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'with' field contents for IPI annotations

Petri, Victoria VPetri at
Wed Mar 1 07:40:22 PST 2006

Hi Doug,

If the paper does not provide clear information regarding the identity
of the interacting partner - which happens quite often - we do not
further investigate. If we use the 'with' column it is the gene ID that
is placed there. On the other hand, if the paper provides good
documentation for the interaction we annotate both rat genes to the
appropriate GO terms (they may use different domains) and reciprocally
use their gene IDs in the 'with' column.


Victoria Petri, Ph.D.
 Scientific Curator for Gene Ontology
 Rat Genome Database (
 Bioinformatics Research Center (
Medical College of Wisconsin 
8701 Watertown PlankRoad, Milwaukee, WI 53208
 (414) 456-7507
 (414) 456-6190 Fax
 vpetri at
vpetri at

-----Original Message-----
From: owner-annotation at
[mailto:owner-annotation at] On Behalf Of Doug howe
Sent: Tuesday, February 28, 2006 4:39 PM
To: GO Annotation list
Subject: 'with' field contents for IPI annotations

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? 


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