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  1. IGB
  2. IGBF-2861

Investigate species synonyms lookup

        Details

        • Type: Improvement
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: The Synonym Lookup module includes several files that are used to compare the species names found in IGB. This includes comparing the contents.txt, species.txt, and synonyms.txt. Genomes can come from Quickloads such as IGB Quickload and also from other services, such as UCSC DAS.

          IGB friendly genome names follow the pattern of G_species_MMM_YYYY. In addition, a variety can be included - G_species_variety_MMM_YYYY.

          While updating genomes for IGBF-781 an edge case was discovered. The opossum genome provided by UCSC DAS has an IGB friendly name of M_domestica. This is very similar to the IGB provided genome for apple, which is M_domestica_Borkh. However, IGB appears to ignore the variety and is just comparing the M_domestica, which is incorrect. As a workaround, a variety was added to the opossum genome to keep them separated.

          Task: Identify why IGB considers the two M_domestica genomes to be the same. This should not be occurring, with or without the variety included.

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              relates to

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-781 Update synonyms.txt for UCSC

              • Major - Major loss of function.
              • Closed

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                nfreese Nowlan Freese added a comment -

                Documentation on synonyms.txt in the IGB users guide
                https://wiki.transvar.org/display/igbman/Use+synonyms.txt+to+link+genome+version+names+to+each+other
                https://wiki.transvar.org/display/igbman/Personal+Synonyms
                https://wiki.transvar.org/display/lorainelab/How+to+add+a+new+synonym+to+IGB

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                nfreese Nowlan Freese added a comment - Documentation on synonyms.txt in the IGB users guide https://wiki.transvar.org/display/igbman/Use+synonyms.txt+to+link+genome+version+names+to+each+other https://wiki.transvar.org/display/igbman/Personal+Synonyms https://wiki.transvar.org/display/lorainelab/How+to+add+a+new+synonym+to+IGB
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                nfreese Nowlan Freese added a comment -

                To replicate the issue:
                Modify the species.txt and synonyms.txt to remove the metatherian variety from Monodelphis domestica.
                In IGB, make sure that the UCSC DAS server is enabled.
                The M_domestica_Borkh genome should now appear as a genome version in the Monodelphis domestica species.

                Show
                nfreese Nowlan Freese added a comment - To replicate the issue: Modify the species.txt and synonyms.txt to remove the metatherian variety from Monodelphis domestica. In IGB, make sure that the UCSC DAS server is enabled. The M_domestica_Borkh genome should now appear as a genome version in the Monodelphis domestica species.

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                  • Assignee:
                    Unassigned
                    Reporter:
                    nfreese Nowlan Freese
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                    Dates

                    • Created:
                      Updated: