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

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