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'with' field contents for IPI annotations
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.
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...
> 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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