Pombase Planning Meeting 29 May 2013

EBI - room? 2-4 pm

Action item review

Outstanding action items from April

  • AI: Document version naming for gene model and annotation updates (Mark)
  • AI: User documentation on version naming for website, should be 'generatable' from Marks documentation (Midori)
  • AI: Automatic updates for the FTP site; script-as-you-go-along with the updates (Mark)
  • AI: Block scary error messages on www from user’s view (Mark).
  • AI: Take a look at the biogrid interaction data and see if some human-friendly text-linkages that imply directionality can be made between interactor A and B (Mark)
  • AI: Curators and Kim to record curation stats. Should separate staff & community.
  • AI: Curators to ask community for pictures to rotate on the front page.
  • AI: Curators to flesh out what to do at the Tuesday lunch-time community curation demo and Thursday lunchtime PomBase? demo at Pombe13
  • Mark to work on automated release pipeline with regression testing. Plan is to have a pipeline ready for the next meeting (Mark - In Progress, see minutes). .
  • Mark to sort out GO slim count anomalies (see PB-1208)
  • Remove ':pep' from identifiers in cDNA FASTA file (Mark or Dan)
  • Find out why Chado uses :pep notation (Val)
  • Mark will do general PomBase poster for Pombe 2013 (especially since old one didn't survive Biocuration 2013 ...)
  • Midori to look into beer mugs and T-shirts (in progress)
  • Organise a large general "PomBase" banner – sort out with people downstairs in Biochem. Go for a long skinny one with PomBase? logo and same color and yeast images as on PomBase? banner (Midori)
  • Curators to draw up a script for the curation video. What steps do we want to show on the video? Discuss at next curator meeting.

Postponed action items

  • Demo of curation tool (postponed)
  • Val/curators will start to send out a large number of community curation sessions (postponed until new session management and documentation is in place. Will continue to send out small numbers of papers) - getting close
  • Mark to liaise with Giulietta to help with making a Pombe community curation video.
  • Dan and Mark to see what files downloadable from PomBase have previously been generated by ensembl. These should be easy to create automatic updates for (In progress?)

New issues


  • ENA linking
  • Juan and Jurg's poly A data. When ready, where do we put it?

And can we get a list of formats for each datatype? "File formats and repositories for HTP data" which unfortunately slipped from the action items.

  • front page news ( keeping it current, could discuss with jira tracker issues below0
  • Configuring the browser and then cookies being reset
  • Kim will summarize a plan to make artemis jave applet available as from GeneDB
  • tag line S resource -> the resource. Confim. jira ticket (what needs to be updated except the header)?
  • ncRNAs and other genomic features in GFF/GTF (Sameet query today)

pombe 2013

  • flier (for conference bags) content, twitter etc
    • #pombe2013 will be the conference hashtag

(Mark you should announce the existence of the twitter account on the mailing list at some point prior to the meeting, and add a link from pombase, we should decide where to put this)

  • banner
  • freebies (dynamo keyfob)
  • demos

Monday 24th June 17.30 -19.30 Welcome reception and PomBase? community curation launch party The PomBase? group will be at a table/stand with the PomBase? banner, signing people up to curate their papers

Tuesday 25th 12.25-1.15 Community Curation Demo Antonia - demo of the interface Midori - some specific examples (normal/ abnormal; cell vs population, differences between phenotypes and GO biological process annotations (direct/indirect), localization dependency etc)

Thursday 27th 12.25-1.15 PomBase? Demo Val - Gene Page walkthrough highlighting features and Advanced search/ List upload feature Mark- Ensembl browser demo (specifically configuring tracks (explain different views and how zoom browse works) and sequence region download, compara, anything else)

(These timings allow people free time before to pick up lunch, and 15 mins. before the conference sessions start again, but we will be able to use this time to answer specific questions if required)

  • posters (need numbers for flier)
  • It would be really useful if an Ensembl developer could come to the Pombase lunchtime session at pombe 2013 and listen to the users who are complaining about the browser.

Update cycle

  • Update cycle appears to be working well. Discuss update prior to pombe 2013 (could delay a little to fit in the changes)


  • Now showing v33 (7th March; 535 fully curated publications)
  • Chado load done for v34; live yet?
  • Data ready for Kim to do v35 chado load
  • Need ftp site update ASAP after v34 live (even if some has to be done manually)
  • Add Jira fix-versions for next couple chado releases
  • MArk to explain and ontology updating PB-1317

Usage stats

GeneDB decommissioned on 14th May. Large increase in users and page accesses


??? see minutes


  • Can we decouple static Drupal page updates (dev --> www) from data updates, so the former don't get delayed if there are problems with the latter? (PB-1270 done, for which thanks; but what about the general case in future?)

what was the response to this? I though this was already possible?

  • ETA/effort estimate for reciprocal interaction annotations (PB-873)?

Should we put this as an action item to follow up next time?

  • Need ftp site update ASAP after v34 live (even if some has to be done manually)

Must be done after 34. For the files that are in the same directory, they can be copied over easily, but I haven’t scripted it yet (mark). Script as you go along with updates (dan). A lot of the outstanding stuff on jira has to do with various things where a version exists but needs updating. Some things are not offered yet by FTP but we want them (midori).

Other general issues

  • transcript type of TR box Mark: I have to add it to a list of features to define which side of the fence they fall, either gene/transcript/translation or if they are simple features, or they are something else that is used else where but does not need to be considered as a gene/simple feature, for example Chromsomes are treated as a special case.
    • This sounds as though it could be easily automated
      • note promoter should be part of gene, not transcript
  • Browser issues and general bad user feedback
    • artemis java applet option easily designing experimental constructs (evaluating crosses, designing primers, targeted mutation etc) etc.




  • Literature (triage) status
    • Nb Midori on leave - more sessions near needing approval/approved status pending fypo terms..
ItemMarch meetingApril meeting May meeting
All publications975597619773
Un-triaged publications042
Curatable publications47354740 4780
Publications with Approved sessions580600 647
Publications with active sessions245247 265
Publications with session needing approval144 4
  • Canto annotations (from 2013-04-26)
nameMarch countApril countMay count
PomBase annotation extension terms144816051651

All annotation types

EC numbers839
PomBase family or domain1873
PomBase gene characterisation status5143
PomBase gene products7018
PomBase annotation extension terms32484

Phenotype ontology

  • #### terms


  • (phenotype date for S for v36...if done)


  • email templates (invitation to curate, session reassignment, etc.) troubleshooting

Next priorities

This is basically same list as from the last meeting, except removed one closed ticket and moved a few of the less urgent download data related changes to Chado future:

  • v35 tickets with high priority for pombe2013



  • Pombe 2013
    • 13 May curator meeting + curator/programmer conf call devoted to planning our activities, esp. lunchtime demos, tutorials, etc.
    • ideally would like Canto tutorial video ready

Next planning meeting

have date, ucl add


Last modified 7 years ago Last modified on May 29, 2013, 9:20:05 AM