Egon,

I've found ChemAxiom [1] efforts quite interesting and wonder if they
are related to Bioclipse.  ChemAxiom has a notion for ChemicalSpecies
and MolecularEntity as well as generic class for Property (with
subclasses to NamedProperty and e.g. MeltingPoint) , and I am trying to
find out how to map into OpenTox Compound/Feature resources.

[1] Nico Adams, Edward O. Cannon & Peter Murray-Rust, ChemAxiom – An
Ontological Framework for Chemistry in Science,
http://precedings.nature.com/documents/3714/version/1

Best regards,
Nina

Nina Jeliazkova wrote:
> Egon Willighagen <egon.willighagen at gmail.com> wrote:
>
>   
>> On Fri, Oct 2, 2009 at 9:24 AM, Nina Jeliazkova <nina at acad.bg> wrote:
>>     
>>> Egon Willighagen <egon.willighagen at gmail.com> wrote:
>>>       
>>>> I can strongly second this suggestion, and help/advise here in these
>>>> matters if you like. Last week I have become official Invited Expert
>>>> to the W3 Health Care and Life Sciences (HCLS) Interest Group, and
>>>> working on RDF in relation to cheminformatics (in the CDK and
>>>> Bioclipse, mostly).
>>>>
>>>>         
>>> Congratulations! It will be really good if you could help us with some
>>> pointers to start with?
>>>       
>> And perhaps collaborate on some things?
>>     
>
> Definitely :) I hope OpenTox partners will join the email exchange soon.
>
>   
>> BTW, the QSAR descriptor ontology is already in OWL.
>>
>>     
>>> OpenTox would be interested in RDF for
>>>
>>> 1) Chemical compounds
>>> 2) Properties of chemical compounds (any kind of; existing ontologies )
>>> 3) Sets of chemical compounds
>>> 4) Sets of chemical compounds + properties
>>> 5) Models
>>> 6) Algorithms (machine learning algorithms as a start)
>>> 7) Model validation
>>>       
>> Yes, what not :)
>>
>> Check my blog for what I have been doing sofar:
>>
>> http://chem-bla-ics.blogspot.com/search?q=rdf
>>
>>     
>
> OK, I am adding few top level pointers as well:
>
> http://www.w3.org/RDF/
> http://www.daml.org/ontologies/
>
>   
>>> I am pretty sure there is lot of work already done 1) and 2) (e.g. RDF
>>>       
> name
>   
>>> space for InChI exists).
>>>
>>>       
>>>>> From technical point of view, RDF/XML can be considered just a XML with
>>>>> specific name spaces.  It seems there are plenty of libraries for
>>>>>           
>>> different
>>>       
>>>>> languages and frameworks.
>>>>>           
>>>> RDF/XML is only one serialization; others exist too, like N3, but even
>>>>         
>> JSON.
>>     
>>> Yes, I pointed to XML serialization, because it might be perceived as a
>>> shorter step from current custom XML schemas. I didn't knew about JSON
>>> serialization (many things to learn these days).
>>>       
>> Yes, XSLT is rather suitable for that. I can also strongly recommend
>> looking at RDFa, though I am not sure Plone has RDFa support yet.
>>
>>     
>
> YAML serialization of RDF seems to exists as well.
>
>
> Regards,
> Nina
>
>   
>>>>> Last but not least RDF offers a way to denote multiple URI point to the
>>>>> same object ;)
>>>>>           
>>>> I assume your refer to owl:sameAs ?
>>>>         
>>> Yes, we had the issue of non-unique URIs discussed several times.
>>>       
>> Yes, OWL is very suited to make such statements.
>>
>>     
>
>   
>> Egon
>>     
>
>
>
>
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