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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 namesynapse table namestandardized schema namerequiredfacetcard locationnotedesired for CSBC/PS-ONconceptexampleGDC equivalentcolumn typesizerestricted valuescommentsin AMP-AD portalin NF portalGDC equivalent
KeywordsKeywords

nosecondary (though I could see these as pills directly beneath the title?)
yesKeywords associated with this publication, some of which may come from a controlled vocabularytumor heterogeneity
string vector
unrestricted

no
AbstractAbstract

noNAok to leave this blank in synapse table for now (robert has concerns about copyright issues,so we may not include in portal)–but if we can include it synapse table efficiently and programmatically, please do so.maybe


largeText





Disease TypediseaseType
yes (as "Diagnosis/Disease" in standard schema)yessecondary
yesThe type of cells that carcinoma arises from.Adenocarcinoma, Anaplastic Astrocytoma 
string vector
many

yesrelated to Disease Type
Experimental StrategyexperimentalStrategy
yes (as "Assay" in standard schema)yessecondary
yes
RNA-seq
string vector
many

norelated to Experimental Strategy
Sitesite

yessecondaryi have trouble differentiating "site" from "tissue/organ." once we adopt GDC, we might better differentiate, for now just copy over the "tissue_or_organ" column to a "site" column in the synapse table. yesThe 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

norelated to Primary Site
Tissuetissue_or_organ

yessecondary
yesThe 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






doidoi doi
noNA
yes

doi without wwww.doi.org/ prefix: eg: 10.1093/neuonc/noy046;

if can't get doi efficiently and programmatically, just use the PubMed field that is already in the table for now








yes
TitleTitleTitle
noprimary
yespublication title

string



no
AuthorsAuthorsAuthor
noprimary
yespublication authors

string vector



no
JournalJournalJournal
noprimary
yespublication journal

string



no
YearPublication YearYearyes?yesprimary
yespublication year

number



no
featured


no

yeswhether the card should be on the homepage (max 3 in table)






yes
GrantCSBC PSON Center
yesno

noLink to a Synapse URL (i.e., a Synapse project or more generally a Synapse Wiki) representing the project/grant.








ProgramConsortium
yes (as "Consortium" in standard schema)yestertiary (possibly don't display on car)
yes


string
CSBC, PSON



Grant TypegrantType

yestertiary (possibly don't display on card)
yes




U54, U01



Datasetsdatasets

nosecondary
yesA comma-delimited list of links to datasets in portal–i.e,. synIds.








Dataset namesdatasetNames

noNA
yesA comma-delimited list of names of datasets in portal (i.e., the string names of the synIds in datasets).








Studiesstudies
yes (as "Study" in standardized schema)nosecondary
yesA comma-delimited list of links to study/studies in portal–i.e., synIds.








Study namesstudyNames

noNA
yesA comma-delimited list of names of studies in portal (i.e., the string names of the synIds in studies).








Grant NumbergrantNumber

notertiary (possibly don't display on card)
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"










Data TypeNA
yes (as "DataType" in standard schema)













Model SystemNA
yes (as "ModelSystem" in standard schema)













Institutioninstituion
yes (as "Institution" in standard schema)


yes









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/

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