WormBase-Caltech Weekly Calls
- 1 Previous Years
- 2 2015 Meetings
- 2.1 August 6, 2015
- 2.2 August 13, 2015
August 6, 2015
- prioritize new data types into WormMine
- RNAi phenotype, interactions, human disease...
- WormMine wiki page: http://wiki.wormbase.org/index.php/WormMine
- 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://188.8.131.52/~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://184.108.40.206/~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
International Biocuration Conference
Propose to submit paper on Community Curation
- Mary Ann happy to lead.
- Daniela on board.