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

We are really sad about our friend Bill Gelbart

We will try to help FlyBase as much as possible

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.
  • We should visit labs to publicize Annotation. target labs with data
  • target senior graduate students.

ModSeek and SPELL updates

  • Wen is working with Seek developer to install a ModSeek mirror, still debugging the software.
  • Wen will try to install a WormSPELL mirror on the Textpresso server because the machine still runs RedHat 5, which is compatible with the requirement of SPELL.