[go] AmiGO beta announcement

[Judith Blake]

Seth, all AmiGOers,

This is great.  Here are some of the many things I like

1.  simplicity to start, nice colors
2.  ability to select output form
3.  ability to customize GOgraphs
4.  tips to tell you where you are going
5.  ability to download gene details by association files or XML, more 
download options
6.  I like the new header bar and the links to tools
7.  I like that the Evidence Codes are spelled out on the Advanced 
Search page.
8. on the gene product search results page, I like the feature 'perform 
an action with selected gene products'
9.  I like this phrase 'in gene association (tab-delimited) file format'



Here are some questions...

1. when getting gene product results from search on home page, how are 
these ordered?  I don't know how the relevance is determined.  For 
example, if I search on Bmp4, I get 5 gene products in the results.  In 
the fourth one, the match is within a synonym term.  Also, the 5th row 
(human) includes both name and synonyms.  I happen to know this, but the 
results are confusing.  I think this is something  GOAis working on.
2.  The term enrichment is presented well, but I find the 'slimmer' too 
confusing.  I actually wonder if we should think of another name.  
'slimmer' is maybe too much GOgroup lingo.  I wonder if others think so 
too. I followed through on the 'more info' and found that the docs 
aren't quite done here.   Maybe this is a place where a 4 click demo 
might work (very short).
3.  When I clicked on 'search' in the dark blue bar, I really expected 
to go to the Home page.  but it went to 'advanced search' instead.  I 
then recognized that the simple search was under the dark blue bar.  As 
a creature of habit, though, I started looking around for a link to the 
Home page...didn't find it.  Hummmmm, disconcerting, but probably ok.
4.  When I mouse over the 'help' page, it says it 'help guide for this 
page', but when I click, that is not what I get.  I get a general help 
page for AmiGO, with nothing about the Advanced Search page.

AND

FASTA files....what are all those identifiers doing in the DE line?  a 
prosite ID is not equivalent to the protein.  ditto ditto on the 
InterPro domains.

Anyway.  Looks great. Lots of improvements.  Great advance.

thanks for all the work on this everyone

Judy

Seth Carbon wrote:
> GO Listers,
>
> New features that you may want to look for and/or test in the AmiGO
> beta:
>
> *) Term Enrichment tool (accessible from the button/link at the top of
> every page).
>
> *) GO Slimmer tool (also accessible from the button/link at the top of
> every page).
>
> *) New Advanced Search page.
>
> *) Searches are now more intelligent (will work harder to get the
> answers that you probably want).
>
> *) Searches are now sorted by relevance.
>
> *) The pie charts have been replaced with bar graphs.
>
> *) Improved download options (more formats more places).
>
> *) Improved user interface (all over the place).
>
> Cheers,
>
> -Seth
>
>
> On Mon, 2007-12-17 at 15:34 -0800, Seth Carbon wrote:
>   
>> GO Listers,
>>
>> The next version of AmiGO is in the final stages and we felt that now
>> would be a good time to open it up to those outside the working group.
>>
>> For those of you interested in trying and testing out the new version of
>> AmiGO, the main testing server is located at:
>>
>> http://goweb-dev.stanford.edu/cgi-bin/amigo/go.cgi
>>
>> Questions, comments, and bug reports should be directed to the Web
>> Presence Working Group:
>>
>>
>>
>> web-presence-working-group at genome.stanford.edu
>>
>> In addition, the testing server at Berkeley is refreshed several times a
>> day from CVS and changes made in response to bug reports can be seen as
>> they are patched:
>>
>> http://toy.lbl.gov:9012/cgi-bin/amigo/go.cgi
>>
>> Cheers,
>>
>> -Seth
>>
>>
>>
>>     
>
>