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  1. IGB
  2. IGBF-4172

STRING for tomato

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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          Description

          GOAL: To get the STRING DB
          https://string-db.org/cgi/input?sessionId=bODA2Ie6lzxH&input_page_show_search=on

          To play nice with our tomato data. According to Kelsey, this worked at one point with SOly IDs. But recently, with a version update, she has not been able to get STRING to work.

          We will test various data inputs to see what can it will accept. If all fail, we ping them and ask what is up!!!

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              robofjoy Robert Reid added a comment -

              SolyIDs no longer work.
              Solgenomics.net is currently borken!!! So we can't use any resource from there for now (I emailed Cornell and asked what is up with being down)

              There is an API and how to retrieve from it here:
              https://string-db.org/help/api/

              It will accept our amino acid sequences. So we could send queries this way.

              Another possibility is to feed our solyIds into DAVID and get uniprot IDs maybe that way?

              Show
              robofjoy Robert Reid added a comment - SolyIDs no longer work. Solgenomics.net is currently borken!!! So we can't use any resource from there for now (I emailed Cornell and asked what is up with being down) There is an API and how to retrieve from it here: https://string-db.org/help/api/ It will accept our amino acid sequences. So we could send queries this way. Another possibility is to feed our solyIds into DAVID and get uniprot IDs maybe that way?
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              robofjoy Robert Reid added a comment -

              Gramene is integrated into interpro.
              Gramene contains SolyIds!!
              So we can use Uniprot to go from SolyID to UniprotID, which is acceptable in string.

              But how do we do this easily?
              I am exploring still.

              Show
              robofjoy Robert Reid added a comment - Gramene is integrated into interpro. Gramene contains SolyIds!! So we can use Uniprot to go from SolyID to UniprotID, which is acceptable in string. But how do we do this easily? I am exploring still.
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              bbendick Brandon Bendickson added a comment -

              I have generated 3hr and 8hr STRING images and popped them into the google slides.

              Show
              bbendick Brandon Bendickson added a comment - I have generated 3hr and 8hr STRING images and popped them into the google slides.

                People

                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated:
                    Resolved: