PomBase Planning Meeting 13 March 2015


Action item review

Outstanding action items carried forward from previous meeting

Action items from

New (and continuing) Agenda items

  • Versioning....
    • (need Mark's help to get this file up to date)
    • 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 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.
    • 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.
    • How does someone get from Schizosaccharomyces_pombe.ASM294v2.25 to know which gene build?
      • i.e where is the historical data about the on the Ensembl site about the gene build that was used in a specific release?
    • figuring the numbering of releases before 32 ( I think maybe we just used a data stamp for these?)
    • It seems that .25 is <eg_version>
    • The gff file should be renamed to capture
    • PomBase? sequence assembly version
    • gene build version
    • annotation version

  • Has the new Ensembl Web-person 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)
  • Compact display progress and outstanding
  • exporting GO and FYPO data in EMBl /Genbank files
  • Document update procedure and time taken (Mark) Done on Confluence (Q how long is this?)

  • EsyN update
  • Display of wild strains, see previous minutes
    • Dan Jefferes paper on genomic and phenotypic diversity is now published.
    • Dan will provide an example of what could be displayed on the PomBase? gene pages.
    • EG to update us on what progress displaying the variation data
      • Need to discuss what we can feasibly display in the light of the volume and scope of the data
      • should we just attach the phenotype trait data to the SNP?
  • Do Ensembl have any plans how to handle chromosome interaction data
    • We had a little discussion about this and Mark suggested
      • In the supplementary file there is an image of the all against all for the likelihood of interaction. It would be possible to have a track that would be a frequency of interaction (irrespective of target), which could be displayed as a gradient track. Then have 3 tracks for each phase of the cell cycle that they analysed
      • Your other option would be a custom display on the PomBase? site using a chord style diagram for regions using colour and thickness to represent the frequency of interaction between 2 positions (eg Chr1:X0-X1==Chr1:Y0-Y1 or Chr1:A0-A1==Chr2:B0-B1). Then have a representation for each phase measured. This would have the advantage of representing a flattened 3D structure and act to give context to the user.
  • Discuss what people think of making "review" versions of curated sessions accessible from literature section ? useful or not?
    • Curation attribution
    • Can flag if a paper is curated or not
    • Raises visibility of what a 'curation session' looks like
    • Can see all annotation from a paper simultaneously

  • When will usage stats be back?
    • IS it possible to provide a list of most frequently accessed pages?

Hosting high throughput datasets

  • None pending at high priority
    • Carr lab replication origins
    • Gx data (postponed waiting for user0
    • Runge lab, pending (transposon insertions?)

Next Priority Jira tickets

  • 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).
  • 2. Query builder related tickets especially to handle GO annotation extensions, phenotype conditions and alleles, multi gene phenotypes and sequence features.
    • Curators need to discuss, and then with Kim and Mark, should have done this before meeting
  • 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).
  • 4. Other tickets related to the term suggestion behaviour.
  • Then tickets in Chado future 3 which appear to be stalled


Usage stats

  • Is it possible to get lists of the most frequently accessed gene pages?



Phenotype ontology


  • Kim is finalising multi gene phenotypes (and their storage in Canto), many annotation transfer speed ups.
    • 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.

Other general issues



Update on community curation

Literature (triage) status

Item March 2013 April 2013 May 2013 Aug 2013 May7 2014 July 23 2014 Oct 2014 March 2015
All publications 9755 9761 9773 9989 10356 10400 10522 10693
Curatable publications 4735 4740 4780 4896 5017 5070 4873 4974
Publications with Approved sessions 580 600 647 712 1083 1187 1598 1983
Publications with active sessions 245 247 265 246 220 246 225 146
Publications with session needing approval 14 4 4 18 6 11 19 4
community curatable publications - - - 351 526 613 733 859
community curated publications with approved sessions - - - 58 159 178 207 253
curatable publications without sessions - - - 3730 3256 3177 2518 2413
  • numbers of annotatable papers have dropped due to re-triage and classification of some papers that are probably of low value for curation.

All annotation types

172764 increased from 170515 in Oct

Next priorities



News and Outreach

Next planning meeting


Last modified 6 years ago Last modified on Mar 11, 2015, 3:51:48 PM