File view driving this tableDEPRECATED: 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):
column portal name: name as it should appear in data portal
current synapse file view column: corresponding name (e.g., for SQL query) in Synapse table view
eventual synapse file view column: name (e.g., for SQL query) in Synapse table view that we will eventually migrate to
difference between current and eventual columns: as we migrate to GDC, we will put new annotation keys in "eventual" column names. for now, use "current."
facet: true if column_name should be faceted in data portal.
card location: primary (i.e., top) or secondary (i.e., bottom) key/annotation
desired for CSBC/PS-ON: should this column be included in the CSBC data portal
...
The following have been added to the synapse table, but are blank. They need to be filled in:
| column name | current synapse file view column | eventualportal name | synapse file view column | facet | card location | 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 | yesname | NAno | U54 or U01 | Grant | yes | NA | Program | yes | NA | CSBC or PSON | The name (or part of a name) of a file (of any type). | file_name | no | no | ||||||||
| Title | Title | no | ||||||||||||||||||||
| Species | species | species | yessecondary | none | yes | |||||||||||||||||
| Scientific Theme | NATheme | theme | yessecondary(or possibly pill directly beneath file name) | tumor-heterogeneity | none | yes | ||||||||||||||||
| Data Category | assayNA | data_category | yes | secondary | 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 | data_type | no? | NA | 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 | data_format | no? | NA | yes | Format of the data files. |
| data_format | yes | yes | ||||||||||||
| Experiment StrategyAssay | assayexperimentalStrategy | experimental_strategy | yessecondary | 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 | no | primary | The name (or part of a name) of a file (of any type). | file_name | no | no | file_size | no | NA_size | NA | no | The size of the data file (object) in bytes. | file_size | no | no | |||||||
| md5sum | NA | no | NA | 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 | yesNANA | no | platform | yes | yes | |||||||||||||||||
| Disease Tumor Type | tumorType | yes | secondary | 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 | yesNA | secondaryno | 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 | NA | 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 | nosex | NAyes | 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 | NA | 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 | yessecondary | 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 | yes (can we facet by range–i.e., between age 20 and 30?) | NA | Age at the time of diagnosis expressed in number of days since birth. | ||||||||||
| 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 | ||||||||||||||||
| Primary Diagnosis | NA | no | NA | 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 | NA | 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 | noNA | 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 | noNA | 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 | noNA | 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 |
...