Publications
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 | 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 |
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Keywords | Keywords |
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| no | 2 | static | yes | Keywords associated with this publication, some of which may come from a controlled vocabulary | metastasis, scRNA-seq |
| string (vector) |
| unrestricted |
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| no |
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Theme | Theme |
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| 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. |
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Abstract | Abstract |
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| no | 1 | static | no | Copyright issues? TBD |
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| largeText |
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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 |
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| 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 |
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| no | related to Experimental Strategy |
Site | site |
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| 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 |
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| many |
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| no | related to Primary Site |
Tissue | tissue_or_organ |
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| 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 |
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DOI | DOI | DOI | yes? | no | N/A | URL for title | yes |
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| yes |
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Title | Title | Title | yes | no | 1 |
| yes | publication title |
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| string |
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| no |
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Authors | Authors | Author | yes | no | 1 |
| yes | publication authors |
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| string vector |
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| no |
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Journal | Journal | Journal |
| no | 1 |
| yes | publication journal |
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| string |
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| no |
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Year | Publication Year | Year | yes? | yes | 1 |
| yes | publication year |
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| number |
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| no |
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featured |
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| no | N/A | checkbox | yes | whether the card should be on the homepage (max 3 in table) |
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| yes |
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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. |
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| entity ID
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Program | Consortium |
| yes (as "Consortium" in standard schema) | yes | 3 | static | yes | (future-state may link to program page if present) |
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| string |
| CSBC, PSON |
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Grant Type | grantType |
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| yes | 3 | static | yes |
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| U54, U01 |
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Datasets | datasets |
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| no | 3 |
| yes | A comma-delimited list of links to datasets in portal–i.e,. synIds. |
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Dataset names | datasetNames |
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| 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). |
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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. |
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Study names | studyNames |
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