WBConfCall 2012.10.18-Agenda and Minutes

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Agenda items WBConferenceCall 2012-10-18

Models Sign Off

  • Mary Ann

In order to cross reference from strains to the CARS Parasite Isolate Database I would like to add the Database tag to the ?Strain model.

DB_info Database ?Database ?Database_field UNIQUE Text

nb. The Database_field needs to be a Text value because their database does not use accession numbers.

MA: The CARS database is no longer supported so we cannot make xrefs to it. I would like to retract this proposal.

  • Karen

Would you please add the following tag to the Molecule model?

Reference  ?Paper  XREF Molecule


  • Daniela

can you add it just below the description, please?

?Movie      Description ?Text
            Name UNIQUE Text


  • Xiaodong / Erich

After a considerable amount of discussion I think the changes were distilled down to this simple change.

Consensus Text

Approved. Interested parties to do final check when models are tagged next week

Pending Helpdesk Tickets

  • Subject: [wormbase-help] On adding a set of novel transcription start sites to WormBase
    • date recieved 18-Oct

Assigned to Gary W

  • Subject: [wormbase-staff] Re: RNAi screen data submission
    • date received 17-Oct
    • reply to be sent after conf. call.

Assigned to Wen

  • Subject: [website] Feature Request: Hi guys it is really di... (#554)
    • date received 17-Oct - ticket #554
    • Todd asked RNAi curator to reply

Assigned to Chris (on leave)

  • Subject: [wormbase-help] How can I find the latest AMI for WormBase in EC2
    • date received 16-Oct
    • MA forwarded to wormbase-staff

Assigned to Todd

  • Subject: Feature Request: Dear WormBase, i am a...(#551)
    • date received 16-Oct - ticket #551
    • website display issue - m.tuli has responded to allele query - can someone else respond to the rest?

Tood in communication with user We will add Phenotype column to Allele table and users can order the table as they wish. Table with have phenotype count.
Raymond: should we have 3 letter codes for phenotypes? Agreed this would be good survey question - how are users using phenotype info? CalTech to consider this proposal

  • Subject: [website] Bug Report: I am unable to load the association... (#550)
    • date received 16-Oct - ticket#550

Assigned to Todd

  • Subject: [website] new wormbase connection (#531)
    • date received 10-Oct
    • for webteam?

Should not be done on the fly - otherwise we risk many broken links. Data should be stored within gene object. Data will be added to Geneace. Assigned to Paul D

Other Items

  • Todd and Abby have been working on website tickets. Many have been kicked back to curators/staff so please keep an eye on the tracker.
  • Sequence Collection is now live

  • Kevin: referring to help ticket #558 - not obvious that WB has same version as UCSC.
  • Was suggested that we use Other_name in ?Sequence_collection to store other name. nb. M.Tuli: I've just checked this and Other_name is not a tag in ?Sequence_collection. Suggest we store this info. in the Database tag
  • databases should tell WB when they update versions, but we should check. USCS only updated ~once a year.
  • User case: uploading RNA-seq data to UCSC browswer. Although users have not been systematically directed to use UCSC by WB, we think this is what people are doing (user survey to confirm)
  • Kevin: We should be directing users to ensembl (especially since WB money is used to build it). ensembl has "slim" version (lacking deep content). Will soon have WS235. Should be able view RNA-seq data in ensembl so we should be directing people here and we should be finding out what people want and making it available in ensembl.
  • gbrowse nearing end of life. Will be replaced with more modern version in first year of next grant cycle.
  • enseml is up to date (updated every 5 WB releases)
  • UCSC is less up to date.
  • should create a wiki page describing resources and pointing users to most appropriate place, but we need to find out what people want/need to do first.

  • Todd: new developer starting next week. Should be an version of Intermine to test by the end of the year

  • Karen and Mark have been working on WBProcess. Mark has seconded back to modencode for 6 months so Karen should now work with Todd or Abby.

  • Wen: ?Oligo_set has no species tag. Identical data from different species could cause problems.
  • Kevin to check on uniqueness. Platform names should be different across species so should be OK.