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.
show on card: whether to show on the corresponding card–no, or show as primary or secondary field.
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 | show on card–no, primary, secondary | concept | example | GDC equivalent | faceted on GDC | facet on CSBC | GDC reference | size | restricted values | comments | in AMP-AD portal | in NF portal |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Species | species | species | yes | primary | none | yes | |||||||||
| Scientific Theme | NA | theme | yes | primary | tumor-heterogeneity | none | yes | ||||||||
| Data Category | assay | data_category | yes | primary | 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) | |||||
| Data Type | NA | data_type | no? | no | Specific content type of the data file. |
| data_type | yes | yes | CSBC will need to add values to those in GDC (which only cover sequencing) | |||||
| Data Format | fileFormat | data_format | no? | no | Format of the data files. |
| data_format | yes | yes | ||||||
| Experiment Strategy | assay | experimental_strategy | yes | primary | 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) | |||||
| file_name | no | primary | The name (or part of a name) of a file (of any type). | file_name | no | no | |||||||||
| file_size | no | no | The size of the data file (object) in bytes. | file_size | no | no | |||||||||
| md5sum | no | no | The 128-bit hash value expressed as a 32 digit hexadecimal number (in lower case) used as a file's digital fingerprint. | md5sum | no | no | |||||||||
| platform | yes | no | platform | yes | yes | ||||||||||
| workflow_type | NA | no | no | Generic name for the workflow used to analyze a data set. |
| yes | ?? | ||||||||
| Disease Type | disease_type | yes | primary | 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 | ||||||
| Tissue | tissue_or_organ_of_origin | yes | primary | 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 | ||||||
| tissue_type | no | no | Text term that represents a description of the kind of tissue collected with respect to disease status or proximity to tumor tissue. |
| sample/tissue_type | no | yes | https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=sample |
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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