Difference between revisions of "WBConfCall 2015.08.20-Agenda and Minutes"
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== JBrowse Update == | == JBrowse Update == | ||
+ | |||
+ | === 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 | ||
+ | |||
== Item 5 == | == Item 5 == | ||
− | |||
=Minutes= | =Minutes= |
Revision as of 15:26, 20 August 2015
Contents
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
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