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 name | synapse table name | standardized schema name | required | facet | card location | note | desired for CSBC/PS-ON | concept | example | required | column type | size | restricted values | comments | in AMP-AD portal | in NF portal | GDC equivalent |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Keywords | Keywords | no | secondary (though I could see these as pills directly beneath the title?) | yes | Keywords associated with this publication, some of which may come from a controlled vocabulary | tumor heterogeneity | yes | string vector | unrestricted | no | |||||||
| Abstract | Abstract | no | NA | no | largeText | ||||||||||||
| Disease Type | diseaseType | yes | secondary | yes | The type of cells that carcinoma arises from. | Adenocarcinoma, Anaplastic Astrocytoma | yes | string vector | many | yes | related to Disease Type | ||||||
| Experimental Strategy | experimentalStrategy | yes | secondary | yes | RNA-seq | no | string vector | many | no | related to Experimental Strategy | |||||||
| Site | tissue_or_organ | yes | secondary | yes | yes | many | no | related to Primary Site | |||||||||
| doi | doi (if can't get doi efficiently and programmatically, just use the pubmed field that is already in the table) | doi | no | no | NA | yes | doi without wwww.doi.org/ prefix: eg: 10.1093/neuonc/noy046 | yes | yes | ||||||||
| Title | Title | Title | yes | no | primary | yes | publication title | yes | string | no | |||||||
| Authors | Authors | Author | yes | no | primary | yes | publication authors | yes | string vector | no | |||||||
| Journal | Journal | Journal | yes | no | primary | yes | publication journal | yes | string | no | |||||||
| Year | Publication Year | Year | no | yes | primary | yes | publication year | yes | number | no | |||||||
| featured | no | yes | whether the card should be on the homepage (max 3 in table) | yes | |||||||||||||
| Link to Synapse site | CSBC PSON Center | no | no | Link to a Synapse URL (i.e., a Synapse project or more generally a Synapse Wiki) representing the project/grant. | |||||||||||||
| Program | Consortium | yes | tertiary (possibly don't display on car) | yes | yes | string | CSBC, PSON | ||||||||||
| Grant Type | grantType | yes | tertiary (possibly don't display on card) | yes | yes | U54, U01 | |||||||||||
| Datasets | datasets | no | secondary | yes | A comma-delimited list of links to datasets in portal–i.e,. synIds. | ||||||||||||
| Dataset names | datasetNames | no | NA | yes | A comma-delimited list of names of datasets in portal (i.e., the string names of the synIds in datasets). | ||||||||||||
| Studies | studies | no | secondary | yes | A comma-delimited list of links to study/studies in portal–i.e., synIds. | ||||||||||||
| Study names | studyNames | no | NA | yes | A comma-delimited list of names of studies in portal (i.e., the string names of the synIds in studies). | ||||||||||||
| Grant | grant | no | tertiary (possibly don't display on card) | yes | U54 or U01 center |
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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