoting the name of the center that has submitted data.", "8-0": "Reference genome", "9-0": "Access level", "8-1": "The reference assembly (such as HG19 or GRCh37) to which the nucleotide sequence of a case can be aligned.", "9-1": "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": 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": 23 } [/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": 10 } [/block] <div align="right"><a href="#top">top</a></div> ##Slide The **slide** entity represents slides, thin slices of a snap-frozen OCT embedded block of tissue sent for imaging. This same tissue also provides DNA and RNA for further analyses after they are reviewed by histopathologists. Members of the **slide** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **slide** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "1-0": "Section location", "2-0": "Number proliferating cells", "3-0": "Percent eosinophil infiltration", "4-0": "Percent granulocyte infiltration", "5-0": "Percent inflam infiltration", "6-0": "Percent lymphocyte infiltration", "7-0": "Percent monocyte infiltration", "8-0": "Percent necrosis", "9-0": "Percent neutrophil infiltration", "10-0": "Percent normal cells", "11-0": "Percent stromal cells", "13-0": "Percent tumor nuclei", "12-0": "Percent tumor cells", "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 section of a tissue that has been imaged. The value denotes top, middle, or bottom.", "2-1": "The number of proliferating cells identified in the slide sample.", "3-1": "The fraction of eosinophil cells to the gross granulocyte component of inflammatory cells seen on a slide.", "4-1": "The fraction of the granulocyte component to the gross inflammatory cells seen on a slide.", "5-1": "The ratio of inflammatory cells to the gross cell population seen on a slide.", "6-1": "The fraction of lymphocyte cells to the gross inflammatory cells seen on a slide.", "7-1": "The fraction of monocyte cells to the gross inflammatory cells seen on a slide.", "8-1": "The percent of identified tumor cell necrosis based on the tissue image.", "9-1": "The fraction of neutrophile cells to the gross granulocyte component of inflammatory cells seen on a slide.", "10-1": "The percent of identified normal cell based on the tissue image.", "11-1": "The ratio of identified stromal cells present on the tissue slide.", "12-1": "The percent of identified tumor cells based on the tissue image.", "13-1": "The percent of identified tumor nuclei based on the tissue image." }, "cols": 2, "rows": 14 } [/block] <div align="right"><a href="#top">top</a></div> ##Analyte The **analyte** entity represents the analytes or molecules, such as DNA or RNA, used for analyses. An analyte is a molecular specimen extracted for analysis from a portion using a specific extraction protocol. Members of the **analyte** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **analyte** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "1-0": "Amount", "2-0": "A260_A280 ratio", "3-0": "Analyte type", "4-0": "Analyte type ID", "5-0": "Concentration", "6-0": "Spectrophotometer method", "7-0": "Well number", "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 amount of a product (in g or volume in mL) prepared for an analysis.", "2-1": "A purity measurement that weighs the absorbance at 260nm (DNA concentration) against the absorbance at 280nm (protein concentration/contamination).", "3-1": "This defines the type of an analyte on molecular bases.", "4-1": "An ID that determines the type of an analyte on molecular bases. A single letter BCR code for the analyte type.", "5-1": "The concentration of a product (in molarity) prepared for an analysis.", "6-1": "A method of quantifying the content of nucleic acids in any sample, used to measure sample purity (e.g. UV spec.)", "7-1": "The number of wells on the plate in which an analyte has been stored for shipment and for the analysis." }, "cols": 2, "rows": 8 } [/block] <div align="right"><a href="#top">top</a></div> ##Aliquot The **aliquot** entity represents to aliquots, products or units extracted from a sample or specimen 's portion and prepared for analysis. Members of the **aliquot** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **aliquot** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "1-0": "Amount", "2-0": "Concentration", "3-0": "Source center", "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": "The amount of a product (in g or volume in mL) prepared for an analysis.", "2-1": "The concentration of a product (in molarity) prepared for an analysis.", "3-1": "The name of the center that provided the item.", "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 determines 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": "The shortened name of the center (e.g. BI)." }, "cols": 2, "rows": 10 } [/block] <div align="right"><a href="#top>top</a></div> ##Read group The **read group** entity refers to the sequencing reads from one lane of an NGS experiment. Members of the **read group** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **read group** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "1-0": "Read group name", "2-0": "Adapter name", "3-0": "Adapter sequence", "4-0": "Base caller name", "5-0": "Base caller version", "6-0": "Experiment name", "7-0": "Flow cell barcode", "8-0": "Includes spike ins", "9-0": "Instrument model", "10-0": "Is paired end", "11-0": "Library name", "12-0": "Library preparation kit catalog number", "13-0": "Library preparation kit name", "14-0": "Library preparation kit vendor", "15-0": "Library preparation kit version", "16-0": "Library selection", "17-0": "Library strand", "18-0": "Library strategy", "19-0": "Platform", "20-0": "Read length", "21-0": "RIN", "22-0": "Sequencing center", "23-0": "Sequencing date", "24-0": "Size selection range", "25-0": "Spike ins concentration", "26-0": "Spike ins fasta", "27-0": "Target capture kit catalog number", "28-0": "Target capture kit name", "29-0": "Target capture kit target region", "30-0": "Target capture kit vendor", "31-0": "Target capture kit version", "32-0": "To trim adapter sequence", "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 name of the read group.", "2-1": "The name of the sequencing adapter.", "3-1": "The base sequence of the sequencing adapter.", "4-1": "The name of the base