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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 namerequiredfacetprioritynotedesired for CSBC/PS-ONconceptexampleGDC equivalentcolumn typesizerestricted valuescommentsin AMP-AD portalin NF portalGDC equivalent
KeywordsKeywords

no2staticyesKeywords associated with this publication, some of which may come from a controlled vocabularymetastasis, scRNA-seq
string (vector)
unrestricted

no
ThemeTheme

yes2staticyesOne of the NCI-defined themes, e.g., tumor heterogeneity. There are about 4 such themes, so it makes sense to facet.








AbstractAbstract

no1staticnoCopyright issues? TBD

largeText





Disease TypediseaseType
yes (as "Diagnosis/Disease" in standard schema)yes2static, multipleyesThe 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)yes2static, multiple valuesyes
RNA-seq
string vector
many

norelated to Experimental Strategy
Sitesite

yes2staticyesThe 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

yes2staticyesThe 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






PMIDPMIDPMIDyes?noN/AURL for titleyes









yes
TitleTitleTitleyesno1
yespublication title

string



no
AuthorsAuthorsAuthoryesno1
yespublication authors

string vector



no
JournalJournalJournal
no1
yespublication journal

string



no
YearPublication YearYearyes?yes1
yespublication year

number



no
featured


noN/Acheckboxyeswhether the card should be on the homepage (max 3 in table)






yes
GrantCSBC PSON Center
yesno2URL'd entity noLink to a Synapse URL (i.e., a Synapse project or more generally a Synapse Wiki) representing the project/grant.

entity ID








ProgramConsortium
yes (as "Consortium" in standard schema)yes3static yes(future-state may link to program page if present)

string
CSBC, PSON



Grant TypegrantType

yes3staticyes




U54, U01



Datasetsdatasets

no3
yesA comma-delimited list of links to datasets in portal–i.e,. synIds.








Dataset namesdatasetNames

noN/A for now?
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)no3
yesA comma-delimited list of links to study/studies in portal–i.e., synIds.








Study namesstudyNames

noN/A for now? 
yesA comma-delimited list of names of studies in portal (i.e., the string names of the synIds in studies).








Grant NumbergrantNumber

no3
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/

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