wiki:PomBasePlanningMeetingMinutes20121004

Version 9 (modified by gomidori, 8 years ago) (diff)

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Planning Meeting Tuesday 11 July 2012 - Minutes


Agenda for this meeting


Tuesday 11 July, 16:00, UCL

Present: Val, Midori, Jürg, Antonia, Mark, Dan, Paul, Steve
Remote: Kim
Part: Dan Jeffares, Giulietta Spudich, Nathan ? Chair: Val
Minutes: Val

Previous Action Items

  • 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)

General

Usage stats

  • discussion about browser access statistics AI provide browser access statistics at some point in the future

  • Discussion about wildcard lucene limitations
    • It appears that EBI ES do not allow lucene set up with wild card searching at the front of a string
    • AI Val, move wild card searching jira ticket to "blue sky" with the proviso that if it is an issue we revisit it later.

Curation update

  • See Agenda

Web site status and next priorities

  • We are ready to go live with the new data (from the curation tool) showing complete phenotype annotations and annotation extensions.
  • There are a couple of bugs related to display in fire fox but pending this we can go live (outstanding pre GeneDB commissioning tasks were moved to pre-GeneDB commissioning
  • Next priorities, after we go live with this dataset are to process the 17 jira tickets to enable GeneDB to be decommissioned
  • Process 16 post GeneDB commissioning tickets (note these were originally pre-decommissioning tasks but were flagged as slightly less urgent)
  • Host some HTP datasets
  • AI chase up Schizo genomes data

Ensembl Functional Genomic module demo

Giulietta provided a demo of the functional genomics module.

http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000079950;r=6:132779054-132834337

  • Appears to provide all the the necessary functionality for representing data on sequence
  • Curators still have concerns that the interface is quite complicated even for simple visualization
  • AI Val will provide the feedback from the fission yeast community on the browser to Giulietta

New action items

  • 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.

AOB

  • Jurg asked about:
    • discussion about how to handle additional genes not present in lab strain
      • identify a non redundant set of genes to represent in PomBase that will be searchable, but not included in totals

  • utilizing text mining (Fritz Roth tool) (this group are interested to do some work?)
  • XCARP ? (jurg will send details)
  • Next meeting Hayley will circulate doodle poll, will be in Cambridge