Dear Christoph, All,

We've finally figured out what was making ambit datasets OWL-Full - it
was because I've failed to declare object-, data- and annotation
properties as such, but was using generic properties. 

The generic principle is to declare all classes and properties as
declared within opentox.owl.  It can actually be achieved by simply
importing opentox.owl into each generated RDF, but I was reluctant to do
so (for performance reasons) - because  not all opentox.owl classes are
relevant for all services.

With some more reading we learned the recommended approach is to split
the ontology into to small interlinked ontologies (e.g. one for
datasets, one for models, etc. and construct the entire opentox.owl by
importing all small ontologies when necessary).  We might do this
splitting in January for the next iteration, and let opentox api
ontologies be accessible via well known URLs.

Here is example of a small dataset (two compounds, 1 property)
http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/16?feature_uris[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12457&max=2
<http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/16?feature_uris%5B%5D=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12457&max=2>


    @prefix ot:      <http://www.opentox.org/api/1.1#> .
    @prefix dc:      <http://purl.org/dc/elements/1.1/> .
    @prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
    @prefix owl:     <http://www.w3.org/2002/07/owl#> .
    @prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .
    @prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .

    ot:Dataset
          a       owl:Class .

    dc:description
          a       owl:AnnotationProperty .

    <http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12457>
          a       ot:Feature ;
          dc:type "http://www.w3.org/2001/XMLSchema#string" .

    ot:dataEntry
          a       owl:ObjectProperty .

    ot:Compound
          a       owl:Class .

    dc:identifier
          a       owl:AnnotationProperty .

    ot:FeatureValue
          a       owl:Class .

    ot:Feature
          a       owl:Class .

    <http://ambit.uni-plovdiv.bg:8080/ambit2/compound/9083/conformer/262039>
          a       ot:Compound ;
          dc:identifier
    "http://ambit.uni-plovdiv.bg:8080/ambit2/compound/9083/conformer/262039"
    .

    dc:type
          a       owl:AnnotationProperty .

    ot:value
          a       owl:DatatypeProperty .

    ot:DataEntry
          a       owl:Class .

    <http://ambit.uni-plovdiv.bg:8080/ambit2/compound/4891/conformer/262038>
          a       ot:Compound ;
          dc:identifier
    "http://ambit.uni-plovdiv.bg:8080/ambit2/compound/4891/conformer/262038"
    .

    <http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/16>
          a       ot:Dataset ;
          dc:description
    "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/16?feature_uris[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12457&max=2"
    ;
          dc:identifier
    "http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/16?feature_uris[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12457&max=2"
    ;
          dc:title "Dataset = 16" ;
          ot:dataEntry
                  [ a       ot:DataEntry ;
                    ot:compound
    <http://ambit.uni-plovdiv.bg:8080/ambit2/compound/4891/conformer/262038>
    ;
                    ot:values
                            [ a       ot:FeatureValue ;
                              ot:feature
    <http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12457> ;
                              ot:value "139-88-8"^^xsd:string
                            ]
                  ] ;
          ot:dataEntry
                  [ a       ot:DataEntry ;
                    ot:compound
    <http://ambit.uni-plovdiv.bg:8080/ambit2/compound/9083/conformer/262039>
    ;
                    ot:values
                            [ a       ot:FeatureValue ;
                              ot:feature
    <http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12457> ;
                              ot:value "600-28-2"^^xsd:string
                            ]
                  ] .

    ot:values
          a       owl:ObjectProperty .

    ot:compound
          a       owl:ObjectProperty .

    dc:title
          a       owl:AnnotationProperty .

    ot:feature
          a       owl:ObjectProperty .


Hopefully, these observations could help other developers as well, so I
am sending this message to the list. 

If you still have OWL validating issues, please work together with
Ivelina towards resolution.

Best regards,
Nina

Christoph Helma wrote:
> Dear Nina,
>
> Can you send me a link to a small classification dataset (i.e.
> compounds and an endpoint like ActivityOutcome_CPDBAS_Hamster) in OWL-DL to
> debug my owl and dataset libraries? 
>
> Thanks,
> Christoph
>