{"_id":"5a45230e51d5d600120ed73c","project":"55faf11ba62ba1170021a9a7","version":{"_id":"55faf11ba62ba1170021a9aa","project":"55faf11ba62ba1170021a9a7","__v":40,"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","5a2a81f688574d001e9934f5","5b080c8d7833b20003ddbb6f"],"is_deprecated":false,"is_hidden":false,"is_beta":true,"is_stable":true,"codename":"","version_clean":"1.0.0","version":"1.0"},"category":{"_id":"58458b4fba4f1c0f009692bb","project":"55faf11ba62ba1170021a9a7","version":"55faf11ba62ba1170021a9aa","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-12-05T15:44:15.650Z","from_sync":false,"order":6,"slug":"datasets-hub","title":"DATASETS HUB"},"user":"5613e4f8fdd08f2b00437620","githubsync":"","__v":0,"parentDoc":null,"updates":[],"next":{"pages":[],"description":""},"createdAt":"2017-12-28T16:59:58.538Z","link_external":false,"link_url":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":19,"body":"##Overview\n\nMetadata is data that describes other data. On this page, we've detailed ICGC metadata that are available for viewing and filtering ICGC data in the Data Browser on the CGC. ICGC metadata on the CGC consists of **properties** which describe the **entities** of the ICGC dataset and their values.\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\nThe ICGC PCAWG Study dataset includes data from 48 different research projects conducted at participating centers around the world, and differences exist in the ontologies used across centers. Note that all metadata values assigned by ICGC research projects are provided via the CGC without modification. When identifying patient cohorts for further study, researchers are encouraged to investigate the full set of available metadata values to ensure that queries return all relevant Cases, Samples, or similar.\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Entities for ICGC\n\nThe following are entities for ICGC. They represent clinical data, biospecimen data, and data about ICGC files. Learn more about ICGC Data.\n\n  * donor\n  * exposure\n  * family\n  * file\n  * project \n  * sample\n  * specimen\n  * surgery\n  * therapy\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##Donor\n\nThe ICGC **donor** entity represents the subject who has taken part in the investigation/program. Members of the **donor** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **donor** entity below. Note that once you copy an ICGC file into a project on the CGC, metadata information pertaining to the **donor** entity will display under the **case** label on the file's page.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Age at diagnosis\",\n    \"0-1\": \"Age at primary diagnosis in years.\",\n    \"1-0\": \"Age at diagnosis group\",\n    \"1-1\": \"Age at primary diagnosis group, range given in years.\",\n    \"2-0\": \"Age at enrollment\",\n    \"3-0\": \"Age at last follow up\",\n    \"3-1\": \"Age (in years) at last followup.\",\n    \"2-1\": \"Age (in years) at which first specimen was collected.\",\n    \"4-0\": \"Available data types\",\n    \"4-1\": \"Possible available data types. A further, more specific classification of the data category, based on the information that it contains.\",\n    \"5-0\": \"Analysis type\",\n    \"6-0\": \"Cancer type prior malignancy\",\n    \"7-0\": \"Diagnosis\",\n    \"8-0\": \"Disease status at last followup\",\n    \"9-0\": \"ICD-10 diagnostic code\",\n    \"10-0\": \"Gender\",\n    \"11-0\": \"History of first degree relative\",\n    \"12-0\": \"Interval of last follow up\",\n    \"13-0\": \"Primary Site\",\n    \"14-0\": \"Prior Malignancy\",\n    \"15-0\": \"Relapse interval\",\n    \"16-0\": \"Relapse type\",\n    \"17-0\": \"Submitted donor ID\",\n    \"18-0\": \"Survival time\",\n    \"19-0\": \"Tumour stage at diagnosis\",\n    \"20-0\": \"Tumour stage supplemental\",\n    \"21-0\": \"Tumour staging system\",\n    \"22-0\": \"Vital status\",\n    \"23-0\": \"State\",\n    \"24-0\": \"Study\",\n    \"6-1\": \"ICD-10 diagnostic code for type of cancer in a prior malignancy.\",\n    \"5-1\": \"The type of analysis applied to the donor's sample.\",\n    \"7-1\": \"The diagnosis for the donor.\",\n    \"8-1\": \"Donor's last known disease status.\",\n    \"9-1\": \"ICD-10 diagnostic code for donor.\",\n    \"10-1\": \"Donor's biological sex. 