CSBC/PSON Publications Schema

Synapse Table: https://www.synapse.org/#!Synapse:syn10923842/tables/

Fields to show: 3

Display Name	Column Name	Facet Y/N	UI Mapping	Destination	Searchable Y/N	Search hint text
	Authors	N	Card_SubTitle		Y	e.g. LastName
Program	Consortium	Y	Secondary_Label_X		Y	e.g. PS-ON
DOI	DOI	N	Secondary_Label_X	doi (with prefix https://dx.doi.org/)	Y	e.g. 10.1158/2159-8290.CD-17-0222
Journal	Journal	N	Secondary_Label_X		Y	e.g. Nucleic Acids Res
PubMed Link	PubMed	N	Secondary_Label_6		N	e.g. https://www.ncbi.nlm.nih.gov/pubmed/28652380
	Title	N	Card_Title	doi (with prefix https://dx.doi.org/)	Y	e.g. methylation
Year	year	Y	Secondary_Label_1		Y	e.g. 2018
Grant	long_amp_ad_grants	Y	Secondary_Label_4		Y	e.g. U01AG046161

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	case/disease_type https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case	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			Not Yet	Not Yet	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			Not Yet	Not Yet	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 https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis&anchor=tissue_or_organ_of_origin
Title	Title	Title	yes	no	1		yes	publication title			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
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"