Hi Nina,

On Tue, Dec 22, 2009 at 8:35 AM, Nina Jeliazkova <nina at acad.bg> wrote:
> This is true for all of us.  A more active participation from your side
> in the API discussions will be helpful, otherwise we might just fail to
> include in the API some essential for your software functionality.
>> 2) Unclear about whether we should fit our algorithm into Blue Obelix
>>
> It might be better suited to describe your algorithms in Algorithm types
> ontology, suggested by TUM , which is expected to include machine
> learning algorithms.  AFAIK Blue Obelisk ontology currently doesn't
> include machine learning algorithms .

The ontology just describes the entities involves... this is
complemented by a dictionary of QSAR descriptors that uses the
ontology to express the knowledge...

Nina, I'd love to set up a dictionary of machine learning
algorithms... let's continue on this.

> An initial version of algorithm types ontology is available here
> http://opentox.org/data/documents/development/RDF%20files/AlgorithmTypes/view
> .  Could you please have a look and then we will discuss where does your
> algorithm fit?

I'll have a look at that.

>> 4) There is no prior experience with RDF/OWL, we will need some help here.
>>
> All the partners started without prior experience with RDF/OWL.    I
> have tried to put together some introduction and Java examples at
> http://www.opentox.org/data/documents/development/RDF%20files/?searchterm=RDF%20files
> - did you look at those?
>
> Could you provide more details on your software development process
> (language, development platforms, specific problems encountered)?

I have quite some experience with RDF, and certainly assist. We are
using RDF in Bioclipse, for example, for dynamically look up QSAR
descriptor information, but you can check my chem-bla-ics blog for
many more applications. I can recommend the following web page for
questions about semantic web, OWL, RDF, etc:

http://www.semanticoverflow.com/

>> 5) Unable to make the R part of the code native to java as yet. Still
>> trying a few things. This hinders our ability to provide the API
>> interface.
>>
> I am aware of at least one Java - R integration, namely The CDK library
> (*http://cdk*.*sourceforge*.*net*/)  has R integration since few years -
> it might help if you consult the code there. And AFAIK the author of
> CDK-R code is on this list as well, so please do ask specific questions
> on the development mailing list.

Not sure if Rajarshi is on the list yet, but he indeed wrote various
levels of integration, calling R from a Java environment is one.

Have a look at http://www.omegahat.org/RSJava/, which has a section on
'Calling R from Java'.

Egon


-- 
Post-doc @ Uppsala University
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
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