'Other' has been removed from the controlled vocabulary due to identifiability concerns.\",\n    \"11-1\": \"Indicates if the patient has a first degree relative with cancer\",\n    \"12-1\": \"Interval from the primary diagnosis date to the last followup date, in days. ICGC requests that patients be followed up every 6 months while alive.\",\n    \"13-1\": \"The anatomical site where the primary tumour is located in the organism.\",\n    \"14-1\": \"Prior malignancy affecting patient.\",\n    \"15-1\": \"If the donor was clinically disease free following primary therapy, and then relapse or progression (for liquid tumours) occurred afterwards, then donor_relapse_interval is the length of disease free interval, in days.\",\n    \"16-1\": \"Type of relapse or progression (for liquid tumours), if applicable.\",\n    \"17-1\": \"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    \"18-1\": \"How long has the donor survived since primary diagnosis, in days.\",\n    \"19-1\": \"This is the pathological tumour stage classification made after the tumour has been surgically removed, and is based on the pathological results of the tumour and other tissues removed during surgery or biopsy. This information is not expected to be the same as donor's tumour stage at diagnosis since the pathological tumour staging information is the combination of the clinical staging information and additional information obtained during surgery. For this field, please indicate pathological tumour stage value using indicated staging system.\",\n    \"20-1\": \"Optional additional staging. For donor, it should be at the time of diagnosis.\",\n    \"21-1\": \"Name of tumour staging system used.\",\n    \"22-1\": \"Donor's last known vital status.\",\n    \"23-1\": \"Indicates the state of the donor.\",\n    \"24-1\": \"The study the donor is involved in.\"\n  },\n  \"cols\": 2,\n  \"rows\": 25\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Exposure\n\nThe **exposure** entity represents details about a donor's antecedent environmental exposures, such as smoking history. See the table below for the clinical properties and descriptions of the **exposure** entity.\n[block:parameters]\n{\n  \"data\": {\n    \"0-0\": \"Alcohol history\",\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-1\": \"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    \"1-0\": \"Alcohol history intensity\",\n    \"1-1\": \"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    \"2-0\": \"Exposure intensity\",\n    \"2-1\": \"Extent of the exposure. Use this field to specify intensity of exposure submitted in 'Exposure type' field.\",\n    \"3-0\": \"Exposure type\",\n    \"4-0\": \"Tobacco smoking history indicator\",\n    \"5-0\": \"Tobacco smoking intensity\",\n    \"3-1\": \"Type of exposure. This field can be used if donor was exposed to something other than tobacco or alcohol.\",\n    \"4-1\": \"Donor's smoking history.\",\n    \"5-1\": \"Smoking intensity in Pack Years: Number of pack years defined as the number of cigarettes smoked per day times (x) the number of years smoked divided (/) by 20.\"\n  },\n  \"cols\": 2,\n  \"rows\": 6\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Family\n\nThe **family** entity represents details of the family history of the donor. Find the properties of the **family** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Relationship age\",\n    \"0-1\": \"Age of the donor's relative at primary diagnosis (in years).\",\n    \"1-0\": \"Relationship disease\",\n    \"1-1\": \"Name of the donor'zs relative's disease.\",\n    \"2-0\": \"Relationship disease ICD-10\",\n    \"2-1\": \"ICD-10 code of disease affecting family member specified in the 'relationship type' field.\",\n    \"3-0\": \"Relationship sex\",\n    \"4-0\": \"Relationship type\",\n    \"5-0\": \"Relative with cancer history\",\n    \"3-1\": \"Biological sex of the donor's relative\",\n    \"4-1\": \"Relationship to the donor.\",\n    \"5-1\": \"Indicates whether the donor has a relative with a history of cancer.\"\n  },\n  \"cols\": 2,\n  \"rows\": 6\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##File\n\nThe **file** entity represents the data files generated as part of this study. 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\": \"Analysis type\",\n    \"0-1\": \"The type of analysis applied to the sample from the donor.