Changes between Version 4 and Version 5 of PombasePlanningMeetingMinutes20140122


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Timestamp:
Jan 22, 2014, 8:15:06 PM (8 years ago)
Author:
val_wood
Comment:

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  • PombasePlanningMeetingMinutes20140122

    v4 v5  
    2222 * AI: Val to Summarize tasks need to be done for the grant proposal. (see below) 
    2323
    24 == Collectd Action items  Jan ==
     24== Collected Action items  Jan ==
    2525
    2626
     
    2929
    3030 * Kim asked if it is possible for every access to curation.pombase.org to go (transparently) via an EBI server which could show a message if sysbiol/oliver0 is offline (more detail from Kim)
    31    * we will revisit this next time there is sceduled down time
     31   * we will revisit this next time there is scheduled down time
    3232
    3333 * Are we still not doing something we are supposed to?
    34  (Re e-mail Mark was surprised about ne features appearing, I think we were supposed to give prior notice, but I don't think there are procedures in place for this?
    35    * IN future curators should curate a jira ticket to alert Mark when new features are created
     34 (Re e-mail Mark was surprised about new features appearing, I think we were supposed to give prior notice, but I don't think there are procedures in place for this?
     35   * In future curators should curate a jira ticket to alert Mark when new features are created
    3636
    3737 * In noticed in a thread about gff3 specification "Can anyone think of a valid case where multiple feature lines might have the same ID, but different SO types"
     
    4747
    4848 * UniProt trying to  generate uniprot -> pombase mappings using PomBAse, also see tickets #362843, #353760, #366965, and Val's email to pombase list from 21 Nov.
    49    * AI Monitor item on tracker, Ensembl will create mapping, Val will check https://www.ebi.ac.uk/panda/jira/browse/PB-1738
     49   * AI Monitor UniProt item on tracker, Ensembl will create mapping, Val will check https://www.ebi.ac.uk/panda/jira/browse/PB-1738
    5050 
    5151 * Query from a user we can't answer: "Resolved: definition of feature types" basically appear to be reporting problems with the gff file
    52    * AI, the new file appears to contian LTRs , UTRs and the correct number of CDS, Mark to  send file/ close ticket
     52   * AI, Re user gff query the new file appears to contian LTRs , UTRs and the correct number of CDS, Mark to  send file/ close ticket
    5353   
    5454  * Speed (ETA around a month?) a new track loader where data is combined so that loading is quicker. (progess?)
     
    7474Pathways will be hosted in a Reactome instance and linked to from PomBase gene pages. also are there any widgets?
    7575
    76  * 6. discussed  network and pathway data visualization
     76 * Discussed  network and pathway data visualization
    7777  * i) low resolution  (PPI data)
    7878  * ii)  medium resolution  (summarising GO data)- separate project?
     
    8989    b) Ability to sort data on all columns (terms alleles etc)
    9090
    91   AI Val to a) document b) make mock ups b) ask for community feedback on proposal
     91  AI Re gene page revisions to deal with increasng page length Val to a) document b) make mock ups b) ask for community feedback on proposal
    9292 
    93  * 8. Curators, mockup of graphical display of modifications and mutations in sequence context
    94 
     93 * Curators, mockup of graphical display of modifications and mutations in sequence context
    9594    * Paul showed us the Ensembl variation display which will largely do the trick.
    9695    * We would additionally like to be able to  filter display for specific phenotypes of interest
     
    104103  * Jurg's polyA data https://www.ebi.ac.uk/panda/jira/browse/PB-1513
    105104  * Nick Rhind transcriptome https://www.ebi.ac.uk/panda/jira/browse/PB-1707
    106 
    107105    * All of these datasets are in progress.
    108106       * AI Problem with Paco's data.  Mark to contact Paco/Luis/Ignacio