Synapse table for this card: https://www.synapse.org/#!Synapse:syn10923842/tables/
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desired for CSBC/PS-ON: should this column be included in the CSBC data portal
The following have been added to the synapse table, but are blank. They need to be filled in: datasets, studies, tissue_or_organ, diseaseType, experimentalStrategy, featured, Abstract
| column name | synapse table name | standardized schema name | required | facet | priority | card locationnote | desired for CSBC/PS-ON | concept | example | requiredGDC equivalent | column type | size | restricted values | comments | in AMP-AD portal | in NF portal | GDC equivalent | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Keywords | Keywords | nosecondary (though I could see these as pills directly beneath the title?) | 2 | static | yes | Keywords associated with this publication, some of which may come from a controlled vocabulary | tumor heterogeneity | yesmetastasis, scRNA-seq | string (vector) | unrestricted | no | |||||||||||||
| Theme | Theme | yes | 2 | static | yes | One of the NCI-defined themes, e.g., tumor heterogeneity. There are about 4 such themes, so it makes sense to facet. | ||||||||||||||||||
| Abstract | Abstract | no | NA1 | static | no | Copyright issues? TBD | largeText | |||||||||||||||||
| Disease Type | diseaseType | yes (as "Diagnosis/Disease" in standard schema) | yes | secondary2 | static, multiple | yes | The type of cells that carcinoma arises from. | Adenocarcinoma, Anaplastic Astrocytoma | yescase/disease_type https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case | string vector | many | yes | related to Disease Type | |||||||||||
| Experimental Strategy | experimentalStrategy | yes secondary(as "Assay" in standard schema) | yes | 2 | static, multiple values | yes | RNA-seq | no | string vector | many | no | related to Experimental Strategy | ||||||||||||
| Site | tissue_or_organ | yes | secondary | yes | yes | site | Not Yet | Not Yet | static | yes | 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). |
| case/primary_site | 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/noy046Tissue | tissue_or_organ | Not Yet | Not Yet | static | yes | 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). |
| diagnosis/tissue_or_organ_of_origin | |||||||||
| DOI | DOI | DOI | yes? | no | N/A | URL for title | yes | yes | ||||||||||||||||
| Title | Title | Title | yes | no | primary1 | yes | publication titleyes | string | no | |||||||||||||||
| Authors | Authors | Author | yes | no | primary1 | yes | publication authors | yes | string vector | no | ||||||||||||||
| Journal | Journal | Journalyes | no | primary1 | yes | publication journalyes | string | no | ||||||||||||||||
| Year | Publication Year | Yearno | yes? | yes | primary1 | yes | publication year | yes | number | no | ||||||||||||||
| featured | no | N/A | checkbox | yes | whether the card should be on the homepage (max 3 in table) | yes | ||||||||||||||||||
| Link to Synapse siteGrant | CSBC PSON Center | yes | no | 2 | URL'd entity | no | Link to a Synapse URL (i.e., a Synapse project or more generally a Synapse Wiki) representing the project/grant. | entity ID | ||||||||||||||||
| Program | Consortium | yes tertiary (possibly don't display on car(as "Consortium" in standard schema) | yes | 3 | static | yes | (future-state may link to program page if present) | string | CSBC, PSON | |||||||||||||||
| Grant Type | grantType | yes | tertiary (possibly don't display on card) | yes3 | static | yes | U54, U01 | |||||||||||||||||
| Datasets | datasets | no | secondary3 | yes | A comma-delimited list of links to datasets in portal–i.e,. synIds. | |||||||||||||||||||
| Dataset names | datasetNames | noNA | N/A for now? | yes | A comma-delimited list of names of datasets in portal (i.e., the string names of the synIds in datasets). | |||||||||||||||||||
| Studies | studies | yes (as "Study" in standardized schema) | no | secondary3 | yes | A comma-delimited list of links to study/studies in portal–i.e., synIds. | ||||||||||||||||||
| Study names | studyNames | noNA | N/A for now? | yes | A comma-delimited list of names of studies in portal (i.e., the string names of the synIds in studies). | |||||||||||||||||||
| Grant Number | grantgrantNumber | no | tertiary (possibly don't display on card)3 | yes | The grant number without the "U54" or U01 center"U01" prefix, e.g., the grant column of this table has "U54 CA217297", we only want "CA217297" |
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.
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