\",\n    \"1-0\": \"Analysis software\",\n    \"1-1\": \"Analysis software used.\",\n    \"2-0\": \"Data type\",\n    \"2-1\": \"A further, more specific classification of the data category, based on the information that it contains.\",\n    \"3-0\": \"Data format\",\n    \"3-1\": \"The type of format that determines data content.\",\n    \"4-0\": \"Experimental strategy\",\n    \"4-1\": \"The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.\",\n    \"5-0\": \"Genome build\",\n    \"5-1\": \"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    \"6-0\": \"File size\",\n    \"6-1\": \"The size of a file measured in bytes (B), kilobytes (KB), megabytes (MB), gigabytes (GB), terabytes (TB), and larger values.\",\n    \"7-0\": \"Study\",\n    \"7-1\": \"The study the donor is involved in.\",\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\": 8\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Project\n\nThe **project** entity represents the project that generated the data. Members of the **project** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **project** entity below. Note that once you copy an ICGC file into a project on the CGC, metadata information pertaining to the **project** entity will display under the investigation label on the file's page.\n[block:parameters]\n{\n  \"data\": {\n    \"0-0\": \"Partner country\",\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-1\": \"Partner country of the cancer project.\",\n    \"1-0\": \"Primary country\",\n    \"1-1\": \"Lead country of the cancer project.\",\n    \"2-0\": \"Primary site\",\n    \"2-1\": \"The anatomical site where the primary tumour is located in the organism.\",\n    \"3-0\": \"Project name\",\n    \"3-1\": \"Name of the project which generated the data.\",\n    \"4-0\": \"Pubmed ID\",\n    \"4-1\": \"ID of the publication at www.ncbi.nlm.nih.gov/pubmed/.\",\n    \"5-0\": \"State\",\n    \"5-1\": \"Indicates the state of the project.\",\n    \"6-0\": \"Tumour type\",\n    \"6-1\": \"The type of the cancer studied.\",\n    \"7-0\": \"Tumour subtype\",\n    \"7-1\": \"Additional information about tumour type.\",\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\": 8\n}\n[/block]\n\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n##Sample\n\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\": \"Sample 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. Note that once you copy an ICGC file into a project on the CGC, metadata information pertaining to the **Sample ID** property will display under the **Aliquot Sample ID** and **Portion Sample ID** labels on the file's page.\",\n    \"1-0\": \"Analyzed sample interval\",\n    \"1-1\": \"Interval from specimen acquisition to sample use in an analytic procedure (e.g. DNA extraction), in days.\",\n    \"2-0\": \"Study\",\n    \"2-1\": \"Study donor is involved in.\",\n    \"3-0\": \"Level of cellularity\",\n    \"3-1\": \"The proportion of tumour nuclei to total number of nuclei in a given specimen/sample. If exact percentage cellularity cannot be determined, submitter has option to use this field to specify a level that defines a range of percentage.\",\n    \"4-0\": \"Percentage of cellularity\",\n    \"5-0\": \"Height\",\n    \"6-0\": \"Weight\",\n    \"7-0\": \"Years smoked\",\n    \"4-1\": \"The ratio of tumour nuclei to total number of nuclei in a given specimen/sample.\",\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\": 5\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Specimen\nThe **specimen** entity represents information about a specimen that was obtained from a donor. There may be several specimens per donor that were obtained concurrently or at different times. Find the properties of the **specimen** entity below.\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"Digital image of stained section\",\n    \"0-1\": \"Linkout(s) to digital image of a stained section, demonstrating a representative section of tumour.\",\n    \"1-0\": \"Level of cellularity\",\n    \"1-1\": \"The proportion of tumour nuclei to total number of nuclei in a given specimen/sample. If exact percentage cellularity cannot be determined, submitter has option to use this field to specify a level that defines a range of percentage.\",\n    \"2-0\": \"Percentage of cellularity\",\n    \"2-1\": \"The ratio of tumour nuclei to total number of nuclei in a given specimen/sample.