The following is a brief description of the relevant columns in the folder view below (by column header):
https://www.synapse.org/#!Synapse:syn18488466/tables/
NOTE: Studies are selected in this view with is.study == TRUE
The legacy table upon which the above project view was created is: https://www.synapse.org/#!Synapse:syn10915872/tables/
data portal name: name as it should appear in data portal
synapse file view column: corresponding name (e.g., for SQL query) in Synapse table view
card location: primary (i.e., top) or secondary (i.e., bottom) key/annotation
facet: true if column_name should be faceted in data portal.
File view driving this table: https://www.synapse.org/#!Synapse:syn9630847/tables/
The following is a brief description of the relevant columns in the table below (by column header):
column name: name as it should appear in data portal
current synapse file view column: corresponding name (e.g., for SQL query) in Synapse table view
eventual synapse file view column: name (e.g., for SQL query) in Synapse table view that we will eventually migrate to
difference between current and eventual columns: as we migrate to GDC, we will put new annotation keys in "eventual" column names. for now, use "current."
facet: true if column_name should be faceted in data portal.
card location: primary (i.e., top) or secondary (i.e., bottom) key/annotation
The following annotations do not exist on file:
The following annotations need to be "ported" to GDC:
The following have been added to the synapse table, but are blank. They need to be filled in:
| column name | current synapse file view column | eventual synapse file view column | facet | card location | concept | example | GDC equivalent | faceted on GDC | facet on CSBC | GDC reference | size | restricted values | comments | in AMP-AD portal | in NF portal |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Grant Type | yes | NA | U54 or U01 | ||||||||||||
| Grant | yes | NA | |||||||||||||
| Program | yes | NA | CSBC or PSON | ||||||||||||
| Species | species | species | yes | secondary | none | yes | |||||||||
| Scientific Theme | NA | theme | yes | secondary (or possibly pill directly beneath file name) | tumor-heterogeneity | none | yes | ||||||||
| Number of Samples | no | secondary | |||||||||||||
| Data Category | assay | data_category | yes | secondary | Broad categorization of the contents of the data file. |
| data_category | yes | yes | CSBC will need to add values to those in GDC (which only cover sequencing) | |||||
| Experiment Strategy | assay | experimental_strategy | yes | secondary | The sequencing strategy used to generate the data file. REMOVE "sequencing" for CSBC. |
| experimental_strategy | yes | yes | CSBC will need to add values to those in GDC (which only cover sequencing) | |||||
| Platform | yes | NA | platform | yes | yes | ||||||||||
| Disease Type | yes | secondary | The text term used to describe the type of malignant disease, as categorized by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O). |
| case/disease_type | yes | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case | |||||||
| Site | yes | secondary | 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 | yes | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=case | |||||||
| Tissue | yes | secondary | 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 | yes | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=diagnosis |
GDC Data Dictionary viewer: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/
GDC Data Dictionary is implemented in YAML files: https://github.com/NCI-GDC/gdcdictionary
GDC submission process (and metadata templates) are described here: https://docs.gdc.cancer.gov/Data_Submission_Portal/Users_Guide/Data_Submission_Overview/
GDC Data Upload Walkthrough: https://docs.gdc.cancer.gov/Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough/#clinical-data-requirements
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