Minutes and Actions

Coordinating datasets for public release

The current difficulty relating PomBase? to EG release relates to the display of GO terms (BioMart? does not allow attachment of GO terms to 2 places i.e. transcript for RNA and protein) fix is in progress

Call for HTP data

Very little response to first pombelist call for submissions, Curators will send out another call when preview is removed. Primary datasets (based on user queries) to see on tracks, are transcriptome and include Jurg's published Solexa (transcriptome) data (in Array express), and the Broad RNA seq data (accession numbers in jira

  • AI Jurg/Curators? dig out the Array Express accession numbers for PMID:18488015
  • AI Mark to add these datasets as tracks

Usage stats

  • AI Val Find out if GeneDB stats record "number of visits" or "unique visitors", get both DONE


  • AI Val/EBI Pass on Conrad Nieduszynski's details to Mark/Paul/Dan? to contact him how best to host data as a track with links into OriDB DONE
  • AI EBI to contact Conrad


Curators have a new procedures in place for answering helpdesk queries and building FAQ. Antonia will assign queries as appropriate and compile responses for Midori to include in FAQ

  • AI All helpdesk personnel. Ensure that user queries answers ASAP, or that users are given an estimate of when their query will be resolved, if possible

Curation tool subdomain

  • AI Kim provide what is needed to EBI DONE
  • AI EBI Action subdomain

Intermittent speed issues

  • AI Curators let EBI know when speed issues arise (Mail Mark directly not through jira)
  • AI Antonia ask Jurg group to report speed issues directly to Mark with details of page/time
  • AI EBI to action selenium testing and check server is sufficiently powered

Difficulty locating configurable tracks, and zoom in browser

This was discussed earlier this week by Mark and curators solution discussed was to change link in to Genome browser to location tab (which has zoom options)

Focused User testing (action items from Paul)

  • AI Midori/Antonia? to propose suggested use cases for discussion (preferably after seeing templates). Use usability issues/use cases reported by users from agenda of 26th Jan as test cases
  • AI Mark to meet with Jenny to discuss use case templates ASAP
  • AI Midori Trial user to be identified for testing the test in Cambridge (in February?)
  • AI Midori/Antonia? 2 dates in March (from Jenny's list of 4) to be agreed for user testing in London (and Cambridge?) - we should try and fix these dates ASAP.  We are looking for a total of 8 users in total, we need ~1 hour of each of their time.

Search issues (Query builder)

Most issues discussed stem from BioMart? not handling our use cases. Fixes are in progress to make the query builder functional for PomBase?

Long term it may be that InfoBrite? provides better functionality?

Blast related

Discussion of Blast issues. Some which are related to output format and usability are general issues which have been raised before and should be fixed for Ensembl generally in the medium term (Note that the Blast formatting issues are not major and some simple fixes like making the raw results more prominent would be very helpful-> add to user testing list)

PomBase? specific items which are specific to this configuration should be addressed:

  • AI Mark/Dan? Difficult to link back to genomic regions with output provided

Results look like this instead of protein product: EG:SPBC14C8.07c.1:pep pep:known chromosome:EF1:II:2215955... 2976 0. 1 see

  • AI Mark Add a link from the protein section of the gene page to a PSI Blast (currently we link to NCBI from PomBase?, but any is OK)

Moving from preview

  • AI Midori raise priority items which result in wrong results to "blocker" as a classification for preview removal, anything which can wait for GeneDB decommissioning can be "critical"
  • AI Val Update notice on GeneDB website to match current status DONE

Better integration between "PomBase?" and "Pombase Ensembl"

Specifically discussed helpdesk contact/ Help/search:

Linking between browser and gene page

  • AI EBI
    • i) provide a "button" to link to Ensembl from Gene pages and vice versa
    • ii) reduce number of linked up/downstream genes
    • iii) place link to Ensembl browser underneath the gene list

Next meeting dates

Technical call is now cancelled, replaced by monthly meetings

  • AI Val meeting changes.venue changes, doodles
Last modified 10 years ago Last modified on Jan 30, 2012, 12:10:17 PM