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Re: Computers may predict drugs’ side effects

From: David Wild <djwild@indiana.edu>
Date: Tue, 12 Jun 2012 12:58:45 -0400
Message-ID: <CANbBT=iAWjU-ecNC8h5mteXoWXEbdhjG=HqqQkF-wOUCCfg8Ag@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>
Here it is -- bad name lookup on our part for sulfuric acid - using CID
instead 1118

http://cheminfov.informatics.indiana.edu:8080/slap/slap.jsp?cid=1118&gene=Insulin

Note the direct relationship is removed in the subgraph / calculation to
show indirect prediction.

David
____________________________________________________

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



On Tue, Jun 12, 2012 at 12:51 PM, Oliver Ruebenacker <curoli@gmail.com>wrote:

>     Hello,
>
> On Tue, Jun 12, 2012 at 12:32 PM, David Wild <djwild@indiana.edu> wrote:
> >> 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.
>
>   Interesting tool!
>
>  I'm not sure I'm using it correctly, though: I entered sulfuric acid
> and insulin, and it found no direct interaction, although I am pretty
> sure sulfuric acid directly reacts with insulin.
>
>     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)
>
Received on Tuesday, 12 June 2012 16:59:19 GMT

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