Feature

— filed under: Ontology, API, wp1, wp2

We still need a way to access information about the Features. Defining Features as rdf:Property (predicates) makes impossible using them as rdf:Classes, which is necessary in many cases. Now Features are defined as owl:Classes.

Feature URI is defined by dc:identifier (Dublin Core namespace)

...
xmlns:dc="http://purl.org/dc/elements/1.1/"
...
<dc:identifier rdf:datatype="&xsd;string"
            >http://myserice/feature/{featureid2}</dc:identifier>

Feature name is defined by dc:title (Dublin Core namespace)

<dc:title rdf:datatype="&xsd;string">XLogP</dc:title>

The origin of the Feature is defined by ot:hasSource (OpenTox namespace) element and can be Algorithm, Model or Dataset
Links with other ontologies are established via RDF subclassing (rdf:type property), or owl:sameAs property.

Examples:

Features, defined as originated from a Dataset or Machine Learning Algorithm

   <ot:Feature rdf:ID="MultiCellCall">

        <dc:identifier rdf:datatype="&xsd;string"
            >http://myservice/feature/{featureid1}</dc:identifier>
        <dc:source rdf:datatype="&xsd;string"
            >http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_MultiCellCall</dc:source>
        <ot:hasSource rdf:resource="#DSSToxCPDBAS"/>
    </ot:Feature>
    <ot:Feature rdf:ID="MultiCellCallPredicted">
        <dc:identifier rdf:datatype="&xsd;string"
            >http://myservice/feature/{featureid3}</dc:identifier>
        <ot:hasSource rdf:resource="#WekaJ48"/>
    </ot:Feature>

Feature, with a descriptor calculation algorithm , defined as a source.

<ot:Feature rdf:ID="XLogPDescriptor">
        <dc:identifier rdf:datatype="&xsd;string"
            >http://myservice/feature/{featureid2}</dc:identifier>
        <dc:title rdf:datatype="&xsd;string">XLogP</dc:title>
        <ot:hasSource rdf:resource="#XLogPCalculation"/>
</ot:Feature>

Features, which are defined as Carcinogenicity endpoints, according to ECHA endpoints ontology

<rdf:RDF xmlns="http://www.opentox.org/example/1.1#"
     xml:base="http://www.opentox.org/example/1.1"
     xmlns:ot="http://www.opentox.org/api/1.1#"
     xmlns:dc="http://purl.org/dc/elements/1.1/"
     xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
     xmlns:p3="&dc;#"
     xmlns:p2="http://www.opentox.org/algorithmTypes.owl#"
     xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
     xmlns:p1="http://www.w3.org/1998/Math/MathML"
     xmlns:otee="http://www.opentox.org/echaEndpoints.owl#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:swrl="http://www.w3.org/2003/11/swrl#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">

    <owl:Ontology rdf:about="">
        <rdfs:comment rdf:datatype="&xsd;string"
            >An example of OpenTox resource ontology usage. Definition of example instances</rdfs:comment>
        <owl:imports rdf:resource="http://www.opentox.org/echaEndpoints.owl"/>
        <owl:imports rdf:resource="http://www.opentox.org/api/1.1"/>
    </owl:Ontology>

    <ot:Feature rdf:ID="CarcinogenicityLazar">
        <dc:identifier rdf:datatype="&xsd;string">/feature/1</dc:identifier>
        <ot:hasSource rdf:resource="#Lazar"/>
        <owl:sameAs rdf:resource="http://www.opentox.org/echaEndpoints.owl#Carcinogenicity"/>
    </ot:Feature>
    <ot:Feature rdf:ID="CarcinogenicityToxtree">
        <dc:identifier rdf:datatype="&xsd;string">/feature/2</dc:identifier>
        <ot:hasSource rdf:resource="#ToxtreeCarcinogenicity"/>
        <owl:sameAs rdf:resource="http://www.opentox.org/echaEndpoints.owl#Carcinogenicity"/>
    </ot:Feature>
</rdf:RDF>

How this relationship is defined in Protege is illustrated below:

Sections

Feature

Examples:

Document Actions

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