WormBase-Caltech Weekly Calls

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August 6, 2015

WormMine

WormMart machine

  • Wen wants to use the machine when WormMart retires

UniProt/wormbase gene class

  • need to talk to UniProt C.elegans curator

Raymond, Chris and Juancarlos are working on phenotype viewer

James: list of genes, enrich in what tissues

  • python code
  • biotype ontology, tissue expression from postgres as input


August 13, 2015

Phenotype term 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

Group comments:

  • key of red vs blue nodes

International Biocuration Conference

Propose to submit paper on Community Curation

  • Mary Ann happy to lead.
  • Daniela on board.
    • push out the emails (Ranjana and Chris are thinking about it) Sept.1 so we can get some submissions in the Sept.