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TCGA metadata

Overview

Metadata is data that describes other data. On this page, we've detailed TCGA metadata that are available for viewing and filtering TCGA data in the Data Browser and the Datasets API. TCGA metadata on the Platform consists of properties which describe the entities of the TCGA dataset.

Entities are particular resources with UUIDs, such as files, cases, samples, and cell lines.

Properties can either describe an entity or relate that entity to another entity. For instance, properties include an entity's vital status, gender, data format, or experimental strategy.

Entities for TCGA

The following are entities for TCGA. They represent clinical data, biospecimen data, and data about TCGA files. Learn more about TCGA data.

  • cases
  • analytes
  • radiation_therapies
  • drug_therapies
  • follow_ups
  • portions
  • aliquots
  • samples
  • slides
  • files
  • new_tumor_events

Below, each of these entities is followed by a table of their related properties.

Case

The Case entity represents TCGA cases. Members of the Case entity can be identified by a Universally Unique Identifier (UUID). 35 properties of the TCGA Case have been included in the CGC for filtering Cases. These properties describe clinical information about a case, such as its demographic, prognosis diagnosis. See the table below for the clinical properties and descriptions of the Case entity.

PropertyDescription
IDA human-readable identifier, such as a number or a string that may contain metadata information. This identifier is often referred as submitter ID.
ProgramThe research program under which the data was generated. See NCI Thesaurus Code: C82662.
InvestigationA value denoting the project or study that generated the data. See NCI Thesaurus Code: C41198.
Batch numberA set of related analytes prepared for further analysis, numbered sequentially, from the same disease. Once a Case has been assigned to a batch, subsequent shipments from that case are assigned the same batch number as the original.
GenderThe 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.
RaceA classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution. See NCI Thesaurus Code: C17049.
EthnicityA socially defined category of people based on common ancestral, cultural, biological, and social factors. See NCI Thesaurus Code: C29933.
Disease typeThe type of the disease or condition studied. See NCI Thesaurus Code: C2991.
Primary siteThe anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761.
Histologic diagnosisDiagnosis of a disease based on the type of tissue, where type is determined based on the microscopic examination of tissue. See NCI Thesaurus Code: C61478.
Other histologic diagnosisAdditional options for histologics diagnosis (see Histologic diagnosis), which have not been pre-determined in the listed values for histologic diagnosis.
Age at diagnosisThe age in years of the case at the initial pathological diagnosis of disease or cancer. See NCI Thesaurus Code: C15220.
ICD-10This value denotes the classification of the disease according to the tenth version of the International Classification of Diseases (ICD), published by the World Health Organization in 1992. See NCI Thesaurus Code: C71892.
ICD-O-3 SiteThe 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.
ICD-O-3 HistologyThe 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).
Clinical stageEstimate of the extent of the cancer based on results of physical exams, imaging tests (x-rays, CT scans, etc.), and tumor biopsies.
Pathologic stagePathologic staging combines the results of both the clinical staging (physical exam, imaging test), see Clinical stage, with surgical results. NCI Thesaurus Code: C28257.
Clinical T (TNM)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 C253840.1321.
Clinical N (TNM)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.
Clinical M (TNM)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.
Pathologic T (TNM)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.
Pathologic N (TNM)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.
Pathologic M (TNM)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.
Performance Status Score: Karnofsky ScoreAn 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.
Performance Status Score: ECOGA performance status scale designed to assess disease progression and its affect on the daily living abilities of the patient. NCI Thesaurus Code: C105721.
Performance Status Score: TimingA time reference for the Karnofsky score and/or the ECOG score using the defined categories.
Days to deathThe number of days from the date of the initial pathological diagnosis to the date of death for the case in the investigation.
Prior diagnosisInforms whether a case has a known history of an earlier diagnosis of disease/cancer.
New tumor event after initial treatmentA boolean value which denotes whether a neoplasm developed after the initial treatment has finished.
New tumor event typeType of newly developed neoplasm after initial treatment has finished.
New tumor anatomic siteAnatomic site of newly developed neoplasm.
Other new tumor anatomic siteAlternative anatomic site of a newly developed neoplasm which has not been listed under "New tumor anatomic site".
Tumor statusThe condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.
Vital statusThe state of being living or deceased for cases that are part of the investigation. See NCI Thesaurus Code: C25717.
Primary therapy outcome successA value denoting the result of therapy for a given disease or condition in a patient or group of patients. See NCI Thesaurus Code: C18919.

