Version 90 (modified by val_wood, 9 years ago) (diff)



Completed action items

  • DONE AI Jurg/Curators? dig out the ArrayExpress accession numbers for PMID:18488015
  • DONE AI EBI Action subdomain, now in use
  • Midori has forwarded around the minutes from when this was discussed for having PomBase Ver. x.y where x is the EG release and y is the Chado dump version number.
    • DONE Speed of the PomBase portal
      • DONE Currently it is still being hosted via the Hinxton servers due to testing in London. Dan and Mark are currently in discussions with the ES team about using PomBase as the test site for moving to London.

Not done, but logged in jira

Outstanding Action items from May

  • Ask Henning Hermjakob about possibility of OLS as webservice to attach annotations to, we will have the next planning meeting at Hinxton and see if Henning can join us for a while.
    • AI EBI to contact Conrad (Arnaud has looked into this and we could potentially load these as a BAM file). (tranfer this to jira item)
    • AI EBI to action selenium testing and check server is sufficiently powered
    • AI Mark/Dan? Difficult to link back to genomic regions with output provided
      • Mark will provide some examples for the next meeting
    • AI Mark - EG Browser and the customisation to make it feel more friendly and to aid in the linking between the Drupal and ensembl services (this seems to be same action item as above)
    • AI EBI Linking between browser and gene page
      • provide a "button" to link to Ensembl from Gene pages and vice versa
      • reduce number of linked up/downstream genes
      • place link to Ensembl browser underneath the gene list (NOTE, THIS IS STILL NOT CLEAR BUT WILL PROBABLY BE DISCUSSED IN FEEDBACK FROM USER TESTING?)
    • AI Currently PK is looking into the interaction between ES and and PomBase. ( Re Long term will *everything* still need to go through External Services?)


Have not done stats updates as will need to redo at month end:

  • Hosting data on tracks (e.g Buck example) .... what is the plan for hosting these types of datasets? Was there an action item here?
  • Item from Mark determine the functionality of the dev site going forward.

Curation update (Val)

  • Skipped, will do update for next meeting

Focused User testing

Mark - outcomes from user testing

Q did all issues get logged (didn't get follow up from 2nd part)

Review "post-preview" and "GeneDB decommissioning" criteria & progress

Preview removal

Discuss preview removal, see email from earlier in week with new propsed priorites, discuss

  • Update notice about preview removal on GeneDB website
  • Inform users of changes/ pending changes (like, new annotation will only go into PomBase)
  • Explain differences in GO totals (later)

Discuss items required for GeneDB decommissioning

  • Will do this next meeting

Other jira items

Current jira status:

  • Open 125 Closed 577 (was 200/511 last meeting)

Usability issues/ issues reported by users (anyone? any not covered above?)

Meetings Attended/ Upcoming

  • proposed Workshop for 2103 (International meeting) straw poll?
  • Proposed Pombase 1-2 hour workshop at CRUK, with 1-2 hour curation tool demo and or jamboree (to precede EMBO)
  • EMBO course (Val teaching) July
  • Others ? (Steve mentioned a yeast meeting but not minuted?)


  • Next meeting (doodle)

PIs meeting (10 minutes)

Postpone until next inperson?

Lower priority /Later?


Browsing Ontologies

  • AmiGO2 demo
    • Need to contact Chris and Seth to make sure stable URL for meeting

Notes: AmiGO2 is generic and can support other ontologies. To get the cool axial, drill down search/filtering working it involved the use of Solr indexes? which need to be built but Chris says it should be relatively straightforward to implement. This should fulfill our requirements which are not met by other available tools (i.e the ability to provide links to gene product at different levels of the heirarchy). It also handles x-products.....

I'll put this for discussion, demo at a future planning meeting. (QuickGO issues include: different gene product names)