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Source data
Synapse Table: https://www.synapse.org/#!Synapse:syn21868591/tables/
DEPRECATED Synapse Table: https://www.synapse.org/#!Synapse:syn10923842/tables/
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Explore page config
Type / name of card: "Publications"
Fields to show: 35
Facets should be ordered in the order they appear in this table.
Any column that should be faceted in the portal (i.e., faceted on an explore page or have a column facet on a table) must be faceted on the corresponding Synapse table/view. There is a performance penalty incurred with each additional facet – hence, facet only those columns needed by the portal and limit to those likely to be useful.
Display Name | Column Name | Column Type | Link Format | Facet Y/N | Facet Order | Card UI Mapping | Destination | Link Query Key | Link Value Column | Searchable Y/N | Search |
|---|
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Authors
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Consortium
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Order | Search Hint Text |
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| authors
| STRING
|
| N | NA | subTitle
|
|
|
| Y | 2 | e.g. |
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NA | secondaryLabels[7]
| DOI (with prefix https://dx.doi.org/) |
| doi
| Y | 5 | e.g. 10.1158/2159-8290.CD-17-0222 |
Journal | journal
| STRING
|
| N |
...
NA | secondaryLabels[0]
|
|
|
| Y | 4 | e.g. |
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Nucleic Acids Res |
| pubMedUrl
| STRING
| url | N |
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...
| NA |
|
Publication Title | publicationTitle
| STRING
|
| N |
...
NA | title
| PubMed record |
| pubMedUrl
| Y | 1 | e.g. |
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methylation |
Publication Year | publicationYear
|
...
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5 | secondaryLabels[1]
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|
| Y | 10 | e.g. 2018 |
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Keywords | keywords
| STRING
|
| N | NA | secondaryLabels[6]
|
|
|
| Y | 3 | e.g. |
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| 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, string (vector) | unrestricted | no | Theme | Theme | yes | 2 | static | yes | One of the NCI-defined themes, Theme | theme
| STRING_LIST*
|
| Y | 1 | secondaryLabels[2]
|
|
|
| Y | 6 | 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). | - Accessory sinuses
- Adrenal gland
- Anus and anal canal
- Base of tongue
- Bladder
| 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). | - Abdomen, NOS
- Abdominal esophagus
- Accessory sinus, NOS
- Acoustic nerve
- Adrenal gland, NOS
| diagnosis/tissue_or_organ_of_origin https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis&anchor=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"tumor-immune |
Tumor Type | tumorType
| STRING_LIST*
|
| Y | 3 | secondaryLabels[3]
|
|
|
| Y | 8 | e.g. Skin Cutaneous Melanoma |
Tissue | tissue
| STRING_LIST*
|
| Y | 4 | secondaryLabels[4]
|
|
|
| Y | 9 | e.g. Prostate gland |
Assay | assay
| STRING_LIST*
|
| Y | 2 | secondaryLabels[5]
|
|
|
| Y | 7 | e.g. RNA-seq |
Grant Name | grantName
| STRING_LIST*
| portal query (each) | Y | 6 | secondaryLabels[8]
| Grants/DetailsPage | grantName | grantName
| Y | 11 | e.g. immunology |
Consortium | consortium
| STRING_LIST*
|
| Y | 7 | secondaryLabels[9]
|
|
|
| N | NA | e.g. PS-ON |
Dataset | dataset
| STRING_LIST*
| portal query (each) | N | NA | secondaryLabels[10]
| Datasets/DetailsPage | datasetAlias | dataset
| N | NA | e.g. syn13857535 |
*<TYPE>_LIST columns for multi-value annotations not yet implemented
