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TCGA GRCh38 metadata

ABOUT METADATA FOR DATASETS > TCGA GRCh38 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 GRCh38

Entities for TCGA GRCh38
The following are entities for TCGA GRCh38. They represent clinical data, biospecimen data, and data about TCGA GRCh38 files. Note that these entities differ from the entities of legacy TCGA data. Learn more about TCGA GRCh38 data.

  • investigation
  • case
  • demographic
  • diagnosis
  • treatment
  • exposure
  • drug_therapy
  • radiation_therapy
  • follow_up
  • new_tumor_event
  • sample
  • portion
  • slide
  • analyte
  • aliquot
  • read_group
  • read_group_qc
  • file
  • analysis

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

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.

Property

Description

dbGaP accession number

The dbGaP accession number provided for each study. See NCI Thesaurus Code: C25402.

Investigation name

The full name of the project or study that generated the data. See NCI Thesaurus Code: C41198.

Submitter ID

A human-readable identifier, such as a number or a string that may contain metadata information for investigations.

Case

The case entity represents TCGA cases. Members of the case entity are subjects who have taken part in an investigation or program and can be identified by a Universally Unique Identifier (UUID). See the table below for the clinical properties and descriptions of the case entity.

Property

Description

Batch number

A set of related analytes prepared for further analysis and numbered sequentially from the same disease. Once a Case has been assigned to a batch number, subsequent shipments from that case are assigned the same batch number as the original. Seven Bridges only field.

Submitter ID

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.

Disease type

The type of the disease or condition studied. See NCI Thesaurus Code: C2991.

Primary site

The anatomical site where the primary tumor is located in the organism. See NCI Thesaurus Code: C43761.

Tissue source site ID

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.

Tissue source site name

The full name of a clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.

Tissue source site code

The alphanumeric code for clinical site that collects and provides patient samples and clinical metadata for research use. See NCI Thesaurus Code: C103264.

Tissue source site BCR ID

The BCR (Biospecimen Core Resource) provided ID for a tissue source site. See NCI Thesaurus Code: C103264.

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.

Property

Description

Submitter ID

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.

Ethnicity

A socially-defined category of people based on common ancestral, cultural, biological, and social factors. See NCI Thesaurus Code: C29933.

Race

A classification of humans characterized by certain heritable traits, common history, nationality, or geographic distribution. See NCI Thesaurus Code: C17049.

Gender

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.

Year of birth

A numeric value to represent the calendar year in which an individual was born. See CDE (Common Data Element) Public ID: 2896954.

Year of death

A numeric value to represent the year of the death of an individual. See CDE (Common Data Element) Public ID: 2897030.

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.

Property

Description

Submitter ID

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.

Age at diagnosis

The age in years of the Case at the initial pathological diagnosis of the disease or cancer. See NCI Thesaurus Code: C15220.

Classification of tumor

Text that describes the kind of disease present in the tumor specimen as related to a specific point in time. See CDE (Common Data Element) Public ID: 3288124.

Days to birth

The time interval from a person's date of birth to the date of initial pathologic diagnosis, represented as a calculated negative number of days. See CDE (Common Data Element) Public ID: 3008233.

Days to death

The time interval from a person's date of death to the date of initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3165475.

Days to last follow up

The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.

Days to last known disease status

The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.

Days to recurrence

The time interval from the date of new tumor event, including progression, recurrence and new primary malignancies, to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3392464.

Last known disease status

The state or condition of an individual's neoplasm at a particular point in time. See CDE (Common Data Element) Public ID: 3392464.

Morphology

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.

Primary diagnosis

Text term for the structural pattern of cancer cells used to define a microscopic diagnosis. See CDE (Common Data Element) Public ID: 3081934.

Prior malignancy

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.

Progression or recurrence

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.

New tumor event after initial treatment

A Boolean value denoting whether a neoplasm developed after the initial treatment was finished.

Site of resection or biopsy

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.

Tissue or organ of origin

The text term that describes the anatomic site of the tumor or disease. See CDE (Common Data Element) Public ID: 3226281.

Tumor grade

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.

Tumor stage

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.

Vital status

The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.

Histological diagnosis

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.

Histological diagnosis other

Additional options for histologics diagnosis (see Histologic diagnosis), which have not been pre-determined in the listed values for histologic diagnosis.

Year of diagnosis

The numeric value to represent the year of an individual's initial pathologic diagnosis of cancer. See CDE (Common Data Element) Public ID: 2896960.

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.

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.

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 stage

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.

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 scale: Timing

A time reference for the Karnofsky score and/or the ECOG score using the defined categories.

Performance status scale: Karnofsky score

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.

Performance status scale: ECOG

A performance status scale designed to assess disease progression and its effect on the daily living abilities of the patient. NCI Thesaurus Code: C105721.

Tumor status

The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.

Primary therapy outcome success

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.

Treatment

The treatment entity represents records of the administration of therapeutic agents to a patient to alter the course of a pathologic process. Members of the treatment entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the treatment entity below.

Property

Description

Submitter ID

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.

Days to treatment

The number of days from the date of the initial pathologic diagnosis that treatment began.

Therapeutic agents

The text identification of the individual agent(s) used as part of a prior treatment regimen. See CDE (Common Data Element) Public ID: 2975232.

Treatment intent type

The text term to identify the reason for the administration of a treatment regimen. [Manually-curated]. See CDE (Common Data Element) Public ID: 2793511.

Treatment or therapy

A yes/no/unknown/not applicable indicator related to the administration of therapeutic agents received before the body specimen was collected. See CDE (Common Data Element) Public ID: 4231463.

Country of specimen procurement

Country where specimen/sample has been procured.

Longest dimension

The longest dimension of sample/specimen (in centimeters).

Intermediate dimension

The intermediate dimension of sample/specimen (in centimeters).

Shortest dimension

The shortest dimension of sample/specimen (in centimeters).

Initial weight

Initial sample/specimen weight (in grams).

Current weight

Current sample/specimen weight (in grams).

Freezing method

The freezing method for sample/specimen.

OCT embedded

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.

Time between clamping and freezing

Time elapsed (in minutes) between clamping (supplying vessel) and freezing a sample.

Time between excision and freezing

Warm ischemia time, elapsed between clamping and freezing a sample, as denoted in minutes.

Days to collection

Days 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 procurement

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.

Is FFPE

A boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).

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.

Property

Description

Submitter ID

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.

Alcohol history

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.

Alcohol intensity

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.

BMI

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.

Cigarettes per day

The average number of cigarettes smoked per day. See CDE (Common Data Element) Public ID: 2001716.

Height

The height of the patient in centimeters. See CDE (Common Data Element) Public ID: 649.

Weight

The weight of the patient measured in kilograms. See CDE (Common Data Element) Public ID: 651.

Years smoked

The numeric value (or unknown) to represent the number of years a person has been smoking. See CDE (Common Data Element) Public ID: 3137957.

Drug therapy

The drug therapy entity represents the use of pharmaceutical products that contains one or more active and/or inactive ingredients to treat, prevent or alleviate the symptoms of disease. A Case can have more them one drug treatment. Members of the drug therapy entity can be identified by a Universally Unique Identifier (UUID).

Property

Description

Submitter ID

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.

Drug name

The most recognizable term associated with a pharmaceutical product used to prevent, diagnose, treat or relieve symptoms of a disease or abnormal condition. NCI Thesaurus Code: C97104.

Pharmaceutical therapy type

The type of treatment of the disease through the use of drugs. NCI Thesaurus Code: C15986.

Percent tumor cells

The percent of tumor cells based on the tissue image.

Percent tumor nuclei

The percent of tumor nuclei based on the tissue image.

Percent normal cells

The percent of normal cell based on the tissue image.

Percent necrosis

The percent of normal cell based on the tissue image.

Percent stromal cells

The ratio of stromal cells present on the tissue slide.

Percent inflam infiltration

The ratio of inflammatory cells to the gross cell population seen on a slide.

Percent lymphocyte infiltration

The fraction of lymphocyte cells to the gross inflammatory cells seen on a slide.

Percent monocyte infiltration

The fraction of monocyte cells to the gross inflammatory cells seen on a slide.

Percent granulocyte infiltration

The fraction of the granulocyte component to the gross inflammatory cells seen on a slide.

Percent neutrophile infiltration

The fraction of neutrophile cells to the gross granulocyte component of inflammatory cells seen on a slide.

