{"_id":"5d27604415b659001a5f83e1","project":"5773dcfc255e820e00e1cd4d","version":{"_id":"5773dcfc255e820e00e1cd50","__v":27,"project":"5773dcfc255e820e00e1cd4d","createdAt":"2016-06-29T14:36:44.812Z","releaseDate":"2016-06-29T14:36:44.812Z","categories":["5773dcfc255e820e00e1cd51","5773df36904b0c0e00ef05ff","577baf92451b1e0e006075ac","577bb183b7ee4a0e007c4e8d","577ce77a1cf3cb0e0048e5ea","577d11865fd4de0e00cc3dab","578e62792c3c790e00937597","578f4fd98335ca0e006d5c84","578f5e5c3d04570e00976ebb","57bc35f7531e000e0075d118","57f801b3760f3a1700219ebb","5804d55d1642890f00803623","581c8d55c0dc651900aa9350","589dcf8ba8c63b3b00c3704f","594cebadd8a2f7001b0b53b2","59a562f46a5d8c00238e309a","5a2aa096e25025003c582b58","5a2e79566c771d003ca0acd4","5a3a5166142db90026f24007","5a3a52b5bcc254001c4bf152","5a3a574a2be213002675c6d2","5a3a66bb2be213002675cb73","5a3a6e4854faf60030b63159","5c8a68278e883901341de571","5cb9971e57bf020024523c7b","5cbf1683e2a36d01d5012ecd","5dc15666a4f788004c5fd7d7"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"57f801b3760f3a1700219ebb","version":"5773dcfc255e820e00e1cd50","__v":0,"project":"5773dcfc255e820e00e1cd4d","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-10-07T20:12:35.170Z","from_sync":false,"order":7,"slug":"browse-datasets","title":"Browse public datasets"},"user":"5767bc73bb15f40e00a28777","__v":0,"parentDoc":null,"metadata":{"title":"","description":"","image":[]},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2019-07-11T16:13:56.190Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":11,"body":"[block:callout]\n{\n  \"type\": \"warning\",\n  \"title\": \"On this page:\",\n  \"body\": \"* [Overview](#section-overview)\\n* [Investigation](#section-investigation)\\n* [Case](#section-case)\\n* [Demographic](#section-demographic)\\n* [Diagnosis](#section-diagnosis)\\n* [Sample](#section-sample)\\n* [Aliquot](#section-aliquot)\\n* [Read group](#section-read-group)\\n* [File](#section-file)\\n* [Analysis](#section-analysis)\\n* [Analyte](#section-analyte)\\n* [Exposure](#section-exposure)\\n* [Portion](#section-portion)\"\n}\n[/block]\n## Overview\nMetadata is data that describes other data. On this page, we've detailed CPTAC-3 metadata that is available for viewing and filtering CPTAC-3 data in the Data Browser. CPTAC-3 metadata on Cavatica consists of properties which describe the entities of the [CPTAC-3 dataset](doc:cptac-data).\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## Entities for CPTAC-3\n\nThe following are entities for CPTAC-3\n  * investigation\n  * case\n  * demographic\n  * diagnosis\n  * sample\n  * aliquot\n  * read_group\n  * file\n  * analysis\n  * analyte \n  * exposure\n  * portion\n \nBelow, each of these entities is followed by a table of their related properties.\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\": \"Investigation name\",\n    \"1-1\": \"The full name of the project or study that generated the data. See NCI Thesaurus Code: C41198.\",\n    \"2-0\": \"Submitter ID\",\n    \"2-1\": \"A human-readable identifier, such as a number or a string that may contain metadata information for investigations.\"\n  },\n  \"cols\": 2,\n  \"rows\": 2\n}\n[/block]\n## Case\nThe **case** entity represents CPTAC-3 cases. Members of the **case** entity are subjects who have taken part in an investigation or program and can be identified by a Universally Unique Identifier (UUID). See the table below for the clinical properties and descriptions of the **case** entity.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Submitter ID\",\n    \"0-1\": \"Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.\",\n    \"3-0\": \"Tissue source site ID\",\n    \"3-1\": \"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    \"4-0\": \"Tissue source site name\",\n    \"5-0\": \"Tissue source site code\",\n    \"6-0\": \"Tissue source site BCR ID\",\n    \"4-1\": \"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    \"5-1\": \"The alphanumeric code for clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.\",\n    \"6-1\": \"The BCR (Biospecimen Core Resource) provided ID for a tissue source site. See NCI Thesaurus Code: C103264.\",\n    \"1-0\": \"Disease type\",\n    \"1-1\": \"The type of the disease or condition studied. See NCI Thesaurus Code: C2991.\",\n    \"2-0\": \"Primary site\",\n    \"2-1\": \"The anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761.\"\n  },\n  \"cols\": 2,\n  \"rows\": 3\n}\n[/block]\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\": 4\n}\n[/block]\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\": \"Days to death\",\n    \"2-1\": \"The time interval from the date of initial pathologic diagnosis to a person's date of death, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3165475.