Hi Surajit,

On Mon, Aug 16, 2010 at 2:41 PM, surajit ray <mr.surajit.ray at gmail.com> wrote:
> Hi Nina,
>
> I am trying to upload a generated feature to an Ambit server. Would
> you have some example class doing this in Java ?
>


> My work flow is
> a) Accept a compound uri and a dataset uri
> b) Retrieve compound smiles from compound from uri
> c) Retrieve dataset from uri
> d) parse dataset representation to get compound URIs
> e) get the smiles of all dataset compounds
> f) run some code ...
> g) upload a feature of this compound to an Ambit location
>
>
> only step g) remains. Therefore it would be great help if you have an
> example. The API page on opentox on feature does not provide any
> examples (link : http://opentox.org/dev/apis/api-1.1/Feature)
>

The basic procedure is you add the new features into the RDF
representation of the dataset and POST (or PUT) the updated dataset
back.
If in c) you retrieve the dataset in Jena model,  you would need to
add an instance of ot:Feature to the model and add to data entries
(ot:DataEntry, think dataset rows) the new feature and its values
(similar to adding new columns to a table ).

Could you have a look at
https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-client/src/test/java/org/opentox/dataset/test/FeatureTest.java
?  I think the method OntModel addFeaturesToDataset(String dataset)
method is what you need.

> also I have a couple of question about datasets etc
> 1) Datasets contain listings of conformers of compounds. I am assuming
> that the conformer uri will produce the same Smile representation as
> the compound uri itself. Is that correct ?

Yes.

> 2) If I have some property like MCSS, I would like to have the same
> feature for the two compounds being compared. Meaning when compared -
> Compound A and Compound B should have the same MCSS right ? So I need
> a feature which belongs to both compounds. Is this possible in the
> present opentox framework ?
>
This is exactly what features are for.  You could define a feature ,
representing particular MCSS, and assign same value (e.g. TRUE ) to
compounds, having the same MCSS, and different value (e.g. FALSE)
otherwise.

A feature by itself is not associated with any compound. The feature
values association is done via data entries in a dataset, and normally
it could be done with as many compounds as necessary.

In the example below, the feature feature/21573

<rdf:RDF
    xmlns:ac="http://apps.ideaconsult.net:8080/ambit2/compound/"
    xmlns:ot="http://www.opentox.org/api/1.1#"
xmlns:af="http://apps.ideaconsult.net:8080/ambit2/feature/"
 -- prefixes skipped --
  xml:base="http://apps.ideaconsult.net:8080/ambit2/">
  <owl:Class rdf:about="http://www.opentox.org/api/1.1#Dataset"/>
  <owl:Class rdf:about="http://www.opentox.org/api/1.1#Compound"/>
  <owl:Class rdf:about="http://www.opentox.org/api/1.1#Feature"/>
  <owl:Class rdf:about="http://www.opentox.org/api/1.1#FeatureValue"/>
  <owl:Class rdf:about="http://www.opentox.org/api/1.1#NumericFeature">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#Feature"/>
  </owl:Class>
  <owl:Class rdf:about="http://www.opentox.org/api/1.1#NominalFeature">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#Feature"/>
  </owl:Class>
  <owl:Class rdf:about="http://www.opentox.org/api/1.1#DataEntry"/>
  <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#acceptValue"/>
  <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#dataEntry"/>
  <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#hasSource"/>
  <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#values"/>
  <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#compound"/>
  <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#feature"/>
  <owl:DatatypeProperty rdf:about="http://www.opentox.org/api/1.1#units"/>
  <owl:DatatypeProperty rdf:about="http://www.opentox.org/api/1.1#value"/>
  <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/type"/>
  <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title"/>
  <owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/description"/>
  <ot:Dataset rdf:about="dataset/9">
    <ot:dataEntry>
      <ot:DataEntry>
        <ot:values>
          <ot:FeatureValue>
            <ot:value rdf:datatype="http://www.w3.org/2001/XMLSchema#double"
            >1.0</ot:value>
            <ot:feature>
              <ot:Feature rdf:about="feature/21573">

<dc:creator>http://www.epa.gov/NCCT/dsstox/sdf_isscan_external.html</dc:creator>

<ot:hasSource>ISSCAN_v3a_1153_19Sept08.1222179139.sdf</ot:hasSource>
                <ot:units></ot:units>
                <owl:sameAs
rdf:resource="http://www.opentox.org/echaEndpoints.owl#Carcinogenicity"/>
                <ot:acceptValue>3.0</ot:acceptValue>
                <rdf:type
rdf:resource="http://www.opentox.org/api/1.1#NominalFeature"/>
                <ot:acceptValue>1.0</ot:acceptValue>
                <rdf:type
rdf:resource="http://www.opentox.org/api/1.1#NumericFeature"/>
                <dc:title>Canc</dc:title>
              </ot:Feature>
            </ot:feature>
          </ot:FeatureValue>
        </ot:values>
        <ot:compound>
          <ot:Compound rdf:about="compound/44497/conformer/409422"/>
        </ot:compound>
      </ot:DataEntry>
    </ot:dataEntry>
    <ot:dataEntry>
      <ot:DataEntry>
        <ot:values>
          <ot:FeatureValue>
            <ot:value rdf:datatype="http://www.w3.org/2001/XMLSchema#double"
            >3.0</ot:value>
            <ot:feature rdf:resource="feature/21573"/>
          </ot:FeatureValue>
        </ot:values>
        <ot:compound>
          <ot:Compound rdf:about="compound/413/conformer/409421"/>
        </ot:compound>
      </ot:DataEntry>
    </ot:dataEntry>
  </ot:Dataset>
</rdf:RDF>


> Thanks
> Surajit
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