Dear Nina, All,

Thanks for the example - it seems that I have figured out how to create
datasets with simple values (I am temporarily including the complete
opentox.owl), but I am still struggeling with tuples and
complex values.

I have also asked Micha to make opentox.owl available under
http://www.opentox.org/api/1.1. Right now you can download the ontology
from this address, but it is not yet possible to include it into 
ontologes. Micha will try to figure out why (maybe it is a mime-type
problem).

Best regards,
Christoph

Excerpts from Nina Jeliazkova's message of Sat Dec 19 08:43:54 +0100 2009:
> 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.u
> ni-plovdiv.bg:8080/ambit2/feature/12457&max=2
> <http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/16?feature_uris%5B%5D=http://am
> bit.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
>