Versions Compared

Old Version 2

changes.mady.by.user Brian White

Saved on

compared with

New Version Current

changes.mady.by.user James Eddy

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Source data 

Synapse Table: https://www.synapse.org/#!Synapse:syn21868591/tables/

DEPRECATED Synapse File View: https://www.synapse.org/#!Synapse:syn18488466/tables/   

NOTE: Studies are selected in this view with is.dataset == TRUE 

DEPRECATED Synapse Table: https://www.synapse.org/#!Synapse:syn21517423/tables/

...

Explore page config

Type / name of card: "Datasets"

Number of Secondary Fields to show: 4

Note that there is no explicit aliasing between Column Name and Display Name. Rather, camelCase Column Names are automatically rendered as Camel Case. The table below just makes that clear.

Facets should be ordered in the order they appear in this table.

Any column that should be faceted in the portal (i.e., faceted on an explore page or have a column facet on a table) must be faceted on the corresponding Synapse table/view. There is a performance penalty incurred with each additional facet – hence, facet only those columns needed by the portal and limit to those likely to be useful.

Display Name

Column Name

Column Type

Link Format

Facet Y/N

Facet Order

Card UI Mapping

Destination

Link Query Key

Link Value Column

Searchable Y/N

Search

hint textIcon

Order

Search Hint Text







icon

default

icon = microscopenameNCard_TitleidYCenter NamecenterNameNCard_SubTitleYidNNDescriptiondescriptionNSecondary_Label_1YThemeThemeYSecondary_Label_2YDiseasetumorTypeYSecondary_Label_3YAssayexperimentalStrategyYSecondary_Label_4YProgramconsortiumYSecondary_Label_5YGrant TypegrantTypeYSecondary_Label_6Ydata portal namesynapse file view columnpriorityfacetconceptexampleGDC equivalentfaceted on GDCfacet on CSBCGDC referencesizerestricted valuescommentsin AMP-AD portalin NF portalDataset namename1noididname and download button should link to thisnofeaturedfeaturedshould the card be displayed?noGrant TypegrantTypeNAnoU54 or U01GrantcenterNameNAnoProgramconsortiumNAnoCSBC or PSONSpeciesspecies2yesnoneyesThemeTheme2yestumor-heterogeneitynoneyesAssayexperimentalStrategy2yesThe sequencing strategy used to generate the data file.  REMOVE "sequencing" for CSBC.
  • RNA-Seq
  • Total RNA-Seq
experimental_strategyyesyesCSBC will need to add values to those in GDC (which only cover sequencing)Platformplatform2yesplatformyesyesDisease TypetumorType2yesThe 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

= disk






Dataset Name

datasetName

STRING


N

NA

title

Datasets/DetailsPage

datasetId

datasetId

Y

1

e.g. migration


datasetId

ENTITY


N

NA





N

NA



datasetAlias

STRING


N

NA





N

NA


Description

description

LARGE_TEXT


N

NA

description




Y

2

e.g. spatiotemporal

Publication

publication

STRING

markdown: 
[publicationTitle](pubMedUrl)

N

NA

secondaryLabels[0]

PubMed record



Y

4

e.g. immune escape

Overall Design

overallDesign

STRING


N

NA

secondaryLabels[1]




Y

3


Theme

theme

STRING_LIST*


Y

1





N

NA

e.g. tumor-immune

Tumor Type

tumorType

STRING_LIST*


Y

3

secondaryLabels[2]




Y

7

e.g. Skin Cutaneous Melanoma

Assay

assay

STRING_LIST*


Y

2

secondaryLabels[3]




Y

6

e.g. RNA-seq

Species

species

STRING_LIST*


Y

4

secondaryLabels[4]




N

NA

e.g. Human

External Link

externalLink

STRING


N

NA

secondaryLabels[5]

URL embedded in HTML



N

NA

e.g. GSE93776

Grant Name

grantName

STRING_LIST*

portal query (each)

Y

5

secondaryLabels[6]

Grants/DetailsPage

grantName

grantName

Y

5

e.g. immunology

Consortium

consortium

STRING_LIST*


Y

6

secondaryLabels[7]




N

NA

e.g. PS-ON

*<TYPE>_LIST columns for multi-value annotations not yet implemented

...

Details page config 

Detail pages should display the above information (i.e., from the card) in the header/banner of the page. The query to get that information should be on this table using datasets:

SELECT * FROM syn18488466 where "datasets" = 'syn7248581'

Additionally, we should display files associated with this dataset by querying the files table using datasets, i.e.,.

files:

SELECT * FROM syn9630847 where "datasets" = 'syn7248581'