caller.", "5-1": "The version of the base caller.", "6-1": "A submitter-defined name for the experiment.", "7-1": "The barcode assigned to flow cell.", "8-1": "A Boolean value which denotes whether a spike-in is included or not.", "9-1": "A specific model of sequencing instrument used.", "10-1": "A Boolean value which denotes whether sequence reads are paired end or not.", "11-1": "The name of the sequencing library preparation.", "12-1": "The catalog number of the sequencing library preparation kit.", "13-1": "The name of the sequencing library preparation kit.", "14-1": "The vendor of the sequencing library preparation kit.", "15-1": "The version of the sequencing library preparation kit.", "16-1": "The method used to select and/or enrich the material being sequenced.", "17-1": "This determines whether the 'first strand' or 'second strand' of cDNA was used to prepare the library.", "18-1": "The sequencing technique intended for the library.", "19-1": "The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.", "20-1": "The length of the reads.", "21-1": "The RNA integrity number.", "22-1": "The name of the center that provided the sequence files.", "23-1": "The date of sequencing.", "24-1": "The range of size selection.", "25-1": "The concentration of a spike-in.", "26-1": "The name of the FASTA file that contains the spike-in sequences.", "27-1": "The catalog number of target capture kit.", "28-1": "The name of the target capture kit.", "29-1": "The target region for target capture kit.", "30-1": "The vendor of target capture kit.", "31-1": "The version of a target capture kit.", "32-1": "A Boolean value for adapter trimming." }, "cols": 2, "rows": 33 } [/block] <div align="right"><a href="#top">top</a></div> ##Read group QC The **read group QC** represents read group quality control. Members of the **read group QC** entity can be identified with a Universally Unique Identifier (UUID). Find the properties of the **read group QC** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Descripton", "0-0": "Submitter ID", "1-0": "Adapter content", "2-0": "Basic statistics", "3-0": "Encoding", "4-0": "FASTQ name", "5-0": "Kmer content", "6-0": "Overrepresented sequences", "7-0": "Per base N content", "8-0": "Per base sequence content", "9-0": "Per base sequence quality", "10-0": "Per sequence GC content", "11-0": "Per sequence quality score", "12-0": "Per tile sequence quality", "13-0": "Percent GC content", "14-0": "Sequence duplication levels", "15-0": "Sequence length distribution", "16-0": "Total sequences", "17-0": "Workflow start datetime", "18-0": "Workflow end datetime", "19-0": "Workflow link", "20-0": "Workflow type", "21-0": "Workflow version", "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": "An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "2-1": "An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "3-1": "The version of ASCII encoding of quality values found in the file.", "4-1": "The names of FASTQs.", "5-1": "The number of times the kmer occurs in the sequence. Analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "6-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "7-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "8-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "9-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "10-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "11-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "12-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "13-1": "The overall %GC of all bases in all sequences.", "14-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "15-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "16-1": "The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.", "17-1": "The start of the analysis workflow in datetime format.", "18-1": "The end of the analysis workflow in datatime format.", "20-1": "A generic name for the workflow used to analyze data.", "21-1": "The version of the workflow used to analyze data.", "19-1": "The link to Github hash for the CWL workflow used (*GDC* related)." }, "cols": 2, "rows": 22 } [/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": "Data category", "2-0": "Data type", "3-0": "Data format", "4-0": "Experimental strategy", "5-0": "File size", "6-0": "Access level", "7-0": "Platform", "8-0": "Genome build", "9-0": "Genome name", "10-0": "GDC file UUID", "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 classification of data used in (or produced by) the analysis, based on its form and content. See NCI Thesaurus Code: C42645.", "2-1": "A further, more specific classification of the data category, based on the information that it contains.", "3-1": "The type of format that determines data content.", "4-1": "The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.", "5-1": "The size of a file measured in bytes (B), kilobytes (KB), megabytes (MB), gigabytes (GB), terabytes (TB), and larger values.", "6-1": "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.", "7-1": "The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.", "8-1": "The reference genome or assembly (such as HG19/GRCh37 or GRCh38) to which the nucleotide sequence of a case/subject/sample can be aligned.", "9-1": "The reference genome or assembly that also contains decoy viral sequence to which the nucleotide sequence of a case/subject/sample can be aligned.", "10-1": "The unique identifier for a file, such as a UUID." }, "cols": 2, "rows": 11 } [/block] <div align="right"><a href="#top">top</a></div> ##Analysis The **analysis** entity represents analysis workflows used for processing data. Members of the **analysis** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **analysis** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "1-0": "Workflow start datetime", "2-0": "Workflow end datetime", "3-0": "Workflow link", "4-0": "Workflow type", "5-0": "Workflow version", "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 start of the analysis workflow in date/time format.", "3-1": "A link to Github hash for the CWL workflow used (GDC related).", "2-1": "The end of the analysis workflow in date/time format.", "4-1": "The generic name for the workflow used to analyze data.", "5-1": "The version of the workflow used to analyze data." }, "cols": 2, "rows": 6 } [/block] <div align="right"><a href="#top">top</a></div>