Re: [Cdk-devel] substructure query data sets

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--- On Fri, 2/13/09, Andrew Dalke <da...@da...> wrote:

> Does anyone have pointers to a better data set? Ideal would
> be 5,000  
> structures randomly selected from PubChem submissions.
> I'm going to  
> ask them, but even though it's public data I suspect
> they might  
> (rightly) consider the submissions as private.

You might check out the links contained in the following - some of them appear to match your criteria:

http://tinyurl.com/chemdatasets

The terms of use for PubChem data are here, AFAIK:

http://www.ncbi.nlm.nih.gov/About/disclaimer.html

You can easily create your own molecular dataset by saving a PubChem query as XML:

http://tinyurl.com/pugml

I'm not quite sure I understand you concern about public/private. What specific right is in your mind in question? Copyright? Patent? Trade secret?

In MX:

http://code.google.com/p/mx-java/

and cheminfbenchmark:

http://github.com/egonw/cheminfbenchmark/tree/master

I've taken the same approach. It's worked pretty well so far. The nice thing is I can keep a copy of the PubChem XML query that generated the results under revision control, for example:

http://tinyurl.com/chemdata

If I ever need a variant of the dataset (more structures, for example), I just edit the query, submit to PubChem, and be done with it.

> I've never heard of such a data set, and looking around
> now I didn't  
> find anything. Most of the fingerprint interest I know of
> is for  
> similarity searching, and so not really appropriate.
> 
> 				Andrew
> 				da...@da...

___________________________________

Richard L. Apodaca

http://depth-first.com      Blog
http://metamolecular.com    Company

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