WBConfCall 2015.06.04-Agenda and Minutes

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please submit your agenda items here

Community Annotation Forms

  • Mary Ann and Sibyl have setup the community curation portal page on staging: http://staging.wormbase.org/about/userguide/submit_data#0--10
  • We want to make sure that when WS248 goes live (this weekend?) that the links to the forms are appropriately updated
  • Question for webteam: It looks like these form links will be editable at any time by curators, is that correct?
    • If so, then we can update the links at our leisure
    • If not, and the links need to be updated before WS248, we need to make sure the links point to Tazendra, not Mangolassi
  • I will be making my poster and preparing the workshop talk next week so the sooner we finalise what we intend to promote (to a greater or lesser degree) the better. (mary ann)

Tempates for IWM

  • Do we have a template for posters and talks for the meeting? (mary ann)

GO term enrichment (TE) tool for WormBase

  • I've done some groundwork on how we could implement the Panther GO TE tool for both C. elegans and the other core species. (Jane Lomax)

Models for WS250

  • Proposed change to ?GO_term model for WS250
  1. Remove the Term tag. The name of the GO_term would be populated in the Name tag. This change will have downstream effects for the build and web display.
  2. Add an Alt_id tag to populate secondary IDs as listed in the GO obo file. This would allow anyone searching WB with a secondary, or alternate, GO ID to still arrive at the correct GO_term page.
  3. Although this doesn't affect any tags in the model, starting with WS250 we will populate the Version tag with the information in the 'data-version:' tag in the obo file, not the 'remark' tag that holds the SVN revision number. All terms have the Version tag populated, so we should remove the comment in the ?GO_term model about version only being stored on the 3 parent terms.
  • Proposed WS250 models dates (from Paul D.'s 13/05/15 message)
    • 12/06/15 - Models Deadline
    • 19/06/15 - Models CVS
    • 23-29/06/15 - IWM

Link Outs to Same Site, Different Base URL

  • See github #3915
  • Can we accomodate different base URLs for the same site, e.g. UniProt, RefSeq


  • GO term enrichment (TE) tool for WormBase
    • database wholesale, easy transition to C. elegans, but we need to be the provider for gene association files, including parasites, core species, ig briggae, no extra work, interpro to go, phenotype to go, not from Tony, gaf is generated at the end when wormbase build.
    • web interface, use Amigo on GO page, panther GO TE

  • WS248 will go live most likely on Saturday morning

*Community annotation forms

    • concise description and allele forms are ready to go.
    • micro publication form is waiting for more feedback from Oliver Hobert and Ian Hope.
    • allele form link has some hard-coded work, Sybyl will help to update the link
    • other forms links can be edit by owner curators.

  • IWM preparation
    • Mary Ann and Scott Cain will present posters
    • Daniela will talk micro publication on workshop as well

  • Link Outs to Same Site, Different Base URL
    • github #3915
    • Todd and Sybyl are looking into it