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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/

data portal name: name as it should appear in data portal

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

card location: primary (i.e., top) or secondary (i.e., bottom) key/annotation

facet: true if column_name should be faceted in data portal.

data portal namesynapse file view columnfacetpriorityconceptexampleGDC equivalentfaceted on GDCfacet on CSBCGDC referencesizerestricted valuescommentsin AMP-AD portalin NF portal
Descriptiondescriptionno1










Study Namenameno1










synapse IDidno1link to Synapse placesyn123








Grant TypegrantTypeyes3
U54 or U01








GrantcenterNameyes1
Stanford Center for Systems Biology








Programconsortiumyes3
CSBC or PSON








SpeciesspeciesN/AN/A

none
yes





ThemeThemeyes2
tumor-heterogeneitynone
yes





Data CategoryassayN/AN/ABroad categorization of the contents of the data file.
  • Transcriptome Profiling
data_categoryyesyes


CSBC will need to add values to those in GDC (which only cover sequencing)

AssayexperimentalStrategyyes2The sequencing strategy used to generate the data file.  REMOVE "sequencing" for CSBC.
  • RNA-Seq
  • Total RNA-Seq
assayyesyes


CSBC will need to add values to those in GDC (which only cover sequencing)

PlatformplatformN/AN/A

platformyesyes





Disease TypetumorTypeyes2The 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_typeyesyeshttps://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case




SiteNAN/AN/AThe 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_siteyesyeshttps://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case




TissueNAN/AN/AThe 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_originyesyeshttps://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis




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