Datasets

The following is a brief description of the relevant columns in the folder view below (by column header):

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	comments
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.	RNA-Seq Total RNA-Seq	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).	Acinar Cell Neoplasms Adenomas and Adenocarcinomas Adnexal and Skin Appendage Neoplasms Basal Cell Neoplasms Blood Vessel Tumors	case/disease_type	yes	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case

GDC Data Dictionary is implemented in YAML files: https://github.com/NCI-GDC/gdcdictionary