wiki:PombasePlanningMeetingAgenda20121109

November 9th 2012

Outstanding Action items from Oct 4th

  • Action: Curators look into acquiring data from strain collection in Japan

(Not done)

  • Action: Curators to monitor web site for problems (ongoing, OK at present)
  • Action: Functional genomics views demo at next meeting (EBI)
  • Action: Val to circulate non-redundant list of genome browser requests & feedback from community (In progress)
  • Action: PK et al. to create Jira tracker for Ensembl genome browser issues; PK to triage tickets
  • Action: Diagnose the cause of the not synching of the update (Mark) (OK)

New Action items from Oct 4th

  • AI provide browser access statistics at some point in the future (put on jira tracker as "blue sky"
  • AI chase up Schizo genomes data
  • AI Val will provide the feedback from the fission yeast community on the browser to Giulietta
  • AI Val, move wild card searching jira ticket to "blue sky" with the proviso that if it is an issue we revisit it later.

General

  • Usage stats http://tinyurl.com/7qs2zap
  • http://www.ebi.ac.uk/panda/jira/browse/PB-1033
  • new blast interface, would like a demo when this becomes avalable
  • Need an action plan of what work is planned, difficult for us to work and keep the community informed
  • Sam's data Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells PMID:23101633 (discuss with Mark)

Updates from various Areas

Curation Update

  • All papers are triaged (upto ~August?) (no change)
  • Of 9511 papers 4604 are "curatable" with gene product specific information (no change)
  • ? annotations in curation tool
  • 613 curation session (papers) in progress (previous 591)
  • 338 approved (previous 299)
  • 14 needing approval (previous 47)
  • Intend to start sending our more papers to community once phenotype annotation visible in PomBase?

Phenotype Ontology (Midori)

  • 1678 phenotype terms
  • Release pipeline using Oort in place (includes reasoning)

Chado loading (Kim)

  • Anything to report ?

Curation tool (Kim)

  • Anything to report

Review "Post-preview" and "GeneDB decommissioning" criteria & progress (Mark)

Current jira status: Open 163 Closed/Resolved? 868 (was 161/808 last meeting, Oct)

Next priorities (Pombase website)

  1. Host new dataset with curation tool annotations

  • The satus at the last meeting was
    • This is now on stage/dev with a few tickets which still need to be cleared to get the new data hosted still waiting to go live...

  • Once NG28 is live, curators can announce phenotypes, annotation extensions and new annotation from curation tool (and promote community curation) via pombelist.
  • Once NG v29 is hosted, human ortholog data can be announced.
  1. GeneDB decommissioning tasks
    • Next prioities for Mark, 32 jira tickets (should we reprioritise these?)
  1. Post GeneDB decommissioning tasks 53 items These are features which are provided by GeneDB, and used, but are not as critical. Provided they are replaced fairly quickly people can probably survive for a while if the old site is taken down

(The above numbers ahave changed because lots of "unscheduled tickets have been scheduled)

  1. Hosting genome wide datasets
  1. Unscheduled items 11 (was 103)

Problems reported

Meetings Attended/ Upcoming

  • GO meeting next week (Pasadena).
    • Curators attended remotely
  • proposed Workshop for 2013 (International meeting) straw poll?
  • Proposed PomBase? 1-2 hour workshop at CRUK, with 1-2 hour curation tool demo and or jamboree

AOB

  • Next meeting (doodle)

PI's meeting

Last modified 8 years ago Last modified on Nov 9, 2012, 3:03:08 PM