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  1. IGB
  2. IGBF-4112

2025 Update Galaxy dbkey values in IGB synonyms.txt

        Details

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

          Description

          Situation: usegalaxy.org website is used frequently by IGB users. When a user views data from Galaxy in IGB we attempt to load the appropriate genome in IGB. Many of the genomes line up with and use the same nomenclature as Galaxy, but there are now many more genomes in Galaxy.

          Task: Update the IGB synonyms.txt with any missing Galaxy synonyms. See IGBF-1879 for additional details.

          Galaxy genome API: https://usegalaxy.org/api/genomes
          Galaxy Europe genome API: https://usegalaxy.eu/api/genomes
          UCSC genome API (for comparison, this should be up to date in IGB already): https://api.genome.ucsc.edu/list/ucscGenomes

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              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-4266 Synchronize species.txt and synonyms.txt between IGB and SVN

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-1879 Ensure Galaxy default dbkey values are in synonyms.txt

              • Major - Major loss of function.
              • Closed

                Activity

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                pkulzer Paige Kulzer (Inactive) added a comment - - edited

                First steps:

                1. From the API, find a genome that's not supported by IGB and see what happens when viewing a Galaxy History file with that dbkey in IGB.
                2. Find a genome that's being added to IGB via UCSC's API and see what happens when viewing a Galaxy History file with that dbkey in IGB.
                3. Compare the API's between Galaxy and UCSC and determine which, if any, genomes are being included only by Galaxy. These are the genomes we'll likely need to update IGB's synonyms.txt file with.
                Show
                pkulzer Paige Kulzer (Inactive) added a comment - - edited First steps: From the API, find a genome that's not supported by IGB and see what happens when viewing a Galaxy History file with that dbkey in IGB. Find a genome that's being added to IGB via UCSC's API and see what happens when viewing a Galaxy History file with that dbkey in IGB. Compare the API's between Galaxy and UCSC and determine which, if any, genomes are being included only by Galaxy. These are the genomes we'll likely need to update IGB's synonyms.txt file with.
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                pkulzer Paige Kulzer (Inactive) added a comment - - edited
                1. This opened a custom genome in IGB.
                2. This opened the correct genome in IGB.
                3. Below is a table summarizing the genomes that we're including in synonyms.txt without the correct Galaxy key:
                Genome Galaxy Key
                A_thaliana_Jan_2004 araTha1***
                A_thaliana_Apr_2008 arabidopsis_tair8
                A_thaliana_Jun_2009 arabidopsis
                H_exemplaris_Z151_Apr_2017 H_exemplaris_Z151
                Y_lipolytica_CLIB122_Jul_2004 GCF_000002525.2

                ***This key (araTha1) is already listed in synonyms.txt with a different genome. Galaxy correlates araTha1 with TAIR7, we've correlated it with TAIR9/TAIR10, and UCSC correlates it with TAIR10. Which is correct? Update: I believe TAIR10 is correct

                Show
                pkulzer Paige Kulzer (Inactive) added a comment - - edited This opened a custom genome in IGB. This opened the correct genome in IGB. Below is a table summarizing the genomes that we're including in synonyms.txt without the correct Galaxy key: Genome Galaxy Key A_thaliana_Jan_2004 araTha1*** A_thaliana_Apr_2008 arabidopsis_tair8 A_thaliana_Jun_2009 arabidopsis H_exemplaris_Z151_Apr_2017 H_exemplaris_Z151 Y_lipolytica_CLIB122_Jul_2004 GCF_000002525.2 ***This key (araTha1) is already listed in synonyms.txt with a different genome. Galaxy correlates araTha1 with TAIR7, we've correlated it with TAIR9/TAIR10, and UCSC correlates it with TAIR10. Which is correct? Update: I believe TAIR10 is correct
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                pkulzer Paige Kulzer (Inactive) added a comment - - edited

                Please see attached for a copy of the spreadsheet I compiled listing the genomes hosted by Galaxy/Galaxy EU as well as the genomes hosted by UCSC and IGB.

                Ready for review!

                Show
                pkulzer Paige Kulzer (Inactive) added a comment - - edited Please see attached for a copy of the spreadsheet I compiled listing the genomes hosted by Galaxy/Galaxy EU as well as the genomes hosted by UCSC and IGB. Ready for review!
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                nfreese Nowlan Freese added a comment - - edited
                Genome Galaxy Key
                A_thaliana_Jan_2004 araTha1***
                • I'm not sure what to think about this one, I would say let's not change it now since that could mess up UCSC and current IGB users
                A_thaliana_Apr_2008 arabidopsis_tair8
                • let's update this in the synonyms.txt on the SVN repository
                A_thaliana_Jun_2009 arabidopsis
                • let's update this in the synonyms.txt on the SVN repository
                H_exemplaris_Z151_Apr_2017 H_exemplaris_Z151
                • I can't find this in either Galaxy API, can you double check it?
                Y_lipolytica_CLIB122_Jul_2004 GCF_000002525.2
                • In the Galaxy API I see the key as (GCF_000002525.2_ASM252v1) can you double check it?

                Paige Kulzer - I marked some above as needing to be double checked, otherwise please go ahead and add the Galaxy key values to the synonyms.txt file in the SVN repository.

                Show
                nfreese Nowlan Freese added a comment - - edited Genome Galaxy Key A_thaliana_Jan_2004 araTha1*** I'm not sure what to think about this one, I would say let's not change it now since that could mess up UCSC and current IGB users A_thaliana_Apr_2008 arabidopsis_tair8 let's update this in the synonyms.txt on the SVN repository A_thaliana_Jun_2009 arabidopsis let's update this in the synonyms.txt on the SVN repository H_exemplaris_Z151_Apr_2017 H_exemplaris_Z151 I can't find this in either Galaxy API, can you double check it? Y_lipolytica_CLIB122_Jul_2004 GCF_000002525.2 In the Galaxy API I see the key as (GCF_000002525.2_ASM252v1) can you double check it ? Paige Kulzer - I marked some above as needing to be double checked, otherwise please go ahead and add the Galaxy key values to the synonyms.txt file in the SVN repository.
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                pkulzer Paige Kulzer (Inactive) added a comment -
                Genome Galaxy Key
                A_thaliana_Apr_2008 arabidopsis_tair8
                A_thaliana_Jun_2009 arabidopsis
                Y_lipolytica_CLIB122_Jul_2004 GCF_000002525.2

                This is the final table with the changes that need to be made to IGB's synonyms.txt. Rather than making these changes via SVN, they will be made to IGB's version of synonyms.txt. That task has been captured by a ticket Dr. Freese just made (IGBF-4266) so I will now close this ticket and work on that one.

                Show
                pkulzer Paige Kulzer (Inactive) added a comment - Genome Galaxy Key A_thaliana_Apr_2008 arabidopsis_tair8 A_thaliana_Jun_2009 arabidopsis Y_lipolytica_CLIB122_Jul_2004 GCF_000002525.2 This is the final table with the changes that need to be made to IGB's synonyms.txt. Rather than making these changes via SVN, they will be made to IGB's version of synonyms.txt. That task has been captured by a ticket Dr. Freese just made ( IGBF-4266 ) so I will now close this ticket and work on that one.

                  People

                  • Assignee:
                    pkulzer Paige Kulzer (Inactive)
                    Reporter:
                    nfreese Nowlan Freese
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                    • Created:
                      Updated:
                      Resolved: