WBConfCall 2012.06.21-Agenda and Minutes

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Several models for sign off this cycle. Please review the file models.wrm in the Sanger CVS if you want to look at any prior to the call.

Unless I hear any objections I think that these can all go in as is.

Curators who have models in


   Isolation  Picture ?Picture


   ?Life _stage
   Public_name UNIQUE Text


      Mapping_primers Left_mapping_primer UNIQUE Text
                                  Right_mapping_primer UNIQUE Text



  Child   CELL_c         ?Anatomy_term     XREF CELL_p
          XUNION_OF_c    ?Anatomy_term     XREF XUNION_OF_p
  Parent  CELL_p         ?Anatomy_term     XREF CELL_c
          XUNION_OF_p    ?Anatomy_term     XREF XUNION_OF_c 


   -D Author
                      Cis_regulated  //existing tag
              Intragenic_effector_variation   ?Variation   XREF   Interactor // New tag
              Intragenic_affected_variation   ?Variation   XREF   Interactor // New tag
       Interaction_phenotype ?Phenotype XREF Interaction //existing tag
       Unaffiliated_variation   ?Variation // New tag
       Unaffiliated_transgene   ?Transgene // New tag
       Unaffiliated_antibody    ?Antibody // New tag
       Unaffiliated_expr_pattern   ?Expr_pattern // New tag
       WBProcess ?WBProcess XREF Interaction    //existing tag
   Interactor Rearrangement ?Rearrangement XREF Interactor #Interactor_info
   PCR_interactor - remove UNIQUE
   Sequence_interactor - remove UNIQUE
   Reporter 3_UTR ?Gene
   Interactor ?Interaction XREF Rearrangement

Item 2

Helpdesk issues:

  • XML link button previously present on the yellow menu bar? Reported by Kazuya Nomura

(e.g., http://legacy.wormbase.org/db/seq/sequence?name=F59G1.1)

  • In "Old Wormbase", phosphopeptides that has been identified in a pilot phosphoproteomic survey of C. elegans were shown (accessible from gene page). I can't seem to locate this information. Will you please tell me where to find it, and/or if it is missing, please restore it? Reported by Anne Villeneuve


  • All models approved and ready to go
  • Kimberly's Species tag in Paper model will be added for WS234
  • Blast transiently not working -> Todd has been working on that
  • Interaction widget not working -> Abby is working on it
  • phosphopeptides issue, Daniela will create a ticket
  • Todd: WS232 staged -> everyone should test
  • Webteam has been working on smoothing out differences between TierI/II and TierIII species. They have been working on indexing the GFF database. If users go to global search and type a gene name could see all species and from there go directly to GBrowse, Blast..This is to make different species easily accessible.
    • Adding TierIII species needs more consideration. Abby not opposed on having a separate TierIII ace database.
    • Paul S suggested to look into Paul Thomas tool that GO uses for phylogenetic crossing of annotation -Paint. Kevin suggested that some of this could be done using ensembl technology as the goa consortium at EBI have guidelines and the data is already/easy to get in/into the ensembl databases Hinxton already has.
    • Kevin concerned about the number of objects-20 species 20k proteins, transcripts.. will it slow down the search? - lots of possible solutions, needs more consideration.