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/

column 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

The following annotations do not exist on file:

The following annotations need to be "ported" to GDC:

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	eventual synapse file view column	facet	priority	concept	example	GDC equivalent	faceted on GDC	facet on CSBC	GDC reference	comments
Description			no	1
Study Name	name		no	1
synapse ID	id		no	1	link to Synapse place	syn123
Grant Type			yes	3		U54 or U01
Grant			no	1		Stanford Center for Systems Biology
Program			yes	3		CSBC or PSON
Species	species	species	N/A	N/A			none		yes
Theme	NA	theme	yes	2		tumor-heterogeneity	none		yes
Data Category	assay	data_category	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	assay	Assay	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			N/A	N/A			platform	yes	yes
Disease Type			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			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			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