Version 10 (modified by al637, 6 years ago) (diff)


PomBase Planning Meeting 17 Oct 2014

Cambridge - Meeting Room * * Building

Action item review

Outstanding action items carried forward from previous meeting

  • Speak to Eugene to group tracks (aka track hub) (Mark) (Q is there an Ensembl jira ticket for this?)
  • Multiple alignments from Compara Check that i) gap squashing and or ii) dynamic alignment generation for subsets of protein in progress (EG, Q check is there a jira ticket for this)

  • AI: (speed issues) Check progress of trackhub for PomBase?? (EG) (jira ticket?)
  • AI: report onto perl bug synonym type not included (who?) - Reported to Ensembl for fixing.

Action items from

  • AI Val or Mark contact Paco
  • AI check Wilhelm track descriptions are OK Circulate Wilhelm and Marguerat data to Jurg, Sam and Brian for feedback, are all tracks useful? Sam’s data: this is only bigwigs, would bam be useful? Still need track descriptions(Mark/curators)
  • EBI set up dummy confluence (not required, have trac)
  • Mark to draft and circulate an outline of NAR paper contents before the next planning meeting (done & dusted)
  • Ensembl will make annotations propagate over regulates for biological process (follow up: we will need to remove associated text for doing both queries from the Query builder, and update the FAQs)
  • Paul will ensure that that the Ensembl browser developers get the PomBase?? suggestions before the browser overhaul
  • Compact display
  • exporting GO and FYPO data in EMBl /Genbank files
  • Timely answering of helpdesk queries

New (and continuing) Agenda items

  • Document update procedure and time taken (Mark) Done on Confluence (Q how long is this?)

  • EsyN description, input data, linkouts from PomBase?

Hosting high throughput datasets

  • None pending at high priority

Display of new data types

Phenotyping of wild strains, how to display these?

From Dan:

Here is what think might be interesting/useful to represent.

The three main ones are:

  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.
  2. Tf1 transposons that are variable between strains as well. Could also be supplied in VCF.
  3. Variation wiggle tracks (like pi, which is the average pairwise differences, for example).

Also: 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. I 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).

I'd be very happy to come along & help/chat about getting this data into pombase.

Priority Jira tickets

  • I have cleared out some of the smaller tickets to V 48, but if they are quick they can be done and closed. 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.
  • Follow up on the items for Ensembl, are they all raised and in progress?


Usage stats



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
All publications 9755 9761 9773 9989 10356 10400 10522
Curatable publications 4735 4740 4780 4896 5017 5070 4873
Publications with Approved sessions 580 600 647 712 1083 1187 1598
Publications with active sessions 245 247 265 246 220 246 225
Publications with session needing approval 14 4 4 18 6 11 19
community curatable publications - - - 351 526 613 733
community curated publications with approved sessions - - - 58 159 178 207
curatable publications without sessions - - - 3730 3256 3177 2518
  • numvers of annotatable papers have dropped due to retriage and classification of some papers that are probably of low value for curation.

All annotation types


Next priorities



News and Outreach

Next planning meeting