[BioC] annotation package for HPRD

Robert Gentleman rgentlem at fhcrc.org
Thu Jul 30 21:57:32 CEST 2009

No we have not made use of HPRD, we do make a bit more use of other 
proteomic resources.  If there are specific things only found there, 
perhaps you could explain what they are, and why we might want to 
include them.

For protein interactions (if that is the part you want) there are a 
number of parsers around that would let you quickly make a database. I 
doubt that it would take too long to create a package which interfaces 
to the org.Hs type packages, but it is not high on our to-do list.  We 
would gladly take a submission of this sort (but who ever does it has to 
be willing to update regularly, and may want to consider more data 

  A few notes:
   The RpsiXML package should help with the parsing.

   There are some packages that have yeast interaction data in them 
(hopefully soon to be at least one more) that you could look at. I 
suggest considering carefully the representation for the interactions, 
as it can be done quite inefficiently.

   best wishes

Rajarshi Guha wrote:
> Hi, is there an annotation packcage on the lines of org.Hs.db that supports
> the HPRD database? I saw a message from 2005 (
> https://stat.ethz.ch/pipermail/bioconductor/2005-March/007972.html) but
> can't seem to find anything after that.
> Any pointers would be appreciated

Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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