Action items from technical meeting

Incomplete actions from technical meetings are included with new issues below

Action items carried forward from 3rd October planning meeting

  • Need to coordinate dataset for regular public release with Ensembl genomes release cycle after the preview (Kim/Mark/Dan?)
  • FYPO will be submitted to OBO foundry shortly which should trickle through to OLS in due course (Midori)


  • Ensembl group tell us which format specification for various HTP datasets. Val will draft an announcement to be approved by Paul/Mark/Dan?


  • Load external GO data into Chado as a priority (Kim)
    • GO data is now loaded, but filters are not implemented (complicated by annotation extensions. Kim will prioritise this when he starts back in October)

DONE and filters implemented, waiting for data to filter through to check but sounds promising based on numbers

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

Carried Forward

  • 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.

Carried Forward


  • pombelist posting from Bioneer (val)
  • OriDB (val) From Conrad Nieduszynski: The database is SQL based. There is a low tech browser as part of OriDB and all of the data is available for users to either download or to visualise in genome browsers as custom tracks. Let's look at how to share the data. (Conrad has evaluated the origin datasets and classified origins)
  • RT: Curators have agreed on a procedure for handling helpdesk queries (brief report) (Val)
    • Outline procedure/ immediate response
  • FAQ: Drupal module now deployed. Common helpdesk queries will generate FAQ entries as needed. (Midori)
  • curation tool sub domain (Kim) (AI from 1st October, notes Mark hasn't heard anything yet. Needs input from Paul, and probably will involve EBI External Services)
  • Intermittent speed issues (as reported by Robin Allshire (Midori)
  • Any progress on setting up focused user testing? (AI from 1st Oct)

Review "post-preview" criteria & progress

Search issues


Blast related

Misc Data problems (wrong/missing data)

Unlikely to discuss any of these in detail, just wanted to flag them

Tasks before GeneDB decommissioned

Ensembl related

Blast related

Misc Data problems (wrong/missing data)

Unlikely to discuss any of these in detail, just wanted to flag them, there may be a few other items but these seem fairly straightforward.

Things which are not crucial for preview removal, or GeneDB decommissioning but we would like to discuss , if time permits

Usability issues/ issues reported by users

Integration (Better integration between the Ensembl part of the site and the Gene pages) especially:

  • helpdesk/help
    • The "Ensembl help" link leads to a general help page for Ensembl genomes, this won't mean much to our users
    • We need an intermediate Pombe specific help page under PomSase? needs to be Pombase specific (it can include items here which are relevant to Pombase but should exclude items which are not related to Pombase (e.g. eHIVE production system for honeybee, Annotation of Ig/Tcr? Segment Genes, and other links in jira item)

  • download

  • Need an intermediate page for site wide download options linked from main page menus

General note for all of the above, it is important that we remove things which are net relevant. There are so many new and hidden features that users should only be presented with the relevant items or they will stop exploring.


  • next technical meeting?

Lower priority so bump to next meeting ?

  • Re-visit Online Meeting software
  • 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 and IDs; only protein; not representing all annotation; how are term names displayed and accessed; update frequency )

Last modified 10 years ago Last modified on Jan 26, 2012, 7:17:54 PM