Hej Nina,

On Wed, Feb 23, 2011 at 10:53 AM, Nina Jeliazkova
<jeliazkova.nina at gmail.com> wrote:
> In an exercise to reproduce an ECOSAR model, I've found the current
> implementation of XLogP (CDK ) performs a bit different compared to KOWWIN
> [1].
>
> http://tinyurl.com/xlogp-kowwin
>
> This makes hard to reproduce the ECOSAR model, since it depends on LogP.
> Also, LogP is an important parameter in many toxicity prediction models.

Yeah, this nicely reflect how 'reproducible' QSAR modeling is. Most
models are so numerically unstable, that exchanging a variable with a
highly correlated one (KOWWIN and CDK LogP's) ruins the prediction...
says more about the QSAR model thatn the LogP descriptors...

> This is why, I think it is an opportunity for everybody within OpenTox (and
> outside) to create a better LogP prediction model from a dataset, which has
> been recently made available to OpenTox . Models would be built preferably
> via OpenTox API , but not necessary (in that case we could consider wrapping
> the models into OpenTox API later) .
>
> Models can be then validated by OpenTox validation service at ALU-Freiburg
> and best one(s) selected.

Does OpenTox also provide the training data?

> The dataset is available via OpenTox dataset service (several formats via
> HTTP Accept:mime-type header  )
>
> http://apps.ideaconsult.net:8080/ambit2/dataset/181563
> http://apps.ideaconsult.net:8080/ambit2/dataset/181563

This is data to be used as training data? Do you have information on
how it was curated? How tautomers were selected? Etc...

It's about 2300 compounds with experimental LogP values... what's the license?

wget --accept application/rdf+xml
http://apps.ideaconsult.net:8080/ambit2/dataset/181563/metadata

did not reveal license/copyright or modify/redistribution rights...

Egon

-- 
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
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