Synapse table for this card: https://www.synapse.org/#!Synapse:syn10923842/tables/
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| column name | synapse table name | standardized schema name | required | facet | card location | note | 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 | 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 | NAno | ok to leave this blank in synapse table for now (robert has concerns about copyright issues,so we may not include in portal)–but if we can include it synapse table efficiently and programmatically, please do so. | maybe | 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 | nostring vector | many | no | related to Experimental Strategy | |||||||||||||
| Site | site | yes | secondary | i have trouble differentiating "site" from "tissue/organ." once we adopt GDC, we might better differentiate, for now just copy over the "tissue_or_organ" column to a "site" column in the synapse table. | yes | secondary | yes | 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) | ||||||
| Tissue | tissue_or_organ | yes | secondary | 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 | no | no | NA | yes | doi without wwww.doi.org/ prefix: eg: 10.1093/neuonc/noy046 yes; if can't get doi efficiently and programmatically, just use the PubMed field that is already in the table for now | yes | ||||||||||||||
| Title | Title | Title | yes | no | primary | yes | publication titleyes | string | no | |||||||||||||
| Authors | Authors | Author | yes | no | primary | yes | publication authorsyes | string vector | no | |||||||||||||
| Journal | Journal | Journal | yes | no | primary | yes | publication journal | yes | string | no | ||||||||||||
| Year | Publication Year | Year | no | yes | primary | yes | publication yearyes | number | no | |||||||||||||
| featured | no | yes | whether the card should be on the homepage (max 3 in table) | yes | ||||||||||||||||||
| Link to Synapse siteGrant | 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 Number | grantgrantNumber | no | tertiary (possibly don't display on card) | 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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