Hello Pantelis, All,

chung wrote:
> Dear Nina, All,
>
> On Tue, 2009-12-01 at 19:21 +0200, Nina Jeliazkova wrote:
>   
>> chung wrote:
>>     
>>> Dear All,
>>>  According to the current API, the objects of all
>>> "values" ( http://opentox.org/api/1.1/#values ) are Resources that have
>>> a "value" ( http://opentox.org/api/1.1/#value ) and a
>>> "feature" ( http://opentox.org/api/1.1/#feature ) which is a Literal.
>>> Wouldn't it be more convenient to consider of features as Resources.
>>> This way we establish the counterparts of the "feature definitions" of
>>> API 1.0. 
>>>   
>>>       
>> In the opentox.owl Feature is a Class, i.e. a Resource.   I support
>> bringing back to API 1.1 the Feature object , in place of API 1.0
>> feature_definition. 
>>
>> http://opentox.org/api/1.1/#feature  is a Property, in fact it should be better named "hasFeature".
>>     
>
> No its not about its name. All in all, its not made to be human readable
> so it doesn't really matter. The issue is that we use Literals to
> describe the Features in a dataset and not Resources. A Literal cannot
> have an RDF description, while a Resource can! [Think of Literals as
> termination points of the RDF...]

If you look closely into opentox.owl 
http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/view
, you will notice Feature is a Resource (owl:Classs to be exact). 
Feature is a subclass of OpenToxResource. Below is an excerpt of
opentox.owl :

      <owl:Class rdf:about="#Feature">
        <owl:disjointWith rdf:resource="#Compound"/>
        <owl:disjointWith>
          <owl:Class rdf:about="#Model"/>
        </owl:disjointWith>
        <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >1.1</owl:versionInfo>
        <dc:source rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        ></dc:source>
        <owl:disjointWith rdf:resource="#FeatureValue"/>
        <rdfs:subClassOf rdf:resource="#OpentoxResource"/>
        <owl:disjointWith>
          <owl:Class rdf:about="#DataEntry"/>
        </owl:disjointWith>
        <dc:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        >/feature/{featureid}</dc:identifier>
        <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        ></dc:title>
        <owl:disjointWith>
          <owl:Class rdf:about="#Parameter"/>
        </owl:disjointWith>
        <owl:disjointWith>
          <owl:Class rdf:about="#Algorithm"/>
        </owl:disjointWith>
        <owl:disjointWith rdf:resource="#Dataset"/>
        <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
        ></dc:description>
      </owl:Class>

There is a screenshot of Feature class in Protege, where it is clear it
is not Literal :
http://opentox.org/data/documents/development/RDF%20files/Screenshots/Feature/image_view_fullscreen

And the overview of relationships between opentox objects clearly shows
Feature is a resource ,with lot of relationships to other objects:
http://opentox.org/data/documents/development/RDF%20files/Screenshots/Overview/image_view_fullscreen

 This is different from ot:feature (lowercase letters), which is a
property (owl:Property), relating FeatureValue (another resource!) to
Feature.

  <owl:ObjectProperty rdf:ID="feature">
    <rdfs:range rdf:resource="#Feature"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >FeatureValue contains a value for specific Feature, specified by this relationship.</rdfs:comment>
    <rdfs:domain rdf:resource="#FeatureValue"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
    <rdfs:isDefinedBy rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
    >http://opentox.org/api/1.1</rdfs:isDefinedBy>

  </owl:ObjectProperty>

Do please look in opentox.owl, this is where the definition of objects
is done.  RDF allows huge variety of syntax, but the objects themselves
and their relationships are clearly defined.

> For example consider of the following triple:
>
> S: <SomeValue> 
> P: <http://opentox.org/api/1.1/#feature> 
> O: "FeatureName"^^xsd:string
>
>   
This triple is not correct, according to opentox.owl , because 

<http://opentox.org/api/1.1/#feature> has <rdfs:range rdf:resource="#Feature"/> and  <rdfs:domain rdf:resource="#FeatureValue"/>.  This means S: can only be FeatureValue and O: can only be Feature.
 

 

> I just say to change this into the following triple:
>
> S: <SomeValue> 
> P: <http://opentox.org/api/1.1/#feature>
> O: <http://someOntologyForFeatures.com/feature/myFavoriteFeature> 
>
> What do you say? 
>   
Please have a look at the examples I've prepared for Feature and other
objects at

http://opentox.org/data/documents/development/RDF%20files/Feature

It is explained how one can relate values with Features and  Features to
other ontologies.

A real case example (from current ambit implementation) is below: 

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

<http://localhost:8080/ambit2-www/feature/1>
      a       ot:Feature .

ot:FeatureValue
      a       owl:Class .

ot:Dataset
      a       owl:Class .

<http://localhost:8080/ambit2-www>
      ot:dataEntry
              [ a       ot:DataEntry ;
                ot:compound <http://localhost:8080/ambit2-www/compound/1> ;
                ot:values
                        [ a       ot:FeatureValue ;
                          ot:feature
<http://localhost:8080/ambit2-www/feature_definition/1> ;
                          ot:value "CH2O"
                        ]
              ] .

ot:Compound
      a       owl:Class .

<http://localhost:8080/ambit2-www/compound/1>
      a       ot:Compound .

ot:Feature
      a       owl:Class .

ot:DataEntry
      a       owl:Class .

> ** I attach an image of the graph of a dataset which complies with the
> specifications of the current API. 
>
>   
A full graph of opentox objects was published last week at
http://opentox.org/data/documents/development/RDF%20files/Screenshots/Overview/view
<http://opentox.org/data/documents/development/RDF%20files/Screenshots/Overview/view>

Best regards,
Nina

>> Best regards,
>> Nina
>>     
>>>   What is more, we're working on an RDF parser for RDF representations
>>> of datasets using Jena (a Java Library for editing and Parsing RDFs).
>>> Should we consider the current specifications as final or we're
>>> expecting for other changes? Regardless of the abstraction level of our
>>> source code, its important to know what input we should expect (in terms
>>> of Dataset RDF representations).
>>>       
>
> Well, that was my main question... Should we consider of the current API
> as final or not? Of course I don't ask for any changes in the interface.
> I simply want to make some points more clear to avoid changes in the
> specifications.
>
> Best Regards,
> Pantelis
>
>   
>>> Best Regards,
>>> Pantelis
>>>
>>> _______________________________________________
>>> Development mailing list
>>> Development at opentox.org
>>> http://www.opentox.org/mailman/listinfo/development
>>>   
>>>       
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>>
>>     
>
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