\",\n    \"3-0\": \"Submitted specimen ID\",\n    \"3-1\": \"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. Note that once you copy an ICGC file into a project on the CGC, metadata information pertaining to the **Submitted specimen ID** property will display under the **Sample Submitter ID** label on the file's page.\",\n    \"4-0\": \"Specimen available\",\n    \"4-1\": \"Whether additional tissue is available for followup studies.\",\n    \"5-0\": \"Specimen biobank\",\n    \"5-1\": \"If the specimen was obtained from a biobank, provide the biobank name here.\",\n    \"6-0\": \"Specimen biobank ID\",\n    \"6-1\": \"If the specimen was obtained from a biobank, provide the biobank accession number here.\",\n    \"7-0\": \"Specimen processing\",\n    \"7-1\": \"Description of technique used to process specimen.\",\n    \"8-0\": \"Specmen processing other\",\n    \"8-1\": \"If other technique specified for specimen processing, may indicate technique here.\",\n    \"9-0\": \"Specimen storage\",\n    \"9-1\": \"Description of how specimen was stored.\",\n    \"10-0\": \"Specimen type\",\n    \"10-1\": \"Controlled vocabulary description of specimen type.\",\n    \"11-0\": \"Therapy type\",\n    \"11-1\": \"Type of treatment the donor received prior to specimen acquisition.\",\n    \"12-0\": \"Treatment type other\",\n    \"12-1\": \"Freetext description of the treatment type.\",\n    \"13-0\": \"Tumour confirmed\",\n    \"13-1\": \"Whether tumour was confirmed in the specimen as malignant by histological examination.\",\n    \"14-0\": \"Tumour grade\",\n    \"15-0\": \"Tumour grading system\",\n    \"16-0\": \"Tumour histological type\",\n    \"17-0\": \"Tumour stage\",\n    \"18-0\": \"Tumour stage supplemental\",\n    \"19-0\": \"Tumour staging system\",\n    \"14-1\": \"Tumour grade using indicated grading system.\",\n    \"15-1\": \"Name of the tumour grading system.\",\n    \"17-1\": \"This is the pathological tumour stage classification made after the tumour has been surgically removed, and is based on the pathological results of the tumour and other tissues removed during surgery or biopsy. This information is not expected to be the same as donor's tumour stage at diagnosis since the pathological tumour staging information is the combination of the clinical staging information and additional information obtained during surgery. For this field, please indicate pathological tumour stage value using indicated staging system.\",\n    \"16-1\": \"WHO International Histological Classification of Tumours code.\",\n    \"18-1\": \"Optional additional staging. For donor, it should be at the time of diagnosis.\",\n    \"19-1\": \"Name of tumour staging system used.\"\n  },\n  \"cols\": 2,\n  \"rows\": 20\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>\n\n###Surgery\n\nThe **surgery** entity represents details about surgical procedures undergone by the donor. Find the properties of the **surgery** entity below.\n\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"1-0\": \"Procedure site\",\n    \"0-0\": \"Procedure interval\",\n    \"0-1\": \"Interval between primary diagnosis and procedure, in days.\",\n    \"1-1\": \"Anatomical site of the procedure. This must use a standard controlled vocabulary which should be reported in advance to the DCC.\",\n    \"2-0\": \"Procedure type\",\n    \"2-1\": \"Controlled vocabulary description of the procedure type. Vocabulary can be extended by disease-specific projects. Prefix extensions with 3-digit center code, e.g. 008.1 Beijing Cancer Hospital, fine needle aspiration of primary.\",\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###Therapy\n\nThe **therapy** entity represents details about the type and duration of the therapy the donor received. Find the properties of the **therapy** entity below.\n\n[block:parameters]\n{\n  \"data\": {\n    \"h-0\": \"Property\",\n    \"h-1\": \"Description\",\n    \"0-0\": \"First therapy duration\",\n    \"0-1\": \"Duration of first postresection therapy, in days.\",\n    \"1-0\": \"First therapy response\",\n    \"1-1\": \"The clinical effect of the first postresection therapy.\",\n    \"2-0\": \"First therapy start interval\",\n    \"2-1\": \"Interval between primary diagnosis and initiation of the first postresection therapy, in days.