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'with' field contents for IPI annotations

Midori Harris midori at ebi.ac.uk
Thu Mar 2 02:22:03 PST 2006


OK; I'll copy the note about using a gene ID if you have to.

thanks!
m

On Wed, 1 Mar 2006, Doug howe wrote:

> The IPI evidence code doc states:
> 
>  "We recommend making an entry in the "with" column when using this 
> evidence code; i.e., include an identifier for the "other" protein (or 
> other macromolecule) involved in the interaction."
> 
>  From this statement, one could conclude that Gene record IDs are not 
> allowed.
> 
> -Doug
> 
> Midori Harris wrote:
> > Can someone point me to the offending bit of documentation? The Annotation 
> > Guide does have this:
> >
> >   "Note that a gene ID may be used in the 'with' column for a IPI 
> >    annotation, or for an ISS annotation based on amino acid sequence or 
> >    protein structure similarity, if the database does not have identifiers
> >    for individual gene products."
> >
> > ... so if there's anyting elsewhere that says otherwise, it needs fixing!  
> >
> > (The existing passage can also be reworded to explicitly allow 'for
> > whatever reason, you can't tell which protein ID to use'.)
> >
> > thanks,
> > m
> >
> > On Tue, 28 Feb 2006, Suzanna Lewis wrote:
> >
> >   
> >> I'm with you on this Karen, but apparently it made it into the 
> >> documentation somewhere.
> >>
> >> On Feb 28, 2006, at 5:01 PM, Karen Christie wrote:
> >>
> >>     
> >>> I don't believe we've ever implemented a restriction that the ID in the
> >>> with column had to be a protein ID for IPI with, because I would have
> >>> objected strenously to the suggestion, especially early on when some 
> >>> SGD
> >>> genes didn't even have corresponding protein IDs.
> >>>
> >>> -Karen
> >>>
> >>>
> >>> On Tue, 28 Feb 2006, Suzanna Lewis wrote:
> >>>
> >>>       
> >>>> BTW, I'm not sure when and where that restriction on the with column
> >>>> arose, it seems quite unnecessary.
> >>>>
> >>>> -S
> >>>>
> >>>> On Feb 28, 2006, at 3:43 PM, 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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