[go] AmiGO beta announcement

[Eurie Hong]

I agree with Rama - the new column configuration implies that it's  
the evidence code that being qualified.  And I prefer the  
organization on the beta, especially with the "contributes_to" and  
"colocalizes_with" qualifiers.

But I agree that counts are misleading.  Can the count for the  
qualified terms be calculated separately from the non-qualified  
terms?  Or just go back to the "view associations" that's currently  
in production.

eurie

On Jan 7, 2008, at 2:19 PM, Alexander Diehl wrote:

> Rama,
>
> I'm sorry if you find this misleading now.  In my earlier post I  
> explained how I found the previous arrangement (in the beta)  
> misleading.  Again, it comes down to trying to convey the maximal  
> amount of information in the least amount of interface space.   
> While I appreciate your concern, I still feel Amelia's new  
> arrangement is less misleading than the previous arrangement of  
> columns, but this is probably quite subjective.
>
> If anyone else is wondering what this about, compare these two  
> displays:
>
> 1)  (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- 
> assoc.cgi?gp=FB:FBgn0027356
>
> 2)  (Amelia's new column configuration) http://toy.lbl.gov:9012/cgi- 
> bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356
>
> or these two:
>
> 1)  (current beta) http://goweb-dev.stanford.edu/cgi-bin/amigo/gp- 
> assoc.cgi?gp=MGI:MGI:2685628
>
> 2)  (Amelia's new column configuration) http://toy.lbl.gov:9012/cgi- 
> bin/amigo/gp-assoc.cgi?gp=MGI:MGI:2685628
>
>
> Thanks,
>
> Alex
>
>
>
> Rama Balakrishnan wrote:
>> Sorry for not piping in earlier on this one. The way you have  
>> reordered it (http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi? 
>> gp=FB:FBgn0027356) with the NOT next to the evidence code, it  
>> looks like the qualifier goes with the evidence code. I think this  
>> is misleading..
>>
>> rama
>>
>>
>>
>> On Jan 7, 2008, at 6:32 AM, Amelia Ireland wrote:
>>
>>> Hi Alex,
>>>>
>>> [displaying NOT annotations and column ordering]
>>>>>> http://goweb-dev.stanford.edu/cgi-bin/amigo/gp-assoc.cgi? 
>>>>>> gp=MGI:MGI:2685628&session_id=1458amigo1197932357
>>>>>>
>>>>>> the first line of the listed associations reads Qualifier:  
>>>>>> NOT, Term: GO:0051092 : activation of NF-kappaB transcription  
>>>>>> factor, link: 63 gene products,
>>>
>>> I've changed the column so that it is hopefully a little clearer  
>>> now.
>>>
>>> Example:
>>> http://toy.lbl.gov:9012/cgi-bin/amigo/gp-assoc.cgi?gp=FB:FBgn0027356
>>>
>>> Does that work?
>>>
>>> Cheers,
>>> Amelia.
>>>
>>> -- 
>>> Amelia Ireland
>>> GO Editorial Office,
>>> European Bioinformatics Institute, UK.
>>> Carbon neutral driving: http://www.targetneutral.com/TONIC/index.jsp
>>>
>>>
>>
>
>
> -- 
> Alexander Diehl, Ph.D.
> Senior Scientific Curator
> Mouse Genome Informatics
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME  04609
>
> email:  adiehl at informatics.jax.org
> work:  +1 (207) 288-6427
> fax:  +1 (207) 288-6131