Managing phenotypical data with Terra data tables

• 

  Anthony DiCi

  • October 25, 2023 16:18

  Hi Nikhil,

  Thanks for writing in with this question! A member of the Terra support team will follow up with you as soon as they are able.

  If relevant, please let us know if there is any urgency around this request so that the team can prioritize it appropriately.

  Kind regards,

  Anthony

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• 

  Josh Evans

  • October 25, 2023 19:43

  Hi Nikhil,

  Thanks again for writing in! Are there any special considerations that need to be made for this data? If not, then the process would be to upload the data to the Workspace's bucket, and then create a data table that has links to the locations of the data in the Workspace Bucket.

  Here are some links to our documentation that I thought you might find helpful:

  • Upload data and populate the table with linked file paths
  • How to add a table to a Terra workspace
  • How to make a data table from scratch or a template
  • How to move data to/from a Google bucket
  • How to move data between local and workspace storage
  • Managing data with tables

  Please take a look at these and let me know if you have any questions.

  Best,

  Josh

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• 

  Nikhil Shingte

  • October 25, 2023 21:12

  Hi Josh, Thanks for your response. We have following types of datasets, which we are planning to upload to Terra and use for analyses. All of this data has been de-identified:

  • Patient natural history data
  • Patient registry data
  • RNA-Seq, WES, WGS data from cell lines, mouse models
  • Patients Genetic testing raw data

  I have below questions at this moment:

  1. Using this data for analyses with Terra, from compliance point of view, any protocols that we need to be mindful about. I know data in google cloud bucket is encrypted at rest and data in transit is encrypted as well. Wanted to make sure that we are fine from legal and compliance point of view when uploading this data to Terra.
  2. Regarding relationships among various data tables, I think document you have shared are helpful. I saw Gen3 as part of Anvil platform provides relationships between data as well. Is it necessary to use Gen3 for our datasets and export to Terra or we should be able to use Terra for our need. Are there any advantages on using Gen3 with Terra.

  Please let me know if more information is needed.

  Thanks

  Nikhil

   

   

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• 

  Josh Evans

  • November 01, 2023 20:07

  Hi Nikhil,

  Thanks for the reply. To answer your first question, here is a link to our documentation about how Terra handles security.  Please let me know if this helps answer the question for you.

  For the second question: Gen3 can be used to process and export data to Terra, but it is not required. It's another way to get data into Terra.  If your data isn't already in Gen3 and you don't need any of the Gen3 tools, then it doesn't have to be used.  That said, here's a link to our documentation that covers how to use Gen3 with Terra. 

  Please let me know if you have any questions.

  Best,

  Josh

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• 

  Nikhil Shingte

  • November 02, 2023 15:00

  Hi Josh, Thanks for the information related to security. For our use case, we will directly use Terra capabilities without Gen3 as we don't have any data there. 

  Regards

  Nikhil

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• 

  Josh Evans

  • November 02, 2023 15:46

  Hi Nikhil,

  You're very welcome! I'm glad I was able to help.

  Please let me know if you have any questions.

  Best,

  Josh

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