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Drug therapy, Radiation therapy, and Follow up are dependents on the Case entity. This means, to query Drug therapy, Radiation therapy, or Follow up, you have to build your query starting from Case.

Drug therapy

Drug therapy is the pharmaceutical product that contains one or more active and/or inactive ingredients. It is intended to treat, prevent or alleviate the symptoms of disease. A case can have more than one drug treatment that can be identified by a UUID.
ntity below.

PropertyDescription
IDA human-readable identifier, such as a number or a string that may contain metadata information. This identifier is often referred as submitter ID.
Drug nameThe most recognizable term associated with a pharmaceutical product used to prevent, diagnose, treat or relieve symptoms of a disease or abnormal condition. NCI Thesaurus Code: C97104.
Pharmaceutical therapy typeThe type of treatment of the disease through the use of drugs. NCI Thesaurus Code: C15986.

Radiation therapy

The radiation therapy entity represents the treatment of a disease with radiation therapy, in which the whole or a portion of the patient's body is exposed to radiation. Members of the radiation therapy entity can be defined by a UUID. Note that a case can have more than one radiation treatment. Find the properties of the radiation therapy entity below.

PropertyDescription
IDA human-readable identifier, such as a number or a string that may contain metadata information. This identifier is often referred as submitter ID.
Radiation typeThe value denotes the type of high-energy radiation used to kill cancer cells and shrink tumors. NCI Thesaurus Code: C15986.
Radiation therapy siteThe location to which radiation therapy was administered.

Follow up

The follow up entity refers to follow ups which monitor a person's health over time after treatment. Members of the follow up entity can be identified by a UUID. A case can have multiple follow ups generated at different time. Find the properties of the follow up entity below.

PropertyDescription
IDA human-readable identifier, such as a number or a string that may contain metadata information. This identifier is often referred as submitter ID.
Days to last follow upTime interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days.
New tumor event after initial treatmentA boolean value which denotes whether a neoplasm developed after the initial treatment has finished.
New tumor event typeType of newly developed neoplasm after initial treatment has finished.
New tumor anatomic siteAnatomic site of newly developed neoplasm.
Other new tumor anatomic siteAlternative anatomic site of a newly developed neoplasm which has not been listed under "New tumor anatomic site".
Tumor statusThe condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.
Vital statusThe state of being living or deceased for cases that are part of the investigation. See NCI Thesaurus Code: C25717.

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 UUID. Find the properties of the sample entity below.

PropertyDescription
IDA human-readable identifier, such as a number or a string that may contain metadata information. This identifier is often referred as submitter ID.
Sample typeThe 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.
Sample type codeCode 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.
Tissue source siteA clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.
Tissue source site codeAlphanumeric code for a clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.
Country of specimen procurementCountry where specimen/sample has been procured.
Longest dimensionThe longest dimension of sample/specimen (in centimeters).
Intermediate dimensionThe intermediate dimension of sample/specimen (in centimeters).
Shortest dimensionThe shortest dimension of sample/specimen (in centimeters).
Initial weightInitial sample/specimen weight (in grams).
Current weightCurrent sample/specimen weight (in grams).
Freezing methodThe freezing method for sample/specimen.
OCT embeddedA boolean value indicating whether the Optimal Cutting Temperature compound (OCT) is used to embed tissue samples prior to frozen sectioning on a microtome-cryostat.
Time between clamping and freezingTime elapsed (in minutes) between clamping (supplying vessel) and freezing a sample.
Time between excision and freezingWarm ischemia time, elapsed between clamping and freezing a sample, as denoted in minutes.
Days to collectionDays to sample collection. Sample can be collected can be prospectively or retrospectively. This can be a negative value for samples taken retrospectively.
Days to sample procurementNumber 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.
Is FFPEA boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).

Portion

The portion entity represents the sequential 100-120 mg sections derived from samples. Members of the portion entity can be identified by a UUID. Find the properties of the portion entity below.

