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August 6, 2015

WormMine

• prioritize new data types into WormMine
  • RNAi phenotype, interactions, human disease...
  • WormMine wiki page: http://wiki.wormbase.org/index.php/WormMine

WormMart machine

• Wen wants to use the machine when WormMart retires

UniProt/wormbase gene class

• need to talk to UniProt C.elegans curator

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.