Tuesday 1 May, 3 pm, EBI A-201

Action items carried forward from before March

  • Follow up desktop sharing software (circulate possibilities, do free trial?) (Midori)
  • 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.

Action items from March

  • AI Jurg/Curators? dig out the ArrayExpress accession numbers for PMID:18488015
    • AI Mark to add these datasets as tracks
  • AI EBI to contact Conrad
    • Arnaud has looked into this and we could potentially load these as a BAM file.
  • AI EBI Action subdomain
    • This is currently active
  • AI EBI to action selenium testing and check server is sufficiently powered
  • AI Mark/Dan? Check that all sequence features are available consistently on location and gene tabs See
    • This is a web-data issue.
  • AI Mark/Dan? Difficult to link back to genomic regions with output provided
    • Will provide some examples for the next meeting
  • 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)
    • This is a long term issue.
  • AI EBI provide a version of Ensembl help
  • 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.
  • Speed of the PomBase portal
    • 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.
    • The reason for the push is that the only difference between Mark's box and the servers at Hinxton is the version of PHP (mine: 5.3; Hx 5.2). Between the releases of 5.2 to 5.3 there have been major changes to the handling of garbage collection and memory management, so moving to the London servers that are using 5.3 might resolve this issue. This should solve the problem, but it is not a guarantee.
  • 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.
  • Long term will *everything* still need to go through External Services?
    • AI Currently PK is looking into the interaction between ES and and PomBase.


  • ftp site migration (see e-mail to PomBase internal)
    • Val is generating a list of files (or tarring them up) ready for transfer (tie this in with discussion about download file options made available, later)
  • Hosting data on tracks (e.g Buck example) .... what is the plan for hosting these types of datasets?
  • Improving communication between curators and programmers - what do we need to do to ensure that curators stay informed of progress (or when to expect slow progress) with the website or data updates?

GO Regulation Issue

Notes from last minutes:

  • Closure tables
    • Careful consideration needs to be made as to the logic behind the querying over closure tables.
    • Potentially can look into having 2 tables and having 2 numbers on the web site, but more thought needs to be placed into the implementation.
  • Sortable tables
    • For some this is already done
  • Loading of the VCF files
    • Potentially Chonkee could do this

Ongoing discussion with GO how to resolve this more generally

Curation update (Val)

  • brief update on curation tool, triage, curation
  • Helpdesk 347 (+38) resolved tickets/ 20 open (+11)
  • Chado 47 (+4) resolved / 32 (+9) open [Chado]
  • One-off Curation tasks 86 (+4) open / 38 closed (+2) [Curation tasks]
  • Curation tool development 60 (+13) open / 101 (+19) closed [Curation Tool]
  • Documentation 9 open / 2 closed (No change)
  • Phenotype ontology 37 (+5) open/ 142 (+49) closed [Phenotype]
  • GO annotation issues 46 open (-1) / 21 closed (+6)
    • plus 10 submitted to GO tracker (1796 total history)
  • Sequence analysis 25 open (-1) / 13 closed (+1)
  • Triage
    • 8108 /9378 triaged
    • 3865 /8108 (Curatable information)
    • 449 Curatable publicatiosn with curation sessions
    • 173 Curation sessions approved
    • 3 Community curatable

Focused User testing

Mark - outcomes from user testing

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

Preview removal (Mark)

  • Update on speed issues, causes and work-arounds
    • move to London, expected speed up, sis this happen yet?
    • speed of initial page being returned
    • speed of complete page loading, especially of references which sometimes appear to never completely load (A few more users have reported ongoing speed issues, what needs to happen next?)
  • Data issues - Should all be resolved by BioMart update (and a few more minor issues by next Chado reload)
    • update on process
  • Any other items critical for preview removal?
    • 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

Discuss items required for GeneDB decommissioning

  • Raise priority of items for GeneDB commissioning

Other jira items (Val or Midori)

Current jira status:

  • Open 200 (170 reported, 5 reopened, 25 resolved)
  • Closed 511

There are a number of jira items relating to relatively small changes

These are not "critical" but they all look as though they would be very quick to fix, would improve useability, satisfy user requests. Post-preview could Mark dedicate a day trying to clear out a lot of these more trivial items which are cluttering up the tracker?

Aesthetics of the gene page (Val)

A few suggestions about spacing, which it would be useful to discuss with the group and implement if agreed. Include, but not limited to:

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

Annotation extensions

A number of outstanding jira items are related to annotation extension display. This is very nearly ready, but is only on dev because it needs a number of minor tweaks before it is publicly released. Once the data comes through from the curation tool, these will be very highly used and without them information will seem duplicated redundant on the page. It might be useful if there is time to go through these issues (we curators can easily do this with Mark after the meeting). I plan to talk about the extensions at a departmental meeting on 18th May and it would be useful to be abl)e to demonstrate real examples on the gene pages. (add examples, rpb10,ace2,cdc2, others in jira tracker

Download options

This should probably also be an off line discussion with Mark. Need to make sure we

  • i) cover static files generated by GeneDB
  • ii) Files which can be generated by the current GeneDB download (so this item partially overlaps with GeneDB commissioning)

Meetings Attended/ Upcoming

  • Biocurator meeting (April) - Antonia presented (2 posters: phenotype and community curation; platform talk on curation tool and community curation)
  • 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?)


  • Any other updates, e.g.
    • variation data hosting
    • synteny vies for S. octosporus and S. japonicus (propose that these stay on hold until we hear that the final assemblies are submitted. should I ask Nick again?
  • Next meeting at UCL, Thurs. 24 May, 3:30 pm (room TBD)

PIs meeting (10 minutes)

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)

Last modified 8 years ago Last modified on May 2, 2012, 10:43:06 AM