Christoph Helma wrote:
> Excerpts from Nina Jeliazkova's message of Fri Nov 06 11:25:14 +0100 2009:
>   
>> Dear Christoph, All,
>>
>> Christoph Helma wrote:
>>     
>>> Dear all,
>>>
>>> I have started to summarize our API discussions in order to finalize
>>> version 1.1. I will try to integrate our discussions into the API
>>> proposals on the website and inform you as soon as a component is ready.
>>> I would like to resolve the last issues as far as possible on the
>>> website and on the mailinglist before heading for a final virtual
>>> meeting.
>>>
>>> Lets start with an easy one: 
>>> http://opentox.org/dev/apis/api-1.1/structure
>>>   
>>>       
>> This should be fine so far, we could add additional mime type for RDF.
>>     
>
> What should be the content of the RDF representation - should it
> indicate eg. external resources for the compound (using e.g. the
> owl:sameAs predicate)?
>
>   
A start point could be the OpenMolecules service Egon ponted at some
time ago,  for example:  http://rdf.openmolecules.net/?InChI=1/CH4/h1H4

    <?xml version="1.0"?>
    <?xml-stylesheet type="text/xsl"
    href="http://rdf.openmolecules.net/html.xsl"?>
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:iupac="http://www.iupac.org/"
    xmlns:rdfomn="http://rdf.openmolecules.net/#"
    xmlns:owl="http://www.w3.org/2002/07/owl#">

    <rdf:Description
     rdf:about="http://rdf.openmolecules.net/?InChI=1/CH4/h1H4">

     <dc:identifier>info:inchi/InChI=1/CH4/h1H4</dc:identifier>
     <iupac:inchi>InChI=1/CH4/h1H4</iupac:inchi>

    </rdf:Description>

    <rdf:Description
     rdf:about="http://rdf.openmolecules.net/?InChI=1/CH4/h1H4">

      <dc:source>Chemical blogspace</dc:source>

    <pubchem:cid
    xmlns:pubchem="http://pubchem.ncbi.nlm.nih.gov/#">297</pubchem:cid>
    <pubchem:name
    xmlns:pubchem="http://pubchem.ncbi.nlm.nih.gov/#">methane</pubchem:name>
    <cb:discussedBy
    xmlns:cb="http://cb.openmolecules.net/#">http://chem-bla-ics.blogspot.com/2008/09/ubiquity-fun-entering-semantic-markup.html</cb:discussedBy>
    <cb:discussedBy
    xmlns:cb="http://cb.openmolecules.net/#">http://chem-bla-ics.blogspot.com/2007/09/tagging-molecules-mashup-of-connotea.html</cb:discussedBy>

    </rdf:Description>

    <rdf:Description
     rdf:about="http://rdf.openmolecules.net/?InChI=1/CH4/h1H4">

      <dc:source>ChEBI</dc:source>

    <rdfomn:chebiid>CHEBI:16183</rdfomn:chebiid><owl:sameAs
    rdf:resource="http://bio2rdf.org/chebi:16183"/>
    </rdf:Description>


    <rdf:Description
      xmlns:owl="http://www.w3.org/2002/07/owl#"
     rdf:about="http://rdf.openmolecules.net/?InChI=1/CH4/h1H4">

      <dc:source>DBPedia</dc:source>
    <owl:sameAs rdf:resource="http://dbpedia.org/resource/Methane"/>

    </rdf:Description>
    <rdf:Description
      xmlns:owl="http://www.w3.org/2002/07/owl#"
     rdf:about="http://rdf.openmolecules.net/?InChI=1/CH4/h1H4">

      <dc:source>NMRShiftDB</dc:source>

    <rdfomn:nmrmolid>20029286</rdfomn:nmrmolid>
    <owl:sameAs
    rdf:resource="http://pele.farmbio.uu.se/nmrshiftdb/?moleculeId=20029286"/>

    </rdf:Description>

    </rdf:RDF>

It contains pointers to same resources, as well as the links to the
source of the information. 
>> Another discussion point is should we add at this place some querying
>> functionality, like in IN-SILICO services 
>> http://webservices.in-silico.ch/compound/v0/c1ccccc1/match/N ?
>>     
>
> I for the next version of our services I have moved substructure
> matching (as well as similarity calculations) to the algorithm component
> (although they are technically performed within the compound
> (substructure matching) and dataset (similarity calculations)
> components.
>   
OK, we'll discuss then there. 

Best regards,
Nina
> Best regards,
> Christoph
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