Hello Egon,

Egon Willighagen wrote:
> On Wed, Mar 31, 2010 at 12:27 PM, Nina Jeliazkova <nina at acad.bg> wrote:
>   
>>> is it possible to run an OpenTox /algorithm directly on an SD or mol
>>> file? Or should that always be uploaded as data set first?
>>>
>>>       
>> The dataset should have an URI, so it should be uploaded, or the dataset
>> constructed from existing compounds/features at a certain dataset service.
>>     
>
> Must the URI point to an OpenTox API service? Or would a URI to just a
> SD file work too?
> Like http://example.org/someFile.sdf ?
>   
For some algorithms it might do, but IMHO most of the services support
only the mandatory RDF format so far.

One note for processing working directly with files rather than URI -
the latest was agreed within OpenTox, for
1) its best fit with the REST architecture - all resources  (regardless
of being data or models) are exposed by URIs
2) these dataset URIs are used to link algorithm, methods and features
within RDF representation. If we drop the requirements of having URIs,
it might be crucial for the  consistency of all OpenTox framework.

As an example ,see  curl -H "Accept:application/rdf+xml"
http://opentox.ntua.gr:3000/model/3  (or just
http://opentox.ntua.gr:3000/model/3  in a browser )

    <rdf:RDF
        xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
        xmlns:ot="http://www.opentox.org/api/1.1#"
        xmlns:ota="http://www.opentox.org/algorithmTypes.owl/#"
        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#" >
    ....
       <ot:trainingDataset
    rdf:resource="http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/269"/>
    ....


Another example is the  descriptor calculation. We are storing the URI
of the descriptor calculation algorithm in the feature RDF, in order to
be able to reuse it for new compounds.  In the RDF representation of a
dataset (below) there are links to the algorithm, used to generate
descriptors , or models, used to predict properties.
Unfortunately, all this "linked data" will break down, if submitting
files, not URIs  is introduced.

    curl -H "Accept:text/n3"
    http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/607

    or

    http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/607

    @prefix ot:      <http://www.opentox.org/api/1.1#> .
    @prefix ad:      <http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/> .
    @prefix af:      <http://ambit.uni-plovdiv.bg:8080/ambit2/feature/> .


    ad:607
          a       ot:Dataset ;
          ot:dataEntry
                  [ a       ot:DataEntry ;
                    ot:compound
    <http://ambit.uni-plovdiv.bg:8080/ambit2/compound/101215/conformer/269405>
    ;
                    ot:values
                            [ a       ot:FeatureValue ;
                              ot:feature af:103141 ;
                              ot:value "0.633"^^xsd:double
                            ] ;
                    ot:values
                            [ a       ot:FeatureValue ;
                              ot:feature af:106946 ;
                              ot:value "2.695"^^xsd:double
                            ]
                  ] .

    ot:hasSource
          a       owl:ObjectProperty .

    af:103141
          a       ot:Feature , ot:NumericFeature ;
          dc:creator "http://ambit.uni-plovdiv.bg:8080/ambit2" ;
          dc:identifier
    "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/103141"^^xsd:anyURI ;
          dc:title "TUM_CDK_XLogP" ;
          ot:hasSource
    <http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/algorithm/CDKPhysChem/XLogPDescriptor>
    ;
          ot:units "" ;
          =       ot:TUM_CDK_XLogP .



    af:106946
          a       ot:Feature , ot:NumericFeature ;
          dc:creator "http://ambit.uni-plovdiv.bg:8080/ambit2" ;
          dc:identifier
    "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/106946"^^xsd:anyURI ;
          dc:title "Empty feature for prediction." ;
          ot:hasSource
    <http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/model/TUMOpenToxModel_kNN_6>
    ;
          ot:units "" ;
          =       ot: .



Looking to your comments,


Nina
> Egon
>
>