\",\n    \"3-0\": \"First therapy therapeutic intent\",\n    \"4-0\": \"First therapy type\",\n    \"5-0\": \"Other therapy\",\n    \"3-1\": \"The therapeutic intent of the first postresection therapy.\",\n    \"4-1\": \"Type of first postresection therapy (ie. therapy given to the patient after the sample was removed from the patient).\",\n    \"5-1\": \"Other postresection therapy.\",\n    \"6-0\": \"Other therapy response\",\n    \"7-0\": \"Second therapy duration\",\n    \"8-0\": \"Second therapy response\",\n    \"9-0\": \"Second therapy start interval\",\n    \"10-0\": \"Second therapy therapeutic intent\",\n    \"11-0\": \"Second therapy type\",\n    \"6-1\": \"The clinical effect of the other postresection therapy.\",\n    \"7-1\": \"Duration of second postresection therapy, in days.\",\n    \"8-1\": \"The clinical effect of the second postresection therapy.\",\n    \"9-1\": \"Interval between primary diagnosis and initiation of the second postresection therapy, in days.\",\n    \"10-1\": \"The therapeutic intent of the second postresection therapy.\",\n    \"11-1\": \"Type of second postresection therapy (ie. therapy given to the patient after the sample was removed from the patient).\"\n  },\n  \"cols\": 2,\n  \"rows\": 12\n}\n[/block]\n<div align=\"right\"><a href=\"#top\">top</a></div>","excerpt":"","slug":"icgc-metadata","type":"basic","title":"ICGC metadata"}
##Overview Metadata is data that describes other data. On this page, we've detailed ICGC metadata that are available for viewing and filtering ICGC data in the Data Browser on the CGC. ICGC metadata on the CGC consists of **properties** which describe the **entities** of the ICGC dataset and their values. **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. The ICGC PCAWG Study dataset includes data from 48 different research projects conducted at participating centers around the world, and differences exist in the ontologies used across centers. Note that all metadata values assigned by ICGC research projects are provided via the CGC without modification. When identifying patient cohorts for further study, researchers are encouraged to investigate the full set of available metadata values to ensure that queries return all relevant Cases, Samples, or similar. <div align="right"><a href="#top">top</a></div> ##Entities for ICGC The following are entities for ICGC. They represent clinical data, biospecimen data, and data about ICGC files. Learn more about ICGC Data. * donor * exposure * family * file * project  * sample * specimen * surgery * therapy Below, each of these entities is followed by a table of their related properties. <div align="right"><a href="#top">top</a></div> ##Donor The ICGC **donor** entity represents the subject who has taken part in the investigation/program. Members of the **donor** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **donor** entity below. Note that once you copy an ICGC file into a project on the CGC, metadata information pertaining to the **donor** entity will display under the **case** label on the file's page. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Age at diagnosis", "0-1": "Age at primary diagnosis in years.", "1-0": "Age at diagnosis group", "1-1": "Age at primary diagnosis group, range given in years.", "2-0": "Age at enrollment", "3-0": "Age at last follow up", "3-1": "Age (in years) at last followup.", "2-1": "Age (in years) at which first specimen was collected.", "4-0": "Available data types", "4-1": "Possible available data types. A further, more specific classification of the data category, based on the information that it contains.", "5-0": "Analysis type", "6-0": "Cancer type prior malignancy", "7-0": "Diagnosis", "8-0": "Disease status at last followup", "9-0": "ICD-10 diagnostic code", "10-0": "Gender", "11-0": "History of first degree relative", "12-0": "Interval of last follow up", "13-0": "Primary Site", "14-0": "Prior Malignancy", "15-0": "Relapse interval", "16-0": "Relapse type", "17-0": "Submitted donor ID", "18-0": "Survival time", "19-0": "Tumour stage at diagnosis", "20-0": "Tumour stage supplemental", "21-0": "Tumour staging system", "22-0": "Vital status", "23-0": "State", "24-0": "Study", "6-1": "ICD-10 diagnostic code for type of cancer in a prior malignancy.", "5-1": "The type of analysis applied to the donor's sample.", "7-1": "The diagnosis for the donor.", "8-1": "Donor's last known disease status.", "9-1": "ICD-10 diagnostic code for donor.", "10-1": "Donor's biological sex. 