Publications

Synapse table for this card: https://www.synapse.org/#!Synapse:syn10923842/tables/

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

column name: name in data portal

synapse table name: corresponding name (e.g., for SQL query) in Synapse table view

required: is this a column that the portal WG has deemed required?

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

column name	synapse table name	standardized schema name	required	facet	priority	note	desired for CSBC/PS-ON	concept	example	GDC equivalent	column type	restricted values	in NF portal	GDC equivalent
Keywords	Keywords			no	2	static	yes	Keywords associated with this publication, some of which may come from a controlled vocabulary	metastasis, scRNA-seq		string (vector)	unrestricted	no
Theme	Theme			yes	2	static	yes	One of the NCI-defined themes, e.g., tumor heterogeneity. There are about 4 such themes, so it makes sense to facet.
Abstract	Abstract			no	1	static	no	Copyright issues? TBD			largeText
Disease Type	diseaseType		yes (as "Diagnosis/Disease" in standard schema)	yes	2	static, multiple	yes	The type of cells that carcinoma arises from.	Adenocarcinoma, Anaplastic Astrocytoma		string vector	many	yes	related to Disease Type
Experimental Strategy	experimentalStrategy		yes (as "Assay" in standard schema)	yes	2	static, multiple values	yes		RNA-seq		string vector	many	no	related to Experimental Strategy
Site	site			yes	2	static	yes	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		many	no	related to Primary Site
Tissue	tissue_or_organ			yes	2	static	yes	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
PMID	PMID	PMID	yes?	no	N/A	URL for title	yes						yes
Title	Title	Title	yes	no	1		yes	publication title			string		no
Authors	Authors	Author	yes	no	1		yes	publication authors			string vector		no
Journal	Journal	Journal		no	1		yes	publication journal			string		no
Year	Publication Year	Year	yes?	yes	1		yes	publication year			number		no
featured				no	N/A	checkbox	yes	whether the card should be on the homepage (max 3 in table)					yes
Grant	CSBC PSON Center		yes	no	2	URL'd entity	no	Link to a Synapse URL (i.e., a Synapse project or more generally a Synapse Wiki) representing the project/grant.			entity ID
Program	Consortium		yes (as "Consortium" in standard schema)	yes	3	static	yes	(future-state may link to program page if present)			string	CSBC, PSON
Grant Type	grantType			yes	3	static	yes					U54, U01
Datasets	datasets			no	3		yes	A comma-delimited list of links to datasets in portal–i.e,. synIds.
Dataset names	datasetNames			no	N/A for now?		yes	A comma-delimited list of names of datasets in portal (i.e., the string names of the synIds in datasets).
Studies	studies		yes (as "Study" in standardized schema)	no	3		yes	A comma-delimited list of links to study/studies in portal–i.e., synIds.
Study names	studyNames			no	N/A for now?		yes	A comma-delimited list of names of studies in portal (i.e., the string names of the synIds in studies).
Grant Number	grantNumber			no	3		yes	The grant number without the "U54" or "U01" prefix, e.g., the grant column of this table has "U54 CA217297", we only want "CA217297"

Until Synapse has a solution for multiple values in a single table cell (i.e., vectors), use pipe " | " to separate multiple values. Eg: fundingAgency: CTF | NTAP.

GDC docs: https://docs.gdc.cancer.gov/

GDC data dictionary browser: https://docs.gdc.cancer.gov/Data_Dictionary/gdcmvs/