Percent eosinophil infiltration

The fraction of eosinophil cells to the gross granulocyte component of inflammatory cells seen on a slide.

Radiation therapy

The radiation therapy entity represents the treatment of a disease with radiation therapy, in which the whole or a portion of the patient's body is exposed to radiation. A Case can have more than one radiation treatment. Members of the radiation therapy entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the radiation therapy entity below.

Property

Description

Submitter ID

This refers to the radiation therapy id, a human-readable identifier, such as a number or a string that may contain metadata information, for the radiation treatment of a disease by means of exposure of the target or the whole body to radiation. NCI Thesaurus Code: C15986.

Radiation type

The value denotes the type of high-energy radiation used to kill cancer cells and shrink tumors. NCI Thesaurus Code: C15986.

Radiation therapy site

The location to which radiation therapy was administered.

Amount

Amount of a product (in μg) prepared for an analysis.

Concentration

Concentration of a product (in μg/μL) prepared for an analysis.

a260_a280 ratio

A numerical value denoting purity assessment using the A260/A280 Ratios.

Well number

The number of wells on the plate in which an analyte has been stored for shipment and for the analysis.

Spectrophotometer method

A method of quantifying the content of nucleic acids in any sample.

Follow up

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

Property

Description

Submitter ID

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.

Days to death

The time interval from a person's date of death to the date of initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3165475.

Days to last follow up

The time interval from the date of the last follow up to the date of the initial pathologic diagnosis, represented as a calculated number of days. See CDE (Common Data Element) Public ID: 3008273.

New tumor event after initial treatment

A Boolean value which denotes whether a neoplasm developed after the initial treatment has finished.

Tumor status

The condition or state of the tumor at a particular time. See NCI Thesaurus Code: C96643.

Vital status

The state of being living or deceased for Cases that are part of the investigation. See NCI Thesaurus Code: C25717.

Performance status scale: ECOG

A performance status scale designed to assess disease progression and its effect on the daily living abilities of the patient. NCI Thesaurus Code: C105721.

Performance status scale: Karnofsky score

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.

Performance status scale: Timing

A time reference for the Karnofsky score and/or the ECOG score using the defined categories.

Other new tumor anatomic site

Alternative anatomic site of a newly developed neoplasm which has not been listed under 'New tumor anatomic site'.

Primary therapy outcome success

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.

New tumor anatomic site

Anatomic site of newly developed neoplasm.

New tumor event type

Type of newly developed neoplasm after initial treatment has finished.

New tumor event

The new tumor event entity represents a newly developed neoplasm after initial treatment has finished. Members of the new tumor event entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the new tumor event entity below.

Property

Description

New tumor anatomic site

Anatomic site of newly developed neoplasm.

Other new tumor anatomic site

Alternative anatomic site of a newly developed neoplasm which has not been listed under 'New tumor anatomic site'.

New tumor event type

Type of newly developed neoplasm after initial treatment has finished.

Experimental strategy

The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.

Platform

The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.

Data type

The classification of data used in (or produced by) the analysis, based on its form and content. See NCI Thesaurus Code: C42645.

Data subtype

A further, more specific classification of the data type, based on the information that it contains.

Data submitting center

This field takes a string denoting the name of the center that has submitted data.

Reference genome

The reference assembly (such as HG19 or GRCh37) to which the nucleotide sequence of a case can be aligned.

Access level

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.

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.

Property

Description

Submitter ID

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.

Sample type

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.

Sample type ID

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.

Composition

The cellular composition of the sample.

Current weight

Current sample/specimen weight (in grams).

Days to collection

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.

Country of sample procurement

Country where the specimen/sample has been procured.

Days to sample procurement

The time interval from the date of sample collection to the date of sample procurement, expressed in days.

Freezing method

Method used to freeze the sample/specimen.

Initial weight

Initial sample/specimen weight (in grams).

Intermediate dimension

The intermediate dimension of sample/specimen (in millimeters).

Is FFFP

A Boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).

Longest dimension

The longest dimension of the sample/specimen, in millimeters.

OCT embedded

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.

Pathology report UUID

UUID of the related pathology report.

Preservation method

The primary preservation method used to store the sample.

Shortest dimension

The shortest dimension of the sample/specimen, in millimeters.