\",\n    \"3-0\": \"Days to last follow up\",\n    \"3-1\": \"The time interval from the date of the last follow up to the date to the current date, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.\",\n    \"4-0\": \"Morphology\",\n    \"5-0\": \"Primary diagnosis\",\n    \"6-0\": \"Site of resection or biopsy\",\n    \"7-0\": \"Tumor stage\",\n    \"8-0\": \"Vital status\",\n    \"9-0\": \"Histological diagnosis\",\n    \"10-0\": \"Histological diagnosis other\",\n    \"11-0\": \"Year of diagnosis\",\n    \"12-0\": \"Clinical T (TNM)\",\n    \"13-0\": \"Clinical M (TNM)\",\n    \"14-0\": \"Clinical N (TNM)\",\n    \"15-0\": \"Clinical stage\",\n    \"16-0\": \"Pathologic T (TNM)\",\n    \"17-0\": \"Pathologic N (TNM)\",\n    \"18-0\": \"Pathologic M (TNM)\",\n    \"19-0\": \"Performance status scale: Timing\",\n    \"20-0\": \"Performance status scale: Karnofsky score\",\n    \"21-0\": \"Performance status scale: ECOG\",\n    \"22-0\": \"Tumor status\",\n    \"23-0\": \"Primary therapy outcome success\",\n    \"4-1\": \"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    \"5-1\": \"Text term for the structural pattern of cancer cells used to define a microscopic diagnosis. See CDE (Common Data Element) Public ID: 3081934.\",\n    \"6-1\": \"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    \"7-1\": \"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    \"8-1\": \"The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.\",\n    \"9-1\": \"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    \"10-1\": \"Additional options for histologics diagnosis (see Histologic diagnosis), which have not been pre-determined in the listed values for histologic diagnosis.\",\n    \"11-1\": \"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    \"12-1\": \"The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C253840.\",\n    \"13-1\": \"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    \"14-1\": \"The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C25384.\",\n    \"15-1\": \"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    \"16-1\": \"The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C48739.\",\n    \"17-1\": \"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    \"18-1\": \"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    \"19-1\": \"A time reference for the Karnofsky score and/or the ECOG score using the defined categories.\",\n    \"20-1\": \"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    \"21-1\": \"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    \"23-1\": \"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    \"22-1\": \"The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.\"\n  },\n  \"cols\": 2,\n  \"rows\": 9\n}\n[/block]\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\": \"Tumor code\",\n    \"4-0\": \"Tumor Code ID\",\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 diagnostic tumor code of the tissue sample source.\",\n    \"4-1\": \"A BCR-defined ID code for the tumor sample.\",\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\": 5\n}\n[/block]\n## Aliquot\nThe **aliquot** entity represents 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\": 1\n}\n[/block]\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\": \"Experiment name\",\n    \"3-0\": \"Instrument model\",\n    \"4-0\": \"Is paired end\",\n    \"5-0\": \"Library name\",\n    \"6-0\": \"Library strategy\",\n    \"7-0\": \"Platform\",\n    \"8-0\": \"Read length\",\n    \"9-0\": \"Sequencing center\",\n    \"10-0\": \"Sequencing date\",\n    \"11-0\": \"Target capture kit catalog number\",\n    \"12-0\": \"Target capture kit name\",\n    \"13-0\": \"Target capture kit target region\",\n    \"14-0\": \"Target capture kit vendor\",\n    \"15-0\": \"Target capture kit 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 name of the read group.\",\n    \"2-1\": \"A submitter-defined name for the experiment.\",\n    \"3-1\": \"A specific model of sequencing instrument used.\",\n    \"4-1\": \"A Boolean value which denotes whether sequence reads are paired end or not.\",\n    \"5-1\": \"The name of the sequencing library preparation.\",\n    \"6-1\": \"The sequencing technique intended for the library.\",\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 length of the reads.\",\n    \"9-1\": \"The name of the center that provided the sequence files.\",\n    \"10-1\": \"The date of sequencing.\",\n    \"11-1\": \"The catalog number of target capture kit.\",\n    \"12-1\": \"The name of the target capture kit.\",\n    \"13-1\": \"The target region for target capture kit.\",\n    \"14-1\": \"The vendor of target capture kit.