WBConfCall 2013.02.07-Agenda and Minutes

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  • 8 models proposals for WS237 inclusion.
    • 2 provisional
      • History_gene connections (multiple classes) - Chris
        • Chris will discuss with relevant curators and confirm with Paul
        • Needs significant testing, Chris will liaise with Paul.
        • probably bump to WS238 as there hasn't been any further discussion since call.
      • Feature_data - Gary
        • Mapping to a condition rather than via a method.
        • Needs testing as may have implications for acedb.
        • probably bump to WS238 as there hasn't been any further discussion since call.
    • 6 scheduled for inclusion.
      • Accession class retirement continues
      • homol_data - Kevin
        • Oligo_set mapping as we do for other classes.
      • Transgene - Karen
        • Construction_summary Text
      • Transcript - Paul
        • Add biotype lincRNA.
      • Oligo_set & Microarray_result - wen/kev
        • Addition of ?Species
      • ?YH & ?Gene_regulation retirement - Chris
        • Complicated change as needs interaction adding in lots of classes.

David Miller cell specific expression data-tiling arrays

From Daniela: WS235 contains the links to WormViz in the anatomy page under the External links widget. David writes: "Although the link is certainly useful in this location its really buried and will not be noticed by most users. why not include a link to wormviz on the expression page for each gene?"

Have the tiling array data been curated already? if so we can point him to SPELL.

From discussions:

Daniela will contact David and point him to the expression cluster page. Data will be in in 237.

Request from Caltech to expand release notes

Caltech has been making a list of datatypes/objects that we would like numbers for, from each build, to be included in release notes. Is this something that Hinxton could do?

See http://wiki.wormbase.org/index.php/Release_note_requests

From discussions:

  • Release notes should be aimed at user community, tag names and some numbers may not be interesting for them.
  • We could generate a separate list for internal use, with all the statistics that curators want.

How to handle predicted interactions

  • Take out all the predicted interactions from the gene page, instead include the link to the external databases that provide these--Gene Orienteer, WormNet etc.
  • Data will be kept in acedb for purposes of Cytoscape?


  • There will be priority data sets that will be loaded first
  • SGD has ready templates
  • JD will give a demo of WormMine, Thursday 14th, at 8.30 PST