WBConfCall 2015.08.20-Agenda and Minutes

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Welcome to Adam Wright

Biocurator Conference

  • Geneva 10th-14th April 2016
  • Should we ask about a Community Curation workshop in order to exchange ideas with other MODs

Change Tool->WormMart link

  • from Caprica@Caltech to @ParaSite
    • Should not call it "WormMart" though, because it does not contain any of the C. elegans genetics data (phenotype etc).

WormMine Development Update

JBrowse Update

  • Most (still not *all*) ModENCODE tracks have been transferred to JBrowse
  • Planning for 250 to include a link from the toolbar for JBrowse as well as links from the location widget (where the GBrowse link is)

Phenotype annotation summary graph

Goal: Provides an ontology-relationship-aware summary view of a gene's phenotype annotations. Prototype link aex-3 (fewer phenotypes) existing phenotype widget <http://www.wormbase.org/species/c_elegans/gene/WBGene00000086#-b-3> summary graph <>

daf-2 (lots of phenotypes) phenotype widget <http://www.wormbase.org/species/c_elegans/gene/WBGene00000898#-b-3> summary <>

Proposed development procedure:
  • standalone prototyping, commenting and improvements within the group.
  • implementation as a widget on dev site (juancarlos.wormbase.org), more testing and soliciting comments from selected end users.
  • committing to main site for general use.
Outline of graph processing:

To gather information:

  • WOBr query to collect all phenotypes annotated to the gene of interest.
  • WOBr query to collect all transitive relationships of the phenotypes from (1) towards the ontology root.

To simplify and to control graph size:

  • Remove all nodes (phenotype terms) that are not directly annotated with or at branching points where two branches of annotations merge (LCA lowest common ancestor, if you will).
  • Scale node size according to annotation count (includes inferred annotations). width of node is (scale multiplier of 1.5 * log(max count in graph)/log(current node) ) + minimum size value (.1)
  • Limit appearance of label to nodes above a given size (roughly big enough to hold term name).
  • Show annotation counts in mouse-over bubble, add hyperlink to term pages to each node


Welcome to Adam Wright

A warm welcome to Adam. As he has helped evaluate candidate replacements for AceDB.....he is not a complete stranger.

Initially, Adam will be working with the Hinxton and OICR teams continuing development on the AceDB -> Datomic project and will be continuing from where Thomas left off with the project (thanks for all your work Thomas). He will be available at approximately 50% capacity while he wraps up loose ends from other projects.

Biocurator Conference

Mary Ann will ask conference organizers (Pascale Gaudet?) if there can be a workshop dedicated to community curation at the Biocurator conference in Geneva in 2016.

Change Tool->WormMart link

Because WormMart is on its last legs and is no longer supported (or updated), we will make an announcement that it is "sailing off into the sunset"..and much of the functionality will be covered in WormMine. Some of the functionality (especially sequences) that are not yet in WormMine can be found at the Parasite Biomart site. Will will have a link for users to Parasite.

We will have a blog post explaining the transition.

So long WormMart.

WormMine Development Update

Todd and Sybil have been working to wrap some things up on the 249 release of WormMine. Although the WS249 website will be out before the 249 release of WormMine, the development they have done will make it easier to update in the future. Sybil will have a better estimate of the 249 release soon, but the release of new versions of WormMine (i.e. 250) will be in sync with the release of the versions for the website (i.e. WS250).

JBrowse Update

Scott gave an update on JBrowse and his work in getting the ModENCODE tracks up......almost there, but config changes between G and J were not straightforward. We will start introducing JBrowse as the GBrowse replacement by making a link in the tools section. The idea is to get users comfortable with JBrowse, before it replaces GBrowse.

Also we really dont what users to think in terms of "G and J Browse"...we just want them to think of it as the "new version of the genome browser".

Phenotype annotation summary graph

Raymond, Chris and Juancarlos have been working on an alternative display of phenotypes that have been annotated to a gene. The impetus was feedback from people at the IWM. Please visit the prototype links below to see the existing phenotype widget and the new summary graph. You can substitute any WBGeneXXXXXX in the link to a summary graph to see it for a different gene. Please send feedback to Raymond, Chris or Juancarlos.

Feedback at the meeting included:

  • Blue vs Red – not intuitive for direct vs indirect annotations.…perhaps use circles and dashed circles
  • Need a clear legend
  • is scaling an issue?


  • aex-3 (fewer phenotypes)
  • daf-2 (lots of phenotypes)