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CPTAC metadata

ABOUT METADATA FOR DATASETS > CPTAC metadata

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Overview

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

The following are entities for CPTAC. Learn more about CPTAC data.

  • investigation
  • case
  • demographic
  • diagnosis
  • sample
  • portion
  • file
  • protocol

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

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.

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

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.

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

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

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.

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.

Vital status

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

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.

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).

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.

File type

The type of file which stores the data.

Data format

The type of format that determines data content.

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.

Protocol

See below for links to the publications that describe the experimental protocols used to generate each subcollection of data.

Updated about a year ago

CPTAC metadata


ABOUT METADATA FOR DATASETS > CPTAC metadata

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