[go] Putting method/program names into the with field for ISS

[Susan Tweedie]

At the risk of returning us to square one on this... I'd like to take a
step back and revisit why we decided it was vital to have something in
the with column for ISS. I thought this stemmed from an attempt at
enforcing quality annotations - we wanted to identify the similar
'thing' for which there is experimental evidence and to use ISS only
where this was available. We then shifted ground a bit to acknowledge
that there are cases where there is a strong case for ISS annotation but
no single sequence can be identified for this column. So what do we
actually achieve by filling-in the slot for these cases? It seems to me
this is more to do with us saying 'yup I'm being stringent about my use
of ISS so I've stuck something in this column to prove it' than actually
helping users. The 'how they did it' in the the paper just like it is
for other evidence codes. I'm not sure we 'gain' enough here to justify
mixing methods and objects in the 'with' column and I am struggling to
see the justification for making ISS a special case in this respect. If
we show a method for ISS, do we set a precedent and run the risk of
users wanting to know whether it was RNAi or knock-out for IMP etc?

I guess I'd just like to know we haven't just made this column mandatory
as a means of policing curators. I strongly agree that we should fill in
a sequence where possible and do our best (within reason) to be sure
there is an experiment there somewhere but, if we are going to accept
that there are cases where we can't identify a suitable sequence, can't
we just trust curator judgement i.e. leave the column blank and let
people read the paper to see details of how it was done? 

If we stick with the plan to keep 'with' mandatory for ISS then Karen's
system is very nice. But what do we do for cases like Michelle's example
where a whole variety of similarity based methods are used. I find this
crops up time after time and I wouldn't want to have to list all methods
in this column and it doesn't seem very satisfactory to pick
representative examples?

Susan

On Tue, 2007-09-11 at 19:03 +0000, Valerie Wood wrote:
> That OK,
> 
> I just think its rather a trawl to have to create something to go in the 'with' field when the PMID of the published algorithm is sufficient.
> 
> My other reasoning was that these aren't purely based on 'sequence similarity', they always include some 'other  additional step' (although I agree they are 'sequence based') 
> 
> and thirdly, this could become hazy, if we got functional prediction methods which combined sequence data with some experimental date (like cellular localization), for example, would be be RCA (I presume). It therefore seemed  that if the distinction was that ISS needed to have some 'object' which represented a sequence in the 'with' column (rather than allowing the with column to contain other types of things, referring to algorithms), it would be quite a nice distinction.  If you can't locate this object  then the method probably includes something else in addition to 'sequence similarity'.
> 
> However, these were just for consideration, I really have no strong preference either way..... although I prefer easy :)
> 
> Val
> 
> 
> "Gwinn-Giglio, Michelle" <MLGwinn at jcvi.org> wrote: 
> > 
> > 
> > Ben,
> > 
> > Yes, sorry to not be clear - I was disagreeing with Val's suggestion to use RCA for things like TMHMM and tRNAscan.  At least I think that was Val's suggestion and that is what I diasagree with.
> > 
> > Sorry to disagree with you Val.  :)
> > 
> > Michelle
> > 
> > 
> > 
> > 
> > -----Original Message-----
> > From: Benjamin Hitz [mailto:hitz at genome.stanford.edu]
> > Sent: Tue 9/11/2007 1:05 PM
> > To: Gwinn-Giglio, Michelle
> > Cc: GO mailing list
> > Subject: Re: [go] Putting method/program names into the with field for ISS
> >  
> > 
> > On Sep 11, 2007, at 7:55 AM, Gwinn-Giglio, Michelle wrote:
> > 
> > >
> > >
> > > Hi,
> > >
> > > I disagree.  I think taking this approach would significantly muddy  
> > > the waters in terms of distinguishing between ISS and RCA.
> > >
> > > Anything that is based only on sequence analysis, be it simple  
> > > Blast or vastly more complicated modeling methods, should be ISS  
> > > because at their heart they are all comparing sequences of known  
> > > function to ones with unknown function.  Whether they do simple  
> > > alignments to make that comparison or more complicated models, it  
> > > is still a sequence based analysis.
> > 
> > I did not suggest otherwise.
> > 
> > Ben
> > 
> > --
> > Ben Hitz
> > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
> > Consortium
> > Stanford University ** hitz at genome.stanford.edu
> > 
> > 
> > 
> > 
>