Nina,

Thanks for the clarification. I think it would greatly improve the user experience if we could add a simple definition of substructures and also to clean the output of existing services from all traces of HTML and leave the rendering to the client. Maybe this is something to discuss at the meeting next week.

/Ola

On 3 aug 2011, at 10.23, Nina Jeliazkova wrote:

> Hi Ola,
> 
> On 3 August 2011 10:58, Ola Spjuth <ola.spjuth at farmbio.uu.se> wrote:
> 
>> Hi,
>> 
>> I was wondering if there is a definition how results from predictions are
>> to be structured in order for clients to interpret it.
> 
> 
> Yes, all should follow ot:Dataset RDF format in opentox API ontology.
> http://opentox.org/api/1.1/opentox.owl
> 
> N3 Example:
> 
> []    a       ot:Dataset ;
>      ot:dataEntry
>              [ a       ot:DataEntry ;
>                ot:compound <
> http://apps.ideaconsult.net:8080/ambit2/compound/100/conformer/143935> ;
>                ot:values
>                        [ a       ot:FeatureValue ;
>                          ot:feature <
> http://apps.ideaconsult.net:8080/ambit2/feature/27457> ;
>                          ot:value "10.335800170898438"^^xsd:double
>                        ]
>              ] .
> 
> 
> <http://apps.ideaconsult.net:8080/ambit2/compound/100/conformer/143935>
>      a       ot:Compound .
> 
> ot:NumericFeature
>      a       owl:Class ;
>      rdfs:subClassOf ot:Feature .
> 
> Where ot:DataEntry is roughly analogous to a row in a spreadsheet , and
> ot:Feature - to a spreadsheet column, ot:FeatureValue - to a spreadsheet
> cell.
> 
> This had been explained in various reports & publications, as well as on
> opentox site.  (Yes, the documentation could be improved :)
> 
> 
> 
>> For example, if a result has a predicted toxicity value (e.g. Double)
> 
> 
> All these are represented as ot:Feature, and values i as ot:FeatureValue
> entries, as in the above example.
> 
> The feature should be instance of any of ot:NumericFeature, ot:StringFeature
> , ot:NominalFeature
> 
> 
>> with accuracy (Double)
> 
> 
> The feature should be instance of ot:ModelConfidenceFeature and links to the
> feature with predicted value via ot:confidenceOf property.
> This is used by the validation service.
> 
> 
>> and a subtructure (set of atoms),
> 
> 
> Apart from agreeing to use additional ot:smarts property for structure
> features , this was not standardised further.
> 
> 
>> how this is defined for clients to reason and visualize it. I now see HTML
>> code in some prediction results, and I'm sure this cannot be the intention.
>> 
> 
> No, it is not :)
> 
> Nina
> 
> [1] http://www.jcheminf.com/content/3/1/18
> 
>> 
>> Cheers,
>> 
>> /Ola
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>> 
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