wiki:PombasePlanningMeetingMinutes20111003

Minutes 03 Oct 2011

  • Midori presented phenotype model for Chado. We now have a model to cover phenotypes for single gene and multiple gene mutants (Link to docs?)
    • AI - add connection to separate table for allele description
      • sequence-position elements
      • SO terms where relevant (or other vocabulary for type of change?)
      • figure out what to store for (e.g.) promoter swaps - how to structure allele description - also relevant to chimeric
    • questions arising:
      • quantitative phenotype data e.g. gene expression in wt vs. mutant (note: quantitative phenotypes are cutting-edge and challenging even phenotype experts)
    • AI - for phenotypes of strains being sequenced, include "natural variations", flagged as such, in allele description
    • AI - add strain ID to genotype (problem: no repository with IDs; NCBI taxonomy too limited; use Japanese collection + Korean deletion repository?)
    • AI - split extensions, at least conditions (could consider lumping expressivity & penetrance) think about whether conditions will need additional table(s) for details
    • AI also include conditional vs. constitutive as phenotype extension
    • AI Longer term, think about quantitative phenotypes of non-reference strains,
    • AI how to handle chimeric sequences
  • Annotation extensions circulated proposal for reformatting this data on the gene pages.
    • AI Antonia, Jurg, Midori, Mark have seen this proposal and agreed that this is OK so will proceed and stick this on Jira tracker. This isn't high priority for the preview or the first release (I would slightly prefer that annotation extensions happen in a later release when we can announce and explain them in detail)

  • Discuss confusing menu options in Ensembl view.
  • seems odd to have links to data types we will not have
  • things which will be curated on the gene pages:
    • external references
      • general Identifiers
      • oligo probes (what is this in the context of an external ref?)
    • regulation (what will be under here?)
    • ontology
    • protein information
    • EBI protein summary
    • protein structure (external link)
    • ID history (Ids are stable, what would this show?)
  • similar issue with "downloads"

Long discussion. We didn't discuss the specifics of these issues, but decided that the way to proceed is to get some user feedback

AI Paul find available dates for testing AI Midori/Val/Antonia? to recruit testers (Cambridge and London based), who have not been exposed to PomBase or specific questions

  • Timelines

Now only have 10 "critical" OR "blocker"

AI We are waiting on Kim implementing the filters on the final GO data (external data) and loading genome wide localization study Once this happens (hopefully late October) we can do a final load with the Chado data. (PomBase will be slightly out of synch annotation wise with EG11, but Paul has approved this, and we will fall into synch with Ensembl later...Things won't be affected by this as we will not have changed any gene structures, or added any new genes so the Compara etc will still be current).

At this stage we will:

  • i) Announce to community for feedback
  • ii) Add links from GeneDB for people to try new site
  • iii) Send out a request for HTP datasets from the community in defined formats (current assembly only at first, this covers most HTP data)

Action items carried forward

  • 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)
  • 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.

New action items

Collect new action items here when approved

Last modified 9 years ago Last modified on Jan 17, 2012, 11:37:11 AM