[go] AmiGO beta announcement

[Mary Dolan]

Seth Carbon <sjcarbon at berkeleybop.org> on Monday, December 17, 2007 at 6:34 PM -0500 wrote:
>http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi

Hi, Seth.
I think it all looks terrific! The pages are clear and inviting.
I like the way AmiGO seems more a part of GO then before but still a self-contained tool. 
Great work! 

A few things...

1. GO Term Enrichment
a. Does not say which evidence codes will be used in the analysis.
b. Will users know what is meant by: "The default settings are sane."

2. Blurbs are reversed for:
http://wiki.geneontology.org/index.php/AmiGO_Manual:_Slimmer
http://wiki.geneontology.org/index.php/AmiGO_Manual:_Term_Enrichment

3. Using "Browse" I got a software error filtering for source "MGI" and species "Mus musculus" and view "compact":
"cannot filter by both speciesdb and taxid at /share/goweb/www-data/html/dev/go-perl/GO/Model/Root.pm line 65"
Maybe that restriction should be made more explicit --or forbidden.

4. So I removed the species restriction, it worked fine. But then gave an error clicking on the bar graph icon for the Bar Chart Viewer:
"Unfortunately AmiGO cannot create a bar chart with the current filter settings."
Again, maybe that restriction should be made more explicit --or forbidden (i.e. no bar chart icon if the user has set filters).

Mary

Mary E. Dolan, Ph.D.
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Mouse Genome Informatics Consortium, The Jackson Laboratory
mdolan at informatics.jax.org
(207)288-6439

Research Faculty, NCGIA
Department of Spatial Information Science and Engineering, University of Maine
Boardman Hall 329
University of Maine
Orono, Maine 04469
fax: 207.581.2206
mary_dolan at umit.maine.edu
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