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Re: Computers may predict drugs’ side effects

From: David Wild <djwild@indiana.edu>
Date: Tue, 12 Jun 2012 12:32:20 -0400
Message-ID: <CANbBT=i-BgA4adH-SxXQugXBybOwoq0BZVXhscg1qE3+QvN5_Q@mail.gmail.com>
To: Oliver Ruebenacker <curoli@gmail.com>
Cc: "Lin MD, Simon" <LINMD.SIMON@mcrf.mfldclin.edu>, Joanne Luciano <jluciano@gmail.com>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
> Hopefully, in the future, we will be able to simulate, for a given
> chemical structure:
>  - which proteins (or other bio-molecules) it interacts with
>  - how that interaction changes the function of the bio-molecule
>  - how changed function of molecules change biological networks and
> systemic function
>  However, what the article says sounds more limited:
>  "... a database of 73 proteins ..."
> > As such, Open Linked Data might offer help!
>   Eventually.

The first (drug-target prediction) is something we're working on at IU -
using a large, heterogenous semantic network of public compound, target,
gene, expression, pathway, disease data to make drug-target predictions
(see http://chem2bio2rdf.org/slap ,
http://slapfordrugtargetprediction.wikispaces.com/ , paper in press at PLoS
Comp. Bio.). Results are promising so far but biggest question is how you
weight different kinds of paths, nodes and edges - there is no one correct
answer, but is dependent on the scientist and application using it. Right
now we're not claiming that it predicts compound-target binding but rather
an "association" which deserves further investigation. Also have to address
preconception by many that "large / integrated dataset" = low quality, high
errors. I argue that if you read 5 papers a day you are overall better
informed than if you read just one of them, even if that one paper is a
very high quality newspaper.

>     Take care
>      Oliver
> --
> Oliver Ruebenacker
> Bioinformatics Consultant (
> http://www.knowomics.com/wiki/Oliver_Ruebenacker)
> Knowomics, The Bioinformatics Network (http://www.knowomics.com)
> SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)

Dr. David J. Wild, djwild@indiana.edu, http://djwild.info @davidjohnwild
Assistant Professor of Informatics & Computing
Director, Cheminformatics & Chemogenomics Research Group
Indiana University School of Informatics and Computing
901 E 10th St Rm 207, Bloomington, IN 47408
Tel. +1 812 856 1848
Received on Tuesday, 12 June 2012 16:32:57 UTC

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