[go] AmiGO beta announcement

[Susan Tweedie]

On Mon, 2008-01-07 at 17:41 -0800, Chris Mungall wrote:
> 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.

Oh dear.... thanks Chris - there is clearly a bug in the script used to
make our ga file which has resulted in a systematic parial duplication
of lines with qualiers. I'll get it fixed. However, we do have some
genuinely contradictory evidence for the same term based on different
papers. Although I would normally prefer to see the qualifier in front
of the GO term, I like the way Amelia's new config has each term only
once. If there is contradictory evidence for a term, it is important to
spot it - this is easier when it is gathered together in a single block
rather than under 2 separate term entries. 

Susan
> 
> 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
> >
> >
>