WBConfCall 2015.08.20-Agenda and Minutes
From WormBaseWiki
Contents
Agenda
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 <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000086>
daf-2 (lots of phenotypes) phenotype widget <http://www.wormbase.org/species/c_elegans/gene/WBGene00000898#-b-3> summary <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898>
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