PFB Handoff to BioData Catalyst Powered by Seven Bridges
The selected participant-level data from PIC-SURE can be handed off to Seven Bridges for analysis in the Portable Format for Bioinformatics, or PFB.
To learn more about the PFB format, please refer to the PFB documentation: https://uc-cdis.github.io/pypfb/
Prepare Data for Analysis from PIC-SURE
Once you have , the data should be prepared for analysis. During this process, be sure to select the "Export as PFB" option. For more information on how to prepare the data for analysis, please refer to Prepare for Analysis.
After going through the process, select the "Export to Seven Bridges" option. This will direct you to the Seven Bridges platform.
Exporting to Seven Bridges
Selecting "Export to Seven Bridges" will direct you to BioData Catalyst Powered by Seven Bridges in a new tab. You may be required to sign in to Seven Bridges.
Select the preferred destination of the data in Seven Bridges. This can be an existing project created previously or a new one. Follow the steps to choose the location.
Once the selection has been made, follow the prompts to go to the destination project, where the file will be loaded.
Data Format in Seven Bridges Project
The data will be stored as an Avro file in your project. You can find this file by navigating to the "Files" tab of your destination project.
Note: You can disregard error messages related to DRS URIs and importing from Gen3. To check if your data was handed off, go to the project and unpack the Avro file.
You can unpack the Avro file using the PFB Unwrapper App in the "Public Apps" section.
Once unpacked, there will be two main data tables: the data and the data dictionary tables.
The data will be labeled as "pic_sure_patients_[dataset ID]" and show the participant-level data from PIC-SURE. The columns of this table are the variables, which are labeled as the PIC-SURE concept paths. For more information about concept paths, see Data Organization in PIC-SURE. The rows of this table represent individual participants.
The data dictionary will be labeled as "pic_sure_data_dicitonary_[dataset ID]" and will contain information about the variables that have been exported. This includes information about each variable, such as the concept path, description, and display name. The data dictionary also includes DRS URIs, or links to the original data file, which can be used to access the files for further analysis in Seven Bridges.
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