\",\n    \"15-1\": \"The version of a target capture kit.\"\n  },\n  \"cols\": 2,\n  \"rows\": 16\n}\n[/block]\n## File\nThe **file** entity refers to the files in CPTAC-3 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## 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 link\",\n    \"2-0\": \"Workflow type\",\n    \"3-0\": \"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\": \"A link to Github hash for the CWL workflow used (GDC related).\",\n    \"2-1\": \"The generic name for the workflow used to analyze data.\",\n    \"3-1\": \"The version of the workflow used to analyze data.\"\n  },\n  \"cols\": 2,\n  \"rows\": 4\n}\n[/block]\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\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\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 determines the 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]","excerpt":"","slug":"cptac-3-metadata","type":"basic","title":"CPTAC-3 metadata"}
[block:callout] { "type": "warning", "title": "On this page:", "body": "* [Overview](#section-overview)\n* [Investigation](#section-investigation)\n* [Case](#section-case)\n* [Demographic](#section-demographic)\n* [Diagnosis](#section-diagnosis)\n* [Sample](#section-sample)\n* [Aliquot](#section-aliquot)\n* [Read group](#section-read-group)\n* [File](#section-file)\n* [Analysis](#section-analysis)\n* [Analyte](#section-analyte)\n* [Exposure](#section-exposure)\n* [Portion](#section-portion)" } [/block] ## Overview Metadata is data that describes other data. On this page, we've detailed CPTAC-3 metadata that is available for viewing and filtering CPTAC-3 data in the Data Browser. CPTAC-3 metadata on Cavatica consists of properties which describe the entities of the [CPTAC-3 dataset](doc:cptac-data). **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. ## Entities for CPTAC-3 The following are entities for CPTAC-3 * investigation * case * demographic * diagnosis * sample * aliquot * read_group * file * analysis * analyte * exposure * portion Below, each of these entities is followed by a table of their related properties. ##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": "Investigation name", "1-1": "The full name of the project or study that generated the data. See NCI Thesaurus Code: C41198.", "2-0": "Submitter ID", "2-1": "A human-readable identifier, such as a number or a string that may contain metadata information for investigations." }, "cols": 2, "rows": 2 } [/block] ## Case The **case** entity represents CPTAC-3 cases. Members of the **case** entity are subjects who have taken part in an investigation or program and can be identified by a Universally Unique Identifier (UUID). See the table below for the clinical properties and descriptions of the **case** entity. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Submitter ID", "0-1": "Usually a human-readable identifier, such as a number or a string that may contain metadata information. In some instances, this can also be a UUID.", "3-0": "Tissue source site ID", "3-1": "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.", "4-0": "Tissue source site name", "5-0": "Tissue source site code", "6-0": "Tissue source site BCR ID", "4-1": "The full name of a clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.", "5-1": "The alphanumeric code for clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.", "6-1": "The BCR (Biospecimen Core Resource) provided ID for a tissue source site. See NCI Thesaurus Code: C103264.", "1-0": "Disease type", "1-1": "The type of the disease or condition studied. See NCI Thesaurus Code: C2991.", "2-0": "Primary site", "2-1": "The anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761." }, "cols": 2, "rows": 3 } [/block] ##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": 4 } [/block] ##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": "Days to death", "2-1": "The time interval from the date of initial pathologic diagnosis to a person's date of death, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3165475.", "3-0": "Days to last follow up", "3-1": "The time interval from the date of the last follow up to the date to the current date, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.", "4-0": "Morphology", "5-0": "Primary diagnosis", "6-0": "Site of resection or biopsy", "7-0": "Tumor stage", "8-0": "Vital status", "9-0": "Histological diagnosis", "10-0": "Histological diagnosis other", "11-0": "Year of diagnosis", "12-0": "Clinical T (TNM)", "13-0": "Clinical M (TNM)", "14-0": "Clinical N (TNM)", "15-0": "Clinical stage", "16-0": "Pathologic T (TNM)", "17-0": "Pathologic N (TNM)", "18-0": "Pathologic M (TNM)", "19-0": "Performance status scale: