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 | GDC 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 | metastasis, scRNA-seq | string vector | unrestricted | no | ||||||||
| Theme | Theme | yes | primary (this might make sense as a "pill" beneath publication title) | 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 | NA | 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. | no | largeText | |||||||||||
| Disease Type | diseaseType | yes (as "Diagnosis/Disease" in standard schema) | yes | secondary | yes | The type of cells that carcinoma arises from. | Adenocarcinoma, Anaplastic Astrocytoma | string vector | many | yes | related to Disease Type | ||||||
| Experimental Strategy | experimentalStrategy | yes (as "Assay" in standard schema) | yes | secondary | yes | RNA-seq | string 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 | 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 | ||||||
| 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 | NA | yes | doi without wwww.doi.org/ prefix: eg: 10.1093/neuonc/noy046; 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 | no | primary | yes | publication title | string | no | |||||||||
| Authors | Authors | Author | no | primary | yes | publication authors | string vector | no | |||||||||
| Journal | Journal | Journal | no | primary | yes | publication journal | string | no | |||||||||
| Year | Publication Year | Year | yes? | yes | primary | yes | publication year | number | no | ||||||||
| featured | no | yes | whether the card should be on the homepage (max 3 in table) | yes | |||||||||||||
| Grant | CSBC PSON Center | yes | 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 (as "Consortium" in standard schema) | yes | tertiary (possibly don't display on car) | yes | string | CSBC, PSON | ||||||||||
| Grant Type | grantType | yes | tertiary (possibly don't display on card) | 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 | yes (as "Study" in standardized schema) | 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 | grantNumber | no | tertiary (possibly don't display on card) | yes | The grant number without the "U54" or "U01" prefix, e.g., the grant column of this table has "U54 CA217297", we only want "CA217297" | ||||||||||||
| Data Type | NA | yes (as "DataType" in standard schema) | |||||||||||||||
| Model System | NA | yes (as "ModelSystem" in standard schema) | |||||||||||||||
| Institution | instituion | yes (as "Institution" in standard schema) | 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/
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