Changes between Initial Version and Version 1 of PombasePlanningMeetingAgenda201402


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Timestamp:
Jan 13, 2015, 6:47:33 PM (7 years ago)
Author:
vw253
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  • PombasePlanningMeetingAgenda201402

    v1 v1  
     1
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     3= !PomBase Planning Meeting ?? Feb 2015 =
     4
     5  ?????
     6
     7= Action item review =
     8
     9 == Outstanding action items carried forward from previous meeting  ==
     10
     11 
     12 == Action items from **** ==
     13 
     14 
     15 
     16= New (and continuing) Agenda items =
     17
     18  *  Has the new person been appointed? Is the browser overhaul in progress? (Re Paul will ensure that that the Ensembl browser developers get the PomBase? suggestions before the browser overhaul)
     19
     20  *  Compact display progess and outstanding
     21
     22  * exporting GO and FYPO data in EMBl /Genbank files
     23
     24  * I still don't see the centromere feature, what was the outcome of this Q? check minutes
     25     Centromere feature is not visible on region in detail view. Do we think it should be?
     26     http://genomebrowser.pombase.org/Schizosaccharomyces_pombe/Location/View?r=I:3735820-3807289;site=ensemblunit
     27
     28   * Document update procedure and time taken (Mark) Done on Confluence (Q how long is this?)
     29
     30   * https://www.ebi.ac.uk/panda/jira/browse/PB-1802  is it best to combine repeats, and ask for average datasets?
     31 
     32   * EsyN  update
     33
     34   
     35 == Hosting high throughput datasets ==
     36
     37 * None pending at high priority
     38
     39== Display of new data types ==
     40Phenotyping of wild strains, how to display these?
     41
     42From Dan:
     43 Here is what  think might be interesting/useful to represent.
     44
     45The three main ones are:
     46
     471. 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.
     482. Tf1 transposons that are variable between strains as well. Could also be supplied in VCF.
     493. Variation wiggle tracks (like pi, which is the average pairwise differences, for example).
     50
     51Also:
     52Some 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.
     53I am not sure how much of this data gets displayed in gene pages. If its des 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
     55I'd be very happy to come along & help/chat about getting this data into pombase.
     56
     57
     58 == Priority Jira tickets ==
     59
     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.
     62
     63    * Follow up on the items for Ensembl, are they all raised and in progress?
     64   
     65 == Chado ==
     66 
     67    * priority ticket https://sourceforge.net/p/pombase/chado/390/
     68
     69 == Usage stats ==
     70
     71 http://tinyurl.com/7qs2zap
     72
     73 == Versioning ==
     74 
     75
     76 == Website ==
     77
     78
     79 == Phenotype ontology ==
     80
     81 == Canto ==
     82
     83   * Kim is finalising multi gene phenotypes (and their storage in Canto), many annotation transfer speed ups.
     84    * We have a large volume of multi gene phenotype data ready to input so this will be the issues to tackle immediately after the compact display. There are related tickets already for how this should look on the gene pages.
     85
     86
     87 == Other general issues ==
     88
     89
     90 == Helpdesk ==
     91
     92 == Curation ==
     93
     94 === Update on community curation ===
     95
     96 ===  Literature (triage) status ===
     97 
     98||Item || March 2013 || April 2013 || May 2013 || Aug 2013 || May7 2014 || July 23 2014|| Oct 2014 ||
     99||All publications || 9755 || 9761 || 9773 || 9989 || 10356 || 10400 || 10522 ||
     100||Curatable publications || 4735 || 4740 || 4780 || 4896 || 5017 || 5070|| 4873 ||
     101||Publications with Approved sessions || 580 || 600 || 647 || 712 || 1083 ||1187 || 1598 ||
     102||Publications with active sessions || 245 || 247 || 265 || 246 || 220 || 246 ||  225 ||
     103||Publications with session needing approval || 14 || 4 || 4 || 18 || 6 || 11 || 19 ||
     104||community curatable publications  || -  || - || - || 351 || 526|| 613 || 733 ||
     105||community curated publications with approved sessions || -  || - || - || 58 || 159 || 178 || 207 ||
     106||curatable publications without sessions  || - || -|| - || 3730 || 3256 || 3177 ||  2518 ||
     107
     108
     109 * numvers of annotatable papers have dropped due to retriage and classification of some papers that  are probably of low value for curation.
     110
     111 === All annotation types ===
     112 170515
     113
     114
     115== Next priorities ==
     116
     117
     118== Publications ==
     119
     120== Meetings ==
     121
     122== News and Outreach ==
     123
     124== Next planning meeting ==
     125
     126= AOB =
     127