[go] AmiGO beta announcement

[Chris Mungall]

Both displays confused me at first, but I believe this to be because  
of a bug in the data. FB appear to be submitting a fake non-NOT  
annotation corresponding to every real NOT annotation. Either that or  
there are a lot of self-contradictory papers.

On Jan 7, 2008, at 3:32 PM, Eurie Hong wrote:

> 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
>
>