Studies

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

https://www.synapse.org/#!Synapse:syn18483791/tables/

NOTE: Studies are selected in this view with is.study == TRUE

The legacy table upon which the above project view was created is: https://www.synapse.org/#!Synapse:syn10915872/tables/

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

card location: primary (i.e., top) or secondary (i.e., bottom) key/annotation

facet: true if column_name should be faceted in data portal.

data portal name	synapse file view column	facet	priority	concept	example	GDC equivalent	faceted on GDC	facet on CSBC	GDC reference	comments
Description	description	no	1
Study Name	name	no	1
synapse ID	id	no	1	link to Synapse place	syn123
Grant Type	grantType	yes	3		U54 or U01
Grant	centerName	yes	1		Stanford Center for Systems Biology
Program	consortium	yes	3		CSBC or PSON
Species	species	N/A	N/A			none		yes
Theme	Theme	yes	2		tumor-heterogeneity	none		yes
Data Category	assay	N/A	N/A	Broad categorization of the contents of the data file.	Transcriptome Profiling	data_category	yes	yes		CSBC will need to add values to those in GDC (which only cover sequencing)
Assay	experimentalStrategy	yes	2	The sequencing strategy used to generate the data file. REMOVE "sequencing" for CSBC.	RNA-Seq Total RNA-Seq	assay	yes	yes		CSBC will need to add values to those in GDC (which only cover sequencing)
Platform	platform	N/A	N/A			platform	yes	yes
Disease Type	tumorType	yes	2	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
Site	NA	N/A	N/A	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).	Accessory sinuses Adrenal gland Anus and anal canal Base of tongue Bladder	case/primary_site	yes	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case
Tissue	NA	N/A	N/A	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).	Abdomen, NOS Abdominal esophagus Accessory sinus, NOS Acoustic nerve Adrenal gland, NOS	diagnosis/tissue_or_organ_of_origin	yes	yes	https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis