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DEPRECATED: Please see Data File entry for CSBC/PSON below with the rest of the portals.
This describes the 'Explore Data' table.
This is not a card, but an explore table.
Table driving this: https://www.synapse.org/#!Synapse:syn21346411/tables/
Previously used a file view to drive Explore Data: https://www.synapse.org/#!Synapse:syn9630847/tables/
The following is a brief description of the relevant columns in the table below (by column header):
portal name: name as it should appear in data portal
synapse file view column: corresponding name (e.g., for SQL query) in Synapse table view
facet: true if column_name should be faceted in data portal.
desired for CSBC/PS-ON: should this column be included in the CSBC data portal
The following annotations do not exist on file: theme
The following annotations need to be "ported" to GDC: Data Category (currently use existing "assay", but eventually use "data_category");
The following have been added to the synapse table, but are blank. They need to be filled in:
| portal name | synapse file view column | facet | concept | example | GDC equivalent | faceted on GDC | facet on CSBC | GDC reference | size | restricted values | comments | in AMP-AD portal | in NF portal | desired for CSBC/PS-ON | GDC equivalent | species | none | data_category|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| File Name | name | no | The name (or part of a name) of a file (of any type). | file_name | no | no | ||||||||||||||||||||
| Title | Title | no | ||||||||||||||||||||||||
| Species | species | yes | none | yes | ||||||||||||||||||||||
| Theme | Theme | yes | tumor-heterogeneity | none | yes | |||||||||||||||||||||
| Data Category | NA | no | Broad categorization of the contents of the data file. |
| data_category | yes | yes | CSBC will need to add values to those in GDC (which only cover sequencing)data_type | ||||||||||||||||||
| Data Type | NA | no | Specific content type of the data file. |
| data_type | yes | yes | CSBC will need to add values to those in GDC (which only cover sequencing)data_format | ||||||||||||||||||
| Data Format | fileFormat | yes | Format of the data files. |
| data_format | yesexperimental_strategy | yes | |||||||||||||||||||
| Assay | experimentalStrategy | yes | The sequencing strategy used to generate the data file. REMOVE "sequencing" for CSBC. |
| experimental_strategy | yes | yes | CSBC will need to add values to those in GDC (which only cover sequencing) | ||||||||||||||||||
| file_name | The name (or part of a name) of a file (of any type). | file_name | no | file_sizesize | NA | no | The size of the data file (object) in bytes. | file_size | no | no | ||||||||||||||||
| md5sum | NA | no | The 128-bit hash value expressed as a 32 digit hexadecimal number (in lower case) used as a file's digital fingerprint. | md5sum | no | platformnoplatform | ||||||||||||||||||||
| Platform | yesNA | workflow_type | Generic name for the workflow used to analyze a data set. |
| yes | disease_type | no | platform | yes | yes | ||||||||||||||||
| Tumor Type | tumorType | yes | The text term used to describe the type of malignant disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). |
| case/disease_type | yes | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case | ||||||||||||||||||
| Sitesite | NA | no | The text term used to describe the general location of the malignant disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). |
| case/primary_site | yes | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case | ||||||||||||||||||
| Ethnicityethnicity | NA | no | An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. |
| demographic/ethnicity | yes | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=demographic | ||||||||||||||||||
| genderGender | sex | yes | Text designations that identify gender. Gender is described as the assemblage of properties that distinguish people on the basis of their societal roles. [Explanatory Comment 1: Identification of gender is based upon self-report and may come from a form, questionnaire, interview, etc.] |
| demographic/gender | yes | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=demographic | ||||||||||||||||||
| Race | NA | raceno | An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. |
| demographic/race | yes | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=demographic | ||||||||||||||||||
| Tissue | tissue_or_organ_of_origin | yes | The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). |
| diagnosis/tissue_or_organ_of_origin | yes | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | age_at_diagnosis | Age at the time of diagnosis expressed in number of days since birth. | diagnosis/age_at_diagnosis | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | days_to_last_follow_up | Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. | diagnosis/days_to_last_follow_up | no | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | days_to_last_known_disease_status | Time interval from the date of last follow up to the date of initial pathologic diagnosis, represented as a calculated number of days. | ||||||
| diagnosis/days_to_last_known_disease_status | no | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | days_to_recurrence | Number of days between the date used for index and the date the patient's disease recurred. | diagnosis/days_to_recurrence | no | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | last_known_disease_status | Text term that describes the last known state or condition of an individual's neoplasm. |
| diagnosis/last_known_disease_status | no | Grant | centerName | yes | |||||||||||
| Grant Type | grantType | yes | U54 or U01 | |||||||||||||||||||||||
| Consortium | consortium | yes | CSBC or PSON | |||||||||||||||||||||||
| Age | NA | no | diagnosis/age_at_diagnosis | yes | ?? | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | morphology | The third edition of the International Classification of Diseases for Oncology, published in 2000 used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms. The study of the structure of the cells and their arrangement to constitute tissues and, finally, the association among these to form organs. In pathology, the microscopic process of identifying normal and abnormal morphologic characteristics in tissues, by employing various cytochemical and immunocytochemical stains. A system of numbered categories for representation of data. | diagnosis/morphology | no | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | |||||||||||||||
| primary_diagnosis | Primary Diagnosis | NA | no | Text term used to describe the patient's histologic diagnosis, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). |
| diagnosis/primary_diagnosis | no | no | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosisprogression_or_recurrence | |||||||||||||||||
| Progression | NA | no | Yes/No/Unknown indicator to identify whether a patient has had a new tumor event after initial treatment. |
| diagnosis/progression_or_recurrence | nohttps://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | site_of_resection_or_biopsy | The text term used to describe the anatomic site of origin, of the patient's malignant disease, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). |
| diagnosis/site_of_resection_or_biopsy | no | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | tumor_grade | Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness. |
| diagnosis/tumor_grade | no | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | ||||||||
| 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. The accepted values for tumor_stage depend on the tumor site, type, and accepted staging system. These items should accompany the tumor_stage value as associated metadata. | diagnosis/tumor_stage | no | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | vital_status | Vital Status | NA | no | The survival state of the person registered on the protocol. |
| diagnosis/vital_status | yes | ?? | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | sample_type||||||||||||
| Sample Type | NA | no | Text term to describe the source of a biospecimen used for a laboratory test. |
| sample/sample_type | no | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sampletissue_type | ||||||||||||||||||
| Tissue Type | NA | no | Text term that represents a description of the kind of tissue collected with respect to disease status or proximity to tumor tissue. |
| sample/tissue_type | no | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample |
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GDC Data Dictionary is implemented in YAML files: https://github.com/NCI-GDC/gdcdictionary
GDC submission process (and metadata templates) are described here: https://docs.gdc.cancer.gov/Data_Submission_Portal/Users_Guide/Data_Submission_Overview/
GDC Data Upload Walkthrough: https://docs.gdc.cancer.gov/Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough/#clinical-data-requirements