PropertyDescription
IDA human-readable identifier, such as a number or a string that may contain metadata information. This identifier is often referred as submitter ID.
Portion numberThe numerical value that represents the order of a portion in the series.
WeightWeight of a portion prepared for the analysis (in mg).
Is FFPEA boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).

Slide

The slide entity refers to slides, thin slices of a snap-frozen OCT embedded block of tissue sent for imaging. This same tissue also provides DNA and RNA for further analyses after they are reviewed by histopathologists. Members of the slide entity can be identified by a UUID. Find the properties of the slide entity below.

PropertyDescription
IDA human-readable identifier, such as a number or a string that may contain metadata information. This identifier is often referred as submitter ID.
Section locationThe section of a tissue that has been imaged. The value denotes top, middle, or bottom.
Number proliferating cellsThe number of proliferating cells based on the tissue image.
Percent tumor cellsThe percent of tumor cells based on the tissue image.
Percent tumor nucleiThe percent of tumor nuclei based on the tissue image.
Percent normal cellsThe percent of normal cell based on the tissue image.
Percent necrosisThe percent of normal cell based on the tissue image.
Percent stromal cellsThe ratio of stromal cells present on the tissue slide.
Percent inflam infiltrationThe ratio of inflammatory cells to the gross cell population seen on a slide.
Percent lymphocyte infiltrationThe fraction of lymphocyte cells to the gross inflammatory cells seen on a slide.
Percent monocyte infiltrationThe fraction of monocyte cells to the gross inflammatory cells seen on a slide.
Percent granulocyte infiltrationThe fraction of the granulocyte component to the gross inflammatory cells seen on a slide.
Percent neutrophile infiltrationThe fraction of neutrophile cells to the gross granulocyte component of inflammatory cells seen on a slide.
Percent eosinophil infiltrationThe fraction of eosinophil cells to the gross granulocyte component of inflammatory cells seen on a slide.

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 UUID. Find the properties of the analyte entity below.

PropertyDescription
IDA human-readable identifier, such as a number or a string that may contain metadata information. This identifier is often referred as submitter ID.
Analyte typeDefines the type of an analyte on molecular bases.
Analyte type codeDetermines the analyte type with a code.
AmountAmount of a product (in μg) prepared for an analysis.
ConcentrationConcentration of a product (in μg/μL) prepared for an analysis.
a260_a280 ratioA numerical value denoting purity assessment using the A260/A280 Ratios.
Well numberThe number of wells on the plate in which an analyte has been stored for shipment and for the analysis.
Spectrophotometer methodA method of quantifying the content of nucleic acids in any sample.

Aliquot

The aliquot entity refers to aliquots, products or units extracted from a sample or specimen 's portion and prepared for analysis. Members of the aliquot entity can be identified by a UUID. Find the properties of the aliquot entity below.

PropertyDescription
IDA human-readable identifier, such as a number or a string that may contain metadata information. This identifier is often referred as submitter ID.
AmountAmount of a product (in μg) prepared for an analysis.
ConcentrationConcentration of a product (in μg/μL) prepared for an analysis.

Files

The file entity refers to the files in TCGA produced by aliquot analyses. Files with Controlled Data are stored in the CGHub in xml, and files with Open Data are stored in the DCC in mage-tab. Members of the file entity can be identified by a UUID. Find the properties of the file entity below.

PropertyDescription
GDC File UUIDThe unique identifier for a file, such as a Universally Unique Identifier (UUID).
File sizeSize of a file measured in bytes (B), kilobytes (KB), megabytes (MB), gigabytes (GB), terabytes (TB), and larger values.
Data formatThe type of format that determines data content.
Experimental strategyThe method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.
PlatformThe version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.
Data typeThe classification of data used in (or produced by) the analysis, based on its form and content. See NCI Thesaurus Code: C42645.
Data subtypeA further, more specific classification of the data type, based on the information that it contains.
Data submitting centerThis field takes a string denoting the name of the center that has submitted data.
Reference genomeThe reference assembly (such as HG19 or GRCh37) to which the nucleotide sequence of a case can be aligned.
Access levelA 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.

Updated 11 months ago

TCGA metadata


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