Timing", "20-0": "Performance status scale: Karnofsky score", "21-0": "Performance status scale: ECOG", "22-0": "Tumor status", "23-0": "Primary therapy outcome success", "4-1": "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.", "5-1": "Text term for the structural pattern of cancer cells used to define a microscopic diagnosis. See CDE (Common Data Element) Public ID: 3081934.", "6-1": "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.", "7-1": "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.", "8-1": "The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.", "9-1": "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.", "10-1": "Additional options for histologics diagnosis (see Histologic diagnosis), which have not been pre-determined in the listed values for histologic diagnosis.", "11-1": "The numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. See CDE (Common Data Element) Public ID: 2896960.", "12-1": "The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C253840.", "13-1": "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.", "14-1": "The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The N category describes whether or not the cancer has reached nearby lymph nodes NCI Thesaurus Code: C48881 and C25384.", "15-1": "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.", "16-1": "The TNM Staging System is based on the extent of the tumor (T), the extent of spread to the lymph nodes (N), and the presence of metastasis (M). The T category describes the original (primary) tumor. NCI Thesaurus Code: C48881 and C48739.", "17-1": "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.", "18-1": "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.", "19-1": "A time reference for the Karnofsky score and/or the ECOG score using the defined categories.", "20-1": "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.", "21-1": "A performance status scale designed to assess disease progression and its effect on the daily living abilities of the patient. NCI Thesaurus Code: C105721.", "23-1": "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.", "22-1": "The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643." }, "cols": 2, "rows": 9 } [/block] ##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": "Tumor code", "4-0": "Tumor Code ID", "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 diagnostic tumor code of the tissue sample source.", "4-1": "A BCR-defined ID code for the tumor sample.", "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": 5 } [/block] ## Aliquot The **aliquot** entity represents 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": 1 } [/block] ## 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": "Experiment name", "3-0": "Instrument model", "4-0": "Is paired end", "5-0": "Library name", "6-0": "Library strategy", "7-0": "Platform", "8-0": "Read length", "9-0": "Sequencing center", "10-0": "Sequencing date", "11-0": "Target capture kit catalog number", "12-0": "Target capture kit name", "13-0": "Target capture kit target region", "14-0": "Target capture kit vendor", "15-0": "Target capture kit 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 name of the read group.", "2-1": "A submitter-defined name for the experiment.", "3-1": "A specific model of sequencing instrument used.", "4-1": "A Boolean value which denotes whether sequence reads are paired end or not.", "5-1": "The name of the sequencing library preparation.", "6-1": "The sequencing technique intended for the library.", "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 length of the reads.", "9-1": "The name of the center that provided the sequence files.", "10-1": "The date of sequencing.", "11-1": "The catalog number of target capture kit.", "12-1": "The name of the target capture kit.", "13-1": "The target region for target capture kit.", "14-1": "The vendor of target capture kit.", "15-1": "The version of a target capture kit." }, "cols": 2, "rows": 16 } [/block] ## File The **file** entity refers to the files in CPTAC-3 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] ## 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 link", "2-0": "Workflow type", "3-0": "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": "A link to Github hash for the CWL workflow used (GDC related).", "2-1": "The generic name for the workflow used to analyze data.", "3-1": "The version of the workflow used to analyze data." }, "cols": 2, "rows": 4 } [/block] ## 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] ## 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] ##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 determines the 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]