[OTDev] Performance testing and monitoring

Nina Jeliazkova nina at acad.bg
Thu Mar 18 16:58:04 CET 2010


Hello Surajit,

>>     
>
> curl http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model<http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/rest/model>
>
>
> should return what you want .... just remove the rest word in the middle
> ....
>   
Having a look at RDF output of the model  
http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model  , I
have the following comments :


    <rdf:RDF
        xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
        xmlns:ot="http://www.opentox.org/api/1.1#"
        xmlns:owl="http://www.w3.org/2002/07/owl#"
        xmlns:dc="http://purl.org/dc/elements/1.1/"
        xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
        xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
      <owl:Class rdf:about="http://www.opentox.org/api/1.1#Model"/>
    // this is fine
      <ot:Model
    rdf:about="http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model/1">
    //ot:parameters are meant to hold parameters specific for model
    calculations, e.g. max number of decision tree nodes , not clear how
    dc:description and dc:title here are related to parameters
        <ot:parameters rdf:parseType="Resource">
          <dc:description
    rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
          >mutagenic activity in Salmonella typhimurium
    TA100</dc:description>
          <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
          >ToxicityEndpoint</dc:title>
        </ot:parameters>

/*The dataset should be defined as ot:Dataset object and the
trainingDataset property should look like
<ot:trainingDataset>      <ot:Dataset
rdf:about="http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/194"/>   
</ot:trainingDataset>     

otherwise, as it is written currently, it will not be recognized as a
dataset (and owl validation might fail )
*/


        <ot:trainingDataset rdf:parseType="Resource">
          <dc:identifier
    rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI"
         
    >http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/dataset/FT_1</dc:identifier>
          <dc:description
    rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
          >The dataset which shows all the fragments in the
    dictionary</dc:description>
          <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
          >fragmentDataset</dc:title>
        </ot:trainingDataset>
        <ot:trainingDataset rdf:parseType="Resource">
          <dc:identifier
    rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI"
         
    >http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/dataset/MT_1</dc:identifier>
          <dc:description
    rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
          >The dataset which was used to get the fragments in the
    dictionary for this model</dc:description>
          <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
          >dictionaryProducingDataset</dc:title>
        </ot:trainingDataset>

/*
There is  no modelTypes.owl defined - could you consider extending
AlgorithmTypes.owl or BlueObelisk descriptors.owl instead , and change
the reference.
*/

       
    <ot:isA>http://www.opentox.org/modelTypes.owl#MCSSBasedToxicityPredictor</ot:isA>
        <dc:identifier
    rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI"
       
    >http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model/1</dc:identifier>
        <dc:description
    rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >Model and dictionary built from 55 active and 55 inactive
    compounds</dc:description>
        <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >Model Number : 1</dc:title>

/*
This representation does not contain ot:independentVariables,
ot:dependentVariables nor ot:predictedVariables.  While
ot:independentVariables can be skipped, if you are generating
descriptors on the fly, it is important to include the rest two,
otherwise the clients will not be able to find out where the results are
stored.  Please consult the existing services of other partners for
examples.
*/

      </ot:Model>
    </rdf:RDF>



Best regards,
Nina
> cheers
> Surajit
>
>
>   
>> http://ambit.uni-plovdiv.bg:8080/ambit2/ontology/test?search=+http%3A%2F%2Fopentox2.informatik.uni-freiburg.de%3A8080%2FMaxtoxTest%2Frest%2Fmodel
>>
>> In particular, when you fix the problem, a reference to model 1 should
>> appear in the "Model [http://www.opentox.org/api/1.1#Model]"  section
>> at the bottom of the ontology playground page.
>>
>> According to opentox.owl, the RDF represnetation of a model should
>> include a statement that the model is of type
>> <http://www.opentox.org/api/1.1#Model> (or if abbreviated - ot:Model)
>> , e.g. there should be a triple like
>>
>> <http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model/1>
>> rdf:type ot:Model .
>>
>> Kind regards,
>> Vedrin
>>
>> PS: You might want to check the output of the following two queries as
>> an example of RDF representations of list of models and specific
>> model:
>>
>> curl -H "Accept:application/rdf+xml"
>> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/model
>> curl -H "Accept:application/rdf+xml"
>>
>> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/model/TUMOpenToxModel_kNN_6
>> _______________________________________________
>> Development mailing list
>> Development at opentox.org
>> http://www.opentox.org/mailman/listinfo/development
>>
>>     
>
>
>
>   



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