[go] AmiGO beta announcement

[Harold Drabkin]

I think the counts are only confusing when the qualifier is a NOT. So, 
if you want to show # of genes annotated to "nucleus"; if you have a NOT 
nucleus, reading it one way is confusing. The fact is you do have x 
number annotated using "nucleus"; but one has a NOT, there are still X 
annotations  using the GO term but the meaning of one of the annotation 
sis different. This isn't as much of a conflict for the contributes_to 
and co_localizes_with, since nether  are negation statements.

The second display does suggest the wrong field is being qualified. The 
first URL is better in that respect.

hjd


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
>