The following is a brief description of the relevant columns in the folder view below (by column header):
https://www.synapse.org/#!Synapse:syn18488466/tables/
NOTE: Studies are selected in this view with is.dataset == TRUE
data 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
priority: 1 (i.e., top), 2 (i.e., bottom) key/annotation, or 3 (i.e., more ...).
facet: true if column_name should be faceted in data portal.
| data portal name | synapse file view column | priority | facet | concept | example | GDC equivalent | faceted on GDC | facet on CSBC | GDC reference | size | restricted values | comments | in AMP-AD portal | in NF portal |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Dataset name | name | 1 | no | |||||||||||
| id | id | name and download button should link to this | no | |||||||||||
| Grant Type | grantType | 3 | yes | U54 or U01 | ||||||||||
| Grant | centerName | 3 | yes | |||||||||||
| Program | consortium | 3 | yes | CSBC or PSON | ||||||||||
| Species | species | 2 | yes | none | yes | |||||||||
| Theme | Theme | 2 | yes | tumor-heterogeneity | none | yes | ||||||||
| Assay | experimentalStrategy | 2 | 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) | |||||
| Platform | platform | 2 | yes | platform | yes | yes | ||||||||
| Disease Type | tumorType | 2 | 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 |
GDC Data Dictionary viewer: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/
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
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