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'with' field contents for IPI annotations

Midori Harris midori at ebi.ac.uk
Wed Mar 1 01:52:35 PST 2006


Seems OK to me, because the ID in the 'with' column always indicates what 
thing interacts with the gene product of interest, even when the 
identification is indirect.

m

On Tue, 28 Feb 2006, Doug howe wrote:

> Perhaps this also relates to the relationship between the evidence code 
> and the allowed type of object in the 'with' column.  Does it create a 
> computational problem if IPI annotations have both protein and gene IDs 
> in the 'with' column since one is sequence and one is DB identifier?  I 
> suppose it isn't all that bad since no matter what you put there, it 
> will have a dbxref associated with it...
> 
> -Doug
> 
> Kimberly Van Auken wrote:
> > Hi Doug--
> >
> > We have come across this situation here at WormBase and have found 
> > that even though we have
> > protein IDs corresponding to all confirmed (or even partially 
> > confirmed) transcripts, it is often
> > difficult, if not impossible, to tell exactly which proteins authors 
> > studied in interaction experiments,
> > be it two-hybrid assays, co-IPs, etc.
> >
> > In these cases, we feel that putting the gene ID in the WITH column is 
> > the best compromise.
> > Doing so still allows users to identify the interacting entities, but 
> > does not make any potentially
> > misleading statements about exactly which proteins were involved.
> >
> > I am also curious to know how other groups handle this. 
> > Best,
> > Kimberly
> >
> >
> >
> > Doug howe wrote:
> >
> >> We (curators working from primary literature) often find 
> >> circumstances for IPI annotation where the authors do not provide 
> >> specific information about exactly which protein they are working 
> >> with...though we usually know which gene it came from.  So when 
> >> making IPI annotations, where the exact sequence of the protein 
> >> involved is questionable, is it better to put a representative 
> >> protein ID in the "with" field, put the ID of the gene itself in the 
> >> with field (is this even valid?), or leave the "with" field empty?
> >>
> >> How often do other groups actually find that they know the exact 
> >> protein sequence ID of the interacting proteins?
> >> -Doug
> >>
> >
> >
> 




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