Changes between Version 5 and Version 6 of PombasePlanningMeetingMinutes20141017


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Timestamp:
Oct 17, 2014, 5:49:16 PM (6 years ago)
Author:
vw253
Comment:

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  • PombasePlanningMeetingMinutes20141017

    v5 v6  
    44 * AI  Val contact Paco
    55
    6 
    7 
    8 What is the status of track-hub?
     6==== What is the status of track-hub? ====
     7What is the status of track-hub, for "collecting" experiments?
    98This will not happen in the near future,  will be done at some point in the future by Ensembl
    109 * AI  Create  jira ticket to ensure this is working correctly when it happens
    1110
    12 
    13 
    14 What is the status of  on the fly multiple alignments from Compara (for gap squashing etc)
     11==== Status of  multiple alignments from Compara  ====
     12What is the status of  on the fly multiple alignments from Compara (for gap squashing etc)
    1513 * AI Create jira ticket for PomBase curators to ensure this is working correctly when it comes through to PomBase
    1614
    17 
    18 
    19 What is the status of storing ontology synonym scope in Ensembl
     15==== Storing ontology synonym scope in Ensembl ====
     16Q What is the status of storing ontology synonym scope in Ensembl?
    2017 * AI Mark will find out the details of the Bio-perl module that is used
    2118 * AI Val will contact author to see if synonym scope can be included
     
    2320
    2421
    25 
    26 What is the status of Sam's data
    27  * AI  Ask Sam for feedback, Jurg will follow up with Sam
     22==== Status of Sam's data ====
     23 * AI  Ask Sam for feedback, Jurg will follow up with Sam (Sam will provide revised data)
    2824
    2925
    30 
    31 What is the status of ensuring that Ensembl  ensuring that annotations are transitive over the "regulates" relationship for biological process?
     26====  Transitivty over the "regulates" relationship for GO BP ====
     27What is the status of  Ensembl  ensuring that annotations are transitive over the "regulates" relationship for biological process?
    3228 * AI Somebody (who?) will create a ticket (where?). We will also need a PomBase jira tracker ticket for this to list the changes which will need to happen PomBase side when this is in place (mainly  test on query builder and documentation)
    3329Discussion- if Ensembl do this in a generic/modular way it will also provide a solution for
     
    3531but this might not be possible....
    3632
     33==== PomBase browser suggestions ====
     34  * AI Paul will ensure that  PomBase browser suggestions are  forwarded to the new point person before browser overhaul begins
     35
     36==== Exporting FYPO and GO IDs in GenBank and  EMBL export files ====
     37  * AI Dan will remove the PomBase IDs from this file
     38
     39==== Centromere features ====
     40Can centromere features be visible in the "detail view"
     41 * AI  Mark will create jira ticket
    3742
    3843
    39 PomBase browser suggestions
    40  * AI Paul will ensure that  PomBase browser suggestions are  forwarded to the new point person before browser overhaul begins
    41 
    42 Exporting FYPO and GO IDs in GenBank and  EMBL export files
    43  * AI Dan will remove the PomBase IDs from this file
    44 
    45 
    46 
    47 Can centromere features be visible in the "detail view"
    48 AI  Mark will create jira ticket
    49 
    50 
     44==== PomBase build time ====
    5145Q How long is a  PomBase build taking from start to finish
    5246A Approximately 2-3 days. It takes about 0.5 days of  Mark's time
    5347
    5448
     49==== Combining  experimental tracks for repeats in the  browser track displays ====
    5550Q Should we be combining  experimental tracks for repeats in the  browser track displays
    5651A. General consensus was yes. Users will be able to refer to publications for details of how the tracks were combined. Only change to track labelling will be to add "combined" or "consensus"
    57 AI Midori  Update any of the submission documentation http://www.pombase.org/submit-data/data-submission-form, and the wiki page which details track descriptions http://curation.pombase.org/pombase-trac/wiki/TrackRelabelling (note: I don't know if this is the right page, its the only one I could find)
     52 * AI Midori  Update any of the submission documentation http://www.pombase.org/submit-data/data-submission-form, and the wiki page which details track descriptions http://curation.pombase.org/pombase-trac/wiki/TrackRelabelling (note: I don't know if this is the right page, its the only one I could find)
    5853
    5954
    60 EsyN, Val described that  various link outs will be needed from the "GO slim" and the physical and genetic interaction sections of the gene pages.
    61 AI Val will open a jira ticket once the teething problems are overcome and the URLs are available ( I will circulate for feedback first).
     55==== EsyN ====
     56
     57Val described that  various link outs will be needed from the "GO slim" and the physical and genetic interaction sections of the gene pages.
     58  * AI Val will open a jira ticket once the teething problems are overcome and the URLs are available ( I will circulate for feedback first).
    6259
    6360
    64 New high-throughput data, upcoming dataset from Runge lab
     61==== New high-throughput data ====
     62Upcoming dataset from Runge lab
    6563 * AI Mark will contact authors with ftp upload details and check file formats
    6664
    6765
    68 Discussion about display of variation and phenotypes for 50+ wild strians in Ensembl.
     66==== Discussion about display of variation and phenotypes ====
     67Data  for 50+ wild strians in Ensembl.
    6968 * AI  EG are keen to host this. Dan Jeffares will submit data.
    7069
    71 
     70====Campact view for FYPO & GO ====
    7271We spent some time going through Marks mockups of the compact view for phenotypes and GO.
    7372 * AI. Mark to make additional mockups based on discussion outcome