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.
File view driving this tableTable 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/
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| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 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 | fileFormat | yes | Format of the data files. |
| data_format | yes | 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_size | 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 | no | |||||||
| Platform | NA | no | platform | yes | yes | ||||||||
| Disease 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 | |||||
| Site | 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 | |||||
| Ethnicity | 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 | |||||
| Gender | 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 | no | 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 | 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 | |||||
| Grant | centerName | yes | |||||||||||
| Grant Type | grantType | yes | U54 or U01 | ||||||||||
| ProgramConsortium | 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 | |||||||
| 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=diagnosis | |||||
| 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 | no | no | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis | |||||
| 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 | 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=sample | |||||
| 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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