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'with' field contents for IPI annotations

Tanya Berardini tberardi at acoma.Stanford.EDU
Wed Mar 1 11:31:41 PST 2006

TAIR annotates as described by Karen below.

My 1 cent,


Karen Christie wrote:
> HI Doug,
> In SGD, we often represent IPI with _____ where we use the ID of the gene,
> not the ID of the protein.  Partly because this using the geneID is easy,
> we maintain the geneID's. Similarly to what you describe, the paper often
> is written in terms of the genes they were working with. Admittedly for
> SGD, it's perhaps not a major issue, as there is almost always a 1-1
> correspondance between genes and possible protein products. 
> In addition, when we started representing with info in SGD, some of our
> genes had not been mapped to protein records by UniProt and thus did not
> have a protein ID.  In any case, the way SGD does this right now, we only
> use the GeneID's for our IPI with _____ when the with thing in the with
> field is an SGD gene/protein.
> -Karen
> On Tue, 28 Feb 2006, 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

Tanya Berardini, Ph.D.            tberardi at
The Arabidopsis Information Resource    FAX: (650) 325-6857
Carnegie Institution of Washington    Tel: (650) 325-1521 ext. 325
Department of Plant Biology        URL:
260 Panama St.
Stanford, CA 94305

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