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
facet: true if column_name should be faceted in data portal.
desired for CSBC/PS-ON: should this column be included in the CSBC data portal
Need to add to the above Synapse table: grantType, datasets, studies, tissue_or_organ, diseaseType, experimentalStrategy, featured, abstract
| column name | synapse table name | facet | 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 | 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 | yes | largeText | |||||||||
| Disease Type | diseaseType | yes | 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 | yes | RNA-seq | no | string vector | many | no | related to Experimental Strategy | ||||
| dataType | no | drugScreen, geneExpression, image | no | string vector | many | no | related to Data Category and Data Type | ||||||
| dataSubtype | no | raw, processed, metadata, dataMatrix | no | string vector | many | no | related to Data Type, Workflow Type, and Data Format | ||||||
| diagnosis | no | Neurofibromatosis 1, Breast Cancer | no | string vector | many | yes, as disease focus | |||||||
| isCellLine | no | no | boolean | true/false | no | ||||||||
| Site | tissue_or_organ | yes | yes | yes | many | no | related to Primary Site | ||||||
| platform | no | HiSeq2000 | no | string vector | no | Platform | |||||||
| tissue | no | no | no | ||||||||||
| doi | PubMed | yes | doi without wwww.doi.org/ prefix: eg: 10.1093/neuonc/noy046 | yes | yes | ||||||||
| projectName | no | display name of project | don't know what this is | yes | |||||||||
| studyId | no | synapse id of Study -Synapse project or folder | no | entity vector | yes, as "id" | ||||||||
| datasetId | no | synapse id of datasets | no | entity vector | |||||||||
| fundingAgency | no | no | yes | ||||||||||
| citation | no | the citation of the study in the format Author1 et al. Title. Journal (Year). | no | yes | |||||||||
| Title | Title | no | yes | publication title | yes | string | no | ||||||
| Authors | Authors | no | yes | publication authors | yes | string vector | no | ||||||
| Journal | Journal | no | yes | publication journal | yes | string | no | ||||||
| Year | Publication Year | yes | 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 | yes | yes | string | CSBC, PSON | |||||||
| Grant Type | grantType | yes | yes | yes | U54, U01 | ||||||||
| Datasets | datasets | no | yes | Links to datasets in portal. How should this be represented? | |||||||||
| Studies | studies | no | yes | Links to study in portal. How should this be represented? |
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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