Synapse Table: https://www.synapse.org/#!Synapse:syn20448807syn10923842/tables/
Fields to show: 3
Display Name | Column Name | Facet Y/N | UI Mapping | Destination | Searchable Y/N | Search hint text |
|---|
Authors | N | Card_SubTitle | Y | e.g. LastName | |
| Program |
Consortium | Y | Secondary_Label_ |
| X | Y | e.g. |
| PS- |
| ON |
| DOI |
DOI | N | Secondary_Label_ |
| X | doi (with prefix https://dx.doi.org/) | Y | e.g. |
| 10. |
| 1158/ |
| 2159- |
| 8290.CD- |
| 17- |
| 0222 | ||||||
| Journal | journal | N | Secondary_Label_2 | Y | e.g. Alzheimers Dement | |
| Pubmed ID | pubmed_id | N | Secondary_Label_6 | N | ||
| title | N | Card_Title | doi (with prefix https://dx.doi.org/) | Y | e.g. network | |
| Year | year | Y | Secondary_Label_1 | Y | e.g. 2018 | |
| Grant | long_amp_ad_grants | Y | Secondary_Label_4 | Y | e.g. U01AG046161 |
| column name | synapse table name | standardized schema name | required | facet | priority | 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 | 2 | static | 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 | 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 | 1 | static | no | Copyright issues? TBD | largeText | ||||||||||
| Disease Type | diseaseType | yes (as "Diagnosis/Disease" in standard schema) | yes | 2 | static, multiple | yes | The type of cells that carcinoma arises from. | Adenocarcinoma, Anaplastic Astrocytoma | case/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 (as "Assay" in standard schema) | yes | 2 | static, multiple values | yes | RNA-seq | string vector | many | no | related to Experimental Strategy | ||||||
| Site | 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 | ||||||
| Tissue | 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 | 1 | yes | publication title | string | no | ||||||||
| Journal | Journal | Journal | no | 1 | yes | publication journal | string | no | |||||||||
| Year | Publication Year | Year | yes? | yes | 1 | yes | publication year | number | no | ||||||||
| featured | no | N/A | checkbox | yes | whether the card should be on the homepage (max 3 in table) | yes | |||||||||||
| Grant | 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 | |||||||||
| Grant Type | grantType | yes | 3 | static | yes | U54, U01 | |||||||||||
| Datasets | datasets | no | 3 | yes | A comma-delimited list of links to datasets in portal–i.e,. synIds. | ||||||||||||
| Dataset names | datasetNames | no | 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 | 3 | yes | A comma-delimited list of links to study/studies in portal–i.e., synIds. | |||||||||||
| Study names | studyNames | no | 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 | grantNumber | no | 3 | 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" |