Difference between revisions of "WBConfCall 2015.08.20-Agenda and Minutes"
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* * existing phenotype widget <http://www.wormbase.org/species/c_elegans/gene/WBGene00000086#-b-3> | * * existing phenotype widget <http://www.wormbase.org/species/c_elegans/gene/WBGene00000086#-b-3> | ||
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+ | * * summary graph <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000086> | ||
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+ | * * phenotype widget <http://www.wormbase.org/species/c_elegans/gene/WBGene00000898#-b-3> | ||
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+ | * * summary <http://131.215.12.204/~azurebrd/cgi-bin/amigo.cgi?action=annotSummaryGraph&focusTermId=WBGene00000898> |
Revision as of 00:28, 22 August 2015
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
Minutes
Welcome to Adam Wright
Biocurator Conference
Change Tool->WormMart link
WormMine Development Update
JBrowse Update
Phenotype annotation summary graph
Raymond, Chris and Juancarlos have been working on an alternative display of phenotypes that have been annotated to a gene. The impetus was feedback people at the IWM. Please visit the prototype links below to see the existing phenotype widget and the new summary graph. You can substitute any WBGeneXXXXXX in the link below to see a different gene. Please send feedback to Raymond, Chris or Juancarlos -
Feedback at the meeting included:
- Blue vs Red – not intuitive for direct vs indirect annotations.…perhaps use circles and dashed circles
- Need a clear legend
- is scaling an issue?
LINKS:
- 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>