The following is a brief description of the relevant columns in the table below (by column header):
https://www.synapse.org/#!Synapse:syn10915872/tables/
column name: name as it should appear in data portal
...
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:
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| 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 | ||||||||
| 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 |
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