Time between clamping and freezing

The time elapsed (in minutes) between clamping (supplying vessel) and freezing a sample.

Time between excision and freezing

Warm ischemia time, elapsed between clamping and freezing a sample, as denoted in minutes.

Tissue type

A description of the tissue type with respect its tumor/normal source.

Tumor code

The diagnostic tumor code of the tissue sample source.

Tumor code ID

A BCR-defined ID code for the tumor sample.

Tumor descriptor

A description of the tumor from which the sample was derived

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.

Property

Description

Submitter ID

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.

Is FFFP

A Boolean value that denotes whether tissue samples used in the analysis were formalin-fixed paraffin-embedded (FFPE).

Portion weight

Weight of a portion prepared for the analysis (in mg).

Portion number

The numerical value that represents the order of a portion in the series.

Center ID

A professional organization or group which has or is able to submit data. It can be identified by a UUID.

Center type

The type classification of the center (e.g. CGCC).

Center code

The code that determins center that has submitted data.

Center name

The name of the center (e.g. Broad Institute of MIT and Harvard).

Center namespace

The domain name of the center (e.g. borad.mit.edu).

Center short name

A shortened name of the center (e.g. BI).

Slide

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

Property

Description

Submitter ID

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.

Section location

The section of a tissue that has been imaged. The value denotes top, middle, or bottom.

Number proliferating cells

The number of proliferating cells identified in the slide sample.

Percent eosinophil infiltration

The fraction of eosinophil cells to the gross granulocyte component of inflammatory cells seen on a slide.

Percent granulocyte infiltration

The fraction of the granulocyte component to the gross inflammatory cells seen on a slide.

Percent inflam infiltration

The ratio of inflammatory cells to the gross cell population seen on a slide.

Percent lymphocyte infiltration

The fraction of lymphocyte cells to the gross inflammatory cells seen on a slide.

Percent monocyte infiltration

The fraction of monocyte cells to the gross inflammatory cells seen on a slide.

Percent necrosis

The percent of identified tumor cell necrosis based on the tissue image.

Percent neutrophil infiltration

The fraction of neutrophile cells to the gross granulocyte component of inflammatory cells seen on a slide.

Percent normal cells

The percent of identified normal cell based on the tissue image.

Percent stromal cells

The ratio of identified stromal cells present on the tissue slide.

Percent tumor cells

The percent of identified tumor cells based on the tissue image.

Percent tumor nuclei

The percent of identified tumor nuclei based on the tissue image.

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.

Property

Description

Submitter ID

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.

Amount

The amount of a product (in g or volume in mL) prepared for an analysis.

A260_A280 ratio

A purity measurement that weighs the absorbance at 260nm (DNA concentration) against the absorbance at 280nm (protein concentration/contamination).

Analyte type

This defines the type of an analyte on molecular bases.

Analyte type ID

An ID that determines the type of an analyte on molecular bases. A single letter BCR code for the analyte type.

Concentration

The concentration of a product (in molarity) prepared for an analysis.

Spectrophotometer method

A method of quantifying the content of nucleic acids in any sample, used to measure sample purity (e.g. UV spec.)

Well number

The number of wells on the plate in which an analyte has been stored for shipment and for the analysis.

Aliquot

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

Property

Description

Submitter ID

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.

Amount

The amount of a product (in g or volume in mL) prepared for an analysis.

Concentration

The concentration of a product (in molarity) prepared for an analysis.

Source center

The name of the center that provided the item.

Center ID

A professional organization or group which has or is able to submit data. It can be identified by a UUID.

Center type

The type classification of the center (e.g. CGCC).

Center code

The code that determines center that has submitted data.

Center name

The name of the center (e.g. Broad Institute of MIT and Harvard).

Center namespace

The domain name of the center (e.g. borad.mit.edu).

Center short name

The shortened name of the center (e.g. BI).

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.

Property

Description

Submitter ID

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.

Read group name

The name of the read group.

Adapter name

The name of the sequencing adapter.

Adapter sequence

The base sequence of the sequencing adapter.

Base caller name

The name of the base caller.

Base caller version

The version of the base caller.

Experiment name

A submitter-defined name for the experiment.

Flow cell barcode

The barcode assigned to flow cell.

