W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > June 2012

(wrong string) ‚€™ side effects

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Tue, 12 Jun 2012 12:51:25 -0400
Message-ID: <CAA=X4OCQT_kq4PNVpkSv8VzAfbO795A05tD8_MMXETvmU+wxRQ@mail.gmail.com>
To: David Wild <djwild@indiana.edu>
Cc: "Lin MD, Simon" <LINMD.SIMON@mcrf.mfldclin.edu>, Joanne Luciano <jluciano@gmail.com>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>

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 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 16:51:58 UTC

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