Changes between Version 31 and Version 32 of PombasePlanningMeetingAgenda201402


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Timestamp:
Mar 10, 2015, 7:15:29 PM (6 years ago)
Author:
vw253
Comment:

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  • PombasePlanningMeetingAgenda201402

    v31 v32  
    2424    * Problem: For example FungiDB use a descriptions  gff file from PomBase, as the main input but this only records the Schizosaccharomyces_pombe.ASM294v2.25.gff3.gz
    2525    which does not change even thought the annotation changes between PomBase versions as time goes on the gene build becomes more static but the annotation changes more. Need a way to capture the annotation version in the gff versioning.
    26    * From Midori: the build number in the table has never corresponded to the number embedded in the GFF file names. According to the Jira ticket, "2.1" was the build number for at least chado versions 38-40, and the GFF files nearest those dates include 2.20 and 2.21.
    27   * How does someone get from  Schizosaccharomyces_pombe.ASM294v2.25 to know  which gene build?
     26    * From Midori: the build number in the table has never corresponded to the number embedded in the GFF file names. According to the Jira ticket, "2.1" was the build number for at least chado versions 38-40, and the GFF files nearest those dates include 2.20 and 2.21.
     27    * How does someone get from  Schizosaccharomyces_pombe.ASM294v2.25 to know  which gene build?
    2828       * i.e where is the historical data about the  on the Ensembl site about the gene build that was used in a specific release?
    29    * figuring the numbering of releases before 32 ( I think maybe we just used a data stamp for these?)
    30 
    31   *  It seems that .25 is <eg_version>
    32   * The gff file should be renamed to capture
    33      * PomBase sequence assembly version
    34      * gene build version
    35      * annotation version
     29    * figuring the numbering of releases before 32 ( I think maybe we just used a data stamp for these?)
     30    *  It seems that .25 is <eg_version>
     31    * The gff file should be renamed to capture
     32    * PomBase sequence assembly version
     33    * gene build version
     34    * annotation version
    3635 
    3736
     
    5554
    5655  * Display of wild strains, see previous minutes
    57    * Dan Jaffres paper on genomic and phenotypic diversity is now published. Asked Jurg/Dan to provide an update of what  they think should be displayed on the PomBase gene pages.
     56   * Dan Jefferes paper on genomic and phenotypic diversity is now published.
     57   * Dan will provide an example of what could  be displayed on the PomBase gene pages.
    5858   * EG to update us on what progress displaying the variation data
    5959   * Need to discuss what we can feasibly display in the light of the volume and scope of the data