'Other' has been removed from the controlled vocabulary due to identifiability concerns.", "11-1": "Indicates if the patient has a first degree relative with cancer", "12-1": "Interval from the primary diagnosis date to the last followup date, in days. ICGC requests that patients be followed up every 6 months while alive.", "13-1": "The anatomical site where the primary tumour is located in the organism.", "14-1": "Prior malignancy affecting patient.", "15-1": "If the donor was clinically disease free following primary therapy, and then relapse or progression (for liquid tumours) occurred afterwards, then donor_relapse_interval is the length of disease free interval, in days.", "16-1": "Type of relapse or progression (for liquid tumours), if applicable.", "17-1": "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.", "18-1": "How long has the donor survived since primary diagnosis, in days.", "19-1": "This is the pathological tumour stage classification made after the tumour has been surgically removed, and is based on the pathological results of the tumour and other tissues removed during surgery or biopsy. This information is not expected to be the same as donor's tumour stage at diagnosis since the pathological tumour staging information is the combination of the clinical staging information and additional information obtained during surgery. For this field, please indicate pathological tumour stage value using indicated staging system.", "20-1": "Optional additional staging. For donor, it should be at the time of diagnosis.", "21-1": "Name of tumour staging system used.", "22-1": "Donor's last known vital status.", "23-1": "Indicates the state of the donor.", "24-1": "The study the donor is involved in." }, "cols": 2, "rows": 25 } [/block] <div align="right"><a href="#top">top</a></div> ##Exposure The **exposure** entity represents details about a donor's antecedent environmental exposures, such as smoking history. See the table below for the clinical properties and descriptions of the **exposure** entity. [block:parameters] { "data": { "0-0": "Alcohol history", "h-0": "Property", "h-1": "Description", "0-1": "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.", "1-0": "Alcohol history intensity", "1-1": "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.", "2-0": "Exposure intensity", "2-1": "Extent of the exposure. Use this field to specify intensity of exposure submitted in 'Exposure type' field.", "3-0": "Exposure type", "4-0": "Tobacco smoking history indicator", "5-0": "Tobacco smoking intensity", "3-1": "Type of exposure. This field can be used if donor was exposed to something other than tobacco or alcohol.", "4-1": "Donor's smoking history.", "5-1": "Smoking intensity in Pack Years: Number of pack years defined as the number of cigarettes smoked per day times (x) the number of years smoked divided (/) by 20." }, "cols": 2, "rows": 6 } [/block] <div align="right"><a href="#top">top</a></div> ##Family The **family** entity represents details of the family history of the donor. Find the properties of the **family** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Relationship age", "0-1": "Age of the donor's relative at primary diagnosis (in years).", "1-0": "Relationship disease", "1-1": "Name of the donor'zs relative's disease.", "2-0": "Relationship disease ICD-10", "2-1": "ICD-10 code of disease affecting family member specified in the 'relationship type' field.", "3-0": "Relationship sex", "4-0": "Relationship type", "5-0": "Relative with cancer history", "3-1": "Biological sex of the donor's relative", "4-1": "Relationship to the donor.", "5-1": "Indicates whether the donor has a relative with a history of cancer." }, "cols": 2, "rows": 6 } [/block] <div align="right"><a href="#top">top</a></div> ##File The **file** entity represents the data files generated as part of this study. 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": "Analysis type", "0-1": "The type of analysis applied to the sample from the donor.", "1-0": "Analysis software", "1-1": "Analysis software used.", "2-0": "Data type", "2-1": "A further, more specific classification of the data category, based on the information that it contains.", "3-0": "Data format", "3-1": "The type of format that determines data content.", "4-0": "Experimental strategy", "4-1": "The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.", "5-0": "Genome build", "5-1": "The reference genome or assembly (such as HG19/GRCh37 or GRCh38) to which the nucleotide sequence of a case/subject/sample can be aligned.", "6-0": "File size", "6-1": "The size of a file measured in bytes (B), kilobytes (KB), megabytes (MB), gigabytes (GB), terabytes (TB), and larger values.", "7-0": "Study", "7-1": "The study the donor is involved in.", "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": 8 } [/block] <div align="right"><a href="#top">top</a></div> ##Project The **project** entity represents the project that generated the data. Members of the **project** entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the **project** entity below. Note that once you copy an ICGC file into a project on the CGC, metadata information pertaining to the **project** entity will display under the investigation label on the file's page. [block:parameters] { "data": { "0-0": "Partner country", "h-0": "Property", "h-1": "Description", "0-1": "Partner country of the cancer project.", "1-0": "Primary country", "1-1": "Lead country of the cancer project.", "2-0": "Primary site", "2-1": "The anatomical site where the primary tumour is located in the organism.", "3-0": "Project name", "3-1": "Name of the project which generated the data.", "4-0": "Pubmed ID", "4-1": "ID of the publication at www.ncbi.nlm.nih.gov/pubmed/.", "5-0": "State", "5-1": "Indicates the state of the project.", "6-0": "Tumour type", "6-1": "The type of the cancer studied.", "7-0": "Tumour subtype", "7-1": "Additional information about tumour type.", "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": 8 } [/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": "Sample 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. Note that once you copy an ICGC file into a project on the CGC, metadata information pertaining to the **Sample ID** property will display under the **Aliquot Sample ID** and **Portion Sample ID** labels on the file's page.", "1-0": "Analyzed sample interval", "1-1": "Interval from specimen acquisition to sample use in an analytic procedure (e.g. DNA extraction), in days.", "2-0": "Study", "2-1": "Study donor is involved in.", "3-0": "Level of cellularity", "3-1": "The proportion of tumour nuclei to total number of nuclei in a given specimen/sample. If exact percentage cellularity cannot be determined, submitter has option to use this field to specify a level that defines a range of percentage.", "4-0": "Percentage of cellularity", "5-0": "Height", "6-0": "Weight", "7-0": "Years smoked", "4-1": "The ratio of tumour nuclei to total number of nuclei in a given specimen/sample.", "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": 5 } [/block] <div align="right"><a href="#top">top</a></div> ###Specimen The **specimen** entity represents information about a specimen that was obtained from a donor. There may be several specimens per donor that were obtained concurrently or at different times. Find the properties of the **specimen** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "Digital image of stained section", "0-1": "Linkout(s) to digital image of a stained section, demonstrating a representative section of tumour.", "1-0": "Level of cellularity", "1-1": "The proportion of tumour nuclei to total number of nuclei in a given specimen/sample. If exact percentage cellularity cannot be determined, submitter has option to use this field to specify a level that defines a range of percentage.", "2-0": "Percentage of cellularity", "2-1": "The ratio of tumour nuclei to total number of nuclei in a given specimen/sample.", "3-0": "Submitted specimen ID", "3-1": "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. Note that once you copy an ICGC file into a project on the CGC, metadata information pertaining to the **Submitted specimen ID** property will display under the **Sample Submitter ID** label on the file's page.", "4-0": "Specimen available", "4-1": "Whether additional tissue is available for followup studies.", "5-0": "Specimen biobank", "5-1": "If the specimen was obtained from a biobank, provide the biobank name here.", "6-0": "Specimen biobank ID", "6-1": "If the specimen was obtained from a biobank, provide the biobank accession number here.", "7-0": "Specimen processing", "7-1": "Description of technique used to process specimen.", "8-0": "Specmen processing other", "8-1": "If other technique specified for specimen processing, may indicate technique here.", "9-0": "Specimen storage", "9-1": "Description of how specimen was stored.", "10-0": "Specimen type", "10-1": "Controlled vocabulary description of specimen type.", "11-0": "Therapy type", "11-1": "Type of treatment the donor received prior to specimen acquisition.", "12-0": "Treatment type other", "12-1": "Freetext description of the treatment type.", "13-0": "Tumour confirmed", "13-1": "Whether tumour was confirmed in the specimen as malignant by histological examination.", "14-0": "Tumour grade", "15-0": "Tumour grading system", "16-0": "Tumour histological type", "17-0": "Tumour stage", "18-0": "Tumour stage supplemental", "19-0": "Tumour staging system", "14-1": "Tumour grade using indicated grading system.", "15-1": "Name of the tumour grading system.", "17-1": "This is the pathological tumour stage classification made after the tumour has been surgically removed, and is based on the pathological results of the tumour and other tissues removed during surgery or biopsy. This information is not expected to be the same as donor's tumour stage at diagnosis since the pathological tumour staging information is the combination of the clinical staging information and additional information obtained during surgery. For this field, please indicate pathological tumour stage value using indicated staging system.", "16-1": "WHO International Histological Classification of Tumours code.", "18-1": "Optional additional staging. For donor, it should be at the time of diagnosis.", "19-1": "Name of tumour staging system used." }, "cols": 2, "rows": 20 } [/block] <div align="right"><a href="#top">top</a></div> ###Surgery The **surgery** entity represents details about surgical procedures undergone by the donor. Find the properties of the **surgery** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "1-0": "Procedure site", "0-0": "Procedure interval", "0-1": "Interval between primary diagnosis and procedure, in days.", "1-1": "Anatomical site of the procedure. This must use a standard controlled vocabulary which should be reported in advance to the DCC.", "2-0": "Procedure type", "2-1": "Controlled vocabulary description of the procedure type. Vocabulary can be extended by disease-specific projects. Prefix extensions with 3-digit center code, e.g. 008.1 Beijing Cancer Hospital, fine needle aspiration of primary.", "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> ###Therapy The **therapy** entity represents details about the type and duration of the therapy the donor received. Find the properties of the **therapy** entity below. [block:parameters] { "data": { "h-0": "Property", "h-1": "Description", "0-0": "First therapy duration", "0-1": "Duration of first postresection therapy, in days.", "1-0": "First therapy response", "1-1": "The clinical effect of the first postresection therapy.", "2-0": "First therapy start interval", "2-1": "Interval between primary diagnosis and initiation of the first postresection therapy, in days.", "3-0": "First therapy therapeutic intent", "4-0": "First therapy type", "5-0": "Other therapy", "3-1": "The therapeutic intent of the first postresection therapy.", "4-1": "Type of first postresection therapy (ie. therapy given to the patient after the sample was removed from the patient).", "5-1": "Other postresection therapy.", "6-0": "Other therapy response", "7-0": "Second therapy duration", "8-0": "Second therapy response", "9-0": "Second therapy start interval", "10-0": "Second therapy therapeutic intent", "11-0": "Second therapy type", "6-1": "The clinical effect of the other postresection therapy.", "7-1": "Duration of second postresection therapy, in days.", "8-1": "The clinical effect of the second postresection therapy.", "9-1": "Interval between primary diagnosis and initiation of the second postresection therapy, in days.", "10-1": "The therapeutic intent of the second postresection therapy.", "11-1": "Type of second postresection therapy (ie. therapy given to the patient after the sample was removed from the patient)." }, "cols": 2, "rows": 12 } [/block] <div align="right"><a href="#top">top</a></div>