Changes between Version 2 and Version 3 of PombasePlanningMeetingAgenda201402


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Timestamp:
Jan 13, 2015, 6:56:27 PM (7 years ago)
Author:
vw253
Comment:

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  • PombasePlanningMeetingAgenda201402

    v2 v3  
    2626     http://genomebrowser.pombase.org/Schizosaccharomyces_pombe/Location/View?r=I:3735820-3807289;site=ensemblunit
    2727
    28    * Document update procedure and time taken (Mark) Done on Confluence (Q how long is this?)
     28  * Document update procedure and time taken (Mark) Done on Confluence (Q how long is this?)
    2929
    30    * https://www.ebi.ac.uk/panda/jira/browse/PB-1802  is it best to combine repeats, and ask for average datasets?
     30  * https://www.ebi.ac.uk/panda/jira/browse/PB-1802  is it best to combine repeats, and ask for average datasets?
    3131 
    32    * EsyN  update
     32  * EsyN  update
     33
     34  * Display of wild strains, see minutes
    3335
    3436   
    3537 == Hosting high throughput datasets ==
    3638
    37  * None pending at high priority
    38 
    39 == Display of new data types ==
    40 Phenotyping of wild strains, how to display these?
    41 
    42 From Dan:
    43  Here is what  think might be interesting/useful to represent.
    44 
    45 The three main ones are:
    46 
    47 1. SNPs, indels using Ensembles variation tools. I think I jhave already sent a VCF for indels and SNPs. If not I'm happy to send this again.
    48 2. Tf1 transposons that are variable between strains as well. Could also be supplied in VCF.
    49 3. Variation wiggle tracks (like pi, which is the average pairwise differences, for example).
    50 
    51 Also:
    52 Some of the variants are associated with one or more traits (they are QTLS). I think QTLs are displayed on some other species. This would be a small amount of data, perhaps 100 or so QTLs.
    53 I am not sure how much of this data gets displayed in gene pages. If its does then fine. Otherwise I could easily make a table of gene-by-gene stats (such as number of Snps, indels, pi, and andy QTLs).
    54 
    55 I'd be very happy to come along & help/chat about getting this data into pombase.
     39 * None pending at high priority (Carr lab replication origins and Gx data)
    5640
    5741
    58  == Priority Jira tickets ==
     42 ==  Next Priority Jira tickets ==
    5943
    60     * I have cleared out some of the smaller tickets to V 48, but if they are quick they can be done and closed.
    61     As the gene pages are getting longer and longer due to the volume of curated data we feel that it is becoming a priority to address the  display of GO and phenotype data and address some of the redundancy in order for the users to be able to consume the data effectively. This should be the next larger project to tackle development wise. Also we should start to add a large volume of multi gene phenotypes in the next couple of months, so the other 2 tickets under the parent PB-1836 (PB-1839 and  PB-1840), so we are happy to punt anything else bar critical bugs until these are done.
     44  *  1. Finalising any gene page display issues related  to summary views etc  (phenotype, GO and multi-gene phenotype). Tickets related to this are  now collected at Chado future 1 (6 tickets).
    6245
    63     * Follow up on the items for Ensembl, are they all raised and in progress?
     46  *  2.  Query builder related tickets especially to handle GO annotation  extensions, phenotype conditions and alleles, multi gene phenotypes and  sequence features.
     47      *  Curators need to discuss, and then with Kim and Mark, should have done this before meeting
     48
     49  *  3. Refining the Query builder results download for the above new query types (and the others which had previously been identified - downloading physical interactions or GO terms associated with a gene list).
     50
     51  *  4. Other tickets related to the term suggestion behaviour.
     52
     53
     54  * Then tickets in Chado future 3 which appear to be stalled
     55 
     56 
    6457   
    6558 == Chado ==