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Studies

Studies

Apr 07, 2019

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 

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 name

synapse file view column

facet

priority

concept

example

GDC equivalent

faceted on GDC

facet on CSBC

GDC reference

size

restricted values

comments

in AMP-AD portal

in NF portal

data portal name

synapse file view column

facet

priority

concept

example

GDC equivalent

faceted on GDC

facet on CSBC

GDC reference

size

restricted values

comments

in AMP-AD portal

in NF portal

Description

description

no

1

 

 

 

 

 

 

 

 

 

 

 

Study Name

name

no

1

 

 

 

 

 

 

 

 

 

 

 

synapse ID

id

no

1

link to Synapse place

syn123

 

 

 

 

 

 

 

 

 

Grant Type

grantType

yes

3

 

U54 or U01

 

 

 

 

 

 

 

 

 

Grant

centerName

yes

1

 

Stanford Center for Systems Biology

 

 

 

 

 

 

 

 

 

Program

consortium

yes

3

 

CSBC or PSON

 

 

 

 

 

 

 

 

 

Species

NA

N/A

N/A

 

 

none

 

yes

 

 

 

 

 

 

Theme

Theme

yes

2

 

tumor-heterogeneity

none

 

yes

 

 

 

 

 

 

Data Category

NA

N/A

N/A

Broad categorization of the contents of the data file.

  • Transcriptome Profiling

data_category

yes

yes

 

 

 

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

 

 

Assay

experimentalStrategy

yes

2

The sequencing strategy used to generate the data file.  REMOVE "sequencing" for CSBC.

  • RNA-Seq

  • Total RNA-Seq

assay

yes

yes

 

 

 

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

 

 

Platform

NA

N/A

N/A

 

 

platform

yes

yes

 

 

 

 

 

 

Disease Type

tumorType

yes

2

The 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_type

yes

yes

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

 

 

 

 

 

Site

NA

N/A

N/A

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

yes

yes

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

 

 

 

 

 

Tissue

NA

N/A

N/A

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

yes

yes

https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis