| column name | concept | example | required | column type | size | restricted values | comments | in AMP-AD portal | in NF portal | desired for CSBC/PS-ON | GDC equivalent |
|---|---|---|---|---|---|---|---|---|---|---|---|
| keywords | Keywords associated with this publication, some of which may come from a controlled vocabulary | tumor heterogeneity | yes | string vector | unrestricted | no | yes | ||||
| tumorType | The type of cells that carcinoma arises from. | Adenocarcinoma, Anaplastic Astrocytoma | yes | string vector | many | yes | yes | related to Disease Type | |||
| assay | RNA-seq | no | string vector | many | no | yes | related to Experimental Strategy | ||||
| dataType | drugScreen, geneExpression, image | no | string vector | many | no | yes | related to Data Category and Data Type | ||||
| dataSubtype | raw, processed, metadata, dataMatrix | no | string vector | many | no | no | related to Data Type, Workflow Type, and Data Format | ||||
| diagnosis | Neurofibromatosis 1, Breast Cancer | no | string vector | many | yes, as disease focus | no | |||||
| isCellLine | no | boolean | true/false | no | |||||||
| organ | yes | many | no | yes | related to Primary Site | ||||||
| platform | HiSeq2000 | no | string vector | no | no | Platform | |||||
| tissue | no | no | no | ||||||||
| doi | doi without wwww.doi.org/ prefix: eg: 10.1093/neuonc/noy046 | yes | yes | yes | |||||||
| projectName | display name of project | don't know what this is | yes | ?? | |||||||
| studyId | synapse id of Study -Synapse project or folder | no | entity vector | yes, as "id" | yes | ||||||
| datasetId | synapse id of datasets | no | entity vector | yes | |||||||
| fundingAgency | no | yes | no | ||||||||
| citation | the citation of the study in the format Author1 et al. Title. Journal (Year). | no | yes | no | |||||||
| pubTitle | publication title | yes | string | no | yes | ||||||
| pubAuthors | publication authors | yes | string vector | no | yes | ||||||
| pubJournal | publication journal | yes | string | no | yes | ||||||
| pubYear | publication year | yes | number | no | yes | ||||||
| featured | whether the card should be on the homepage (max 3 in table) | yes | yes |
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/
Add Comment