Includes spike ins

A Boolean value which denotes whether a spike-in is included or not.

Instrument model

A specific model of sequencing instrument used.

Is paired end

A Boolean value which denotes whether sequence reads are paired end or not.

Library name

The name of the sequencing library preparation.

Library preparation kit catalog number

The catalog number of the sequencing library preparation kit.

Library preparation kit name

The name of the sequencing library preparation kit.

Library preparation kit vendor

The vendor of the sequencing library preparation kit.

Library preparation kit version

The version of the sequencing library preparation kit.

Library selection

The method used to select and/or enrich the material being sequenced.

Library strand

This determines whether the 'first strand' or 'second strand' of cDNA was used to prepare the library.

Library strategy

The sequencing technique intended for the library.

Platform

The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.

Read length

The length of the reads.

RIN

The RNA integrity number.

Sequencing center

The name of the center that provided the sequence files.

Sequencing date

The date of sequencing.

Size selection range

The range of size selection.

Spike ins concentration

The concentration of a spike-in.

Spike ins fasta

The name of the FASTA file that contains the spike-in sequences.

Target capture kit catalog number

The catalog number of target capture kit.

Target capture kit name

The name of the target capture kit.

Target capture kit target region

The target region for target capture kit.

Target capture kit vendor

The vendor of target capture kit.

Target capture kit version

The version of a target capture kit.

To trim adapter sequence

A Boolean value for adapter trimming.

Read group QC

The read group QC represents read group quality control. Members of the read group QC entity can be identified with a Universally Unique Identifier (UUID). Find the properties of the read group QC entity below.

Property

Descripton

Submitter ID

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.

Adapter content

An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Basic statistics

An analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Encoding

The version of ASCII encoding of quality values found in the file.

FASTQ name

The names of FASTQs.

Kmer content

The number of times the kmer occurs in the sequence. Analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Overrepresented sequences

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Per base N content

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Per base sequence content

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Per base sequence quality

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Per sequence GC content

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Per sequence quality score

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Per tile sequence quality

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Percent GC content

The overall %GC of all bases in all sequences.

Sequence duplication levels

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Sequence length distribution

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Total sequences

The analysis module for quality control checks. Please refer to quality control tool for high throughput sequence data at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/.

Workflow start datetime

The start of the analysis workflow in datetime format.

Workflow end datetime

The end of the analysis workflow in datatime format.

Workflow link

The link to Github hash for the CWL workflow used (GDC related).

Workflow type

A generic name for the workflow used to analyze data.

Workflow version

The version of the workflow used to analyze data.

File

The file entity refers to the files in TCGA produced by aliquot analyses. Members of the file entity can be identified by a Universally Unique Identifier (UUID). Find the properties of the file entity below.

Property

Description

Submitter ID

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.

Data category

The classification of data used in (or produced by) the analysis, based on its form and content. See NCI Thesaurus Code: C42645.

Data type

A further, more specific classification of the data category, based on the information that it contains.

Data format

The type of format that determines data content.

Experimental strategy

The method or protocol used to perform the laboratory analysis. See NCI Thesaurus Code: C43622.

File size

The size of a file measured in bytes (B), kilobytes (KB), megabytes (MB), gigabytes (GB), terabytes (TB), and larger values.

Access level

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.

Platform

The version (for instance, manufacturer or model) of the technology that was used for sequencing or assaying. See NCI Thesaurus Code: C45378.

Genome build

The reference genome or assembly (such as HG19/GRCh37 or GRCh38) to which the nucleotide sequence of a case/subject/sample can be aligned.

Genome name

The reference genome or assembly that also contains decoy viral sequence to which the nucleotide sequence of a case/subject/sample can be aligned.

GDC file UUID

The unique identifier for a file, such as a UUID.

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.

Property

Description

Submitter ID

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.

Workflow start datetime

The start of the analysis workflow in date/time format.

Workflow end datetime

The end of the analysis workflow in date/time format.

Workflow link

A link to Github hash for the CWL workflow used (GDC related).

Workflow type

The generic name for the workflow used to analyze data.

Workflow version

The version of the workflow used to analyze data.

Updated about a year ago

TCGA GRCh38 metadata


ABOUT METADATA FOR DATASETS > TCGA GRCh38 metadata

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