Ontology service

UNDER DEVELOPMENT !!!!!!!!!!!

Example ontologies

• ECHA Endpoints ontology
  

• Algorithm Types ontology
  

Example of linking Features

with ECHA endpoint ontology

• by subclassing

• or by using a predicate

Example of linking an ot:Algorithm

with the algorithm types ontology

Note: owl:sameAs doesn't sound right here, more appropriate would be to invent property ot:typeOf

    <ot:Algorithm rdf:ID="WekaJ48">
        <dc:identifier rdf:datatype="&xsd;string"
            >http://myservice/algorithm/{algorithmid}</dc:identifier>
......
        <owl:sameAs rdf:resource="http://www.opentox.org/algorithms.owl#ClassificationEagerSingleTarget"/>
        <rdfs:comment rdf:datatype="&xsd;string"></rdfs:comment>
    </ot:Algorithm>

with Blue obelisk ontology

    <ot:Algorithm rdf:ID="XLogPCalculation">
        <dc:identifier rdf:datatype="&xsd;string"
            >http://myservice/algorithm/{algorithmid}</dc:identifier>
        <dc:title rdf:datatype="&xsd;string">XLogP</dc:title>
        <owl:sameAs rdf:resource="http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#xlogP"/>
    </ot:Algorithm>

Example of querying an Ontology service

All queries assume all of the following ontologies are available in the same repository: OpenTox resource, ECHA endpoints ontology, Algorithm Types ontology , Opentox examples. All queries use SPARQL.

 Retrieve all available ot:Algorithms :

SPARQL

PREFIX ot:<http://www.opentox.org/api/1.1#>

select ?x 
where {
?x rdf:type ot:Algorithm
}

Results:

The query returns references to all ot:Algorithm objects, , as defined in opentox-example ontology.

<http://www.opentox.org/example/1.1#XLogPCalculation>
<http://www.opentox.org/example/1.1#Toxtree>
<http://www.opentox.org/example/1.1#LazarAlgorithm>
<http://www.opentox.org/example/1.1#AlgorithmMLR>
<http://www.opentox.org/example/1.1#AlgorithmSVM>
<http://www.opentox.org/example/1.1#WekaJ48>

Retrieve all available ot:Algorithms, which are same as bo:xlogP algorithm, defined in Blue Obelisk ontology:

SPARQL

PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX ot:<http://www.opentox.org/api/1.1#>

select ?x 
where {
{?x rdf:type ot:Algorithm }
{?x owl:sameAs <http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#xlogP>}
}

Results:

The query returns reference to XLogPCalculation object, as defined in opentox-example ontology.

<http://www.opentox.org/example/1.1#XLogPCalculation>

Retrieve all Classification Algorithms:

SPARQL

PREFIX ota:<http://www.opentox.org/algorithms.owl#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
PREFIX ot:<http://www.opentox.org/api/1.1#>

select ?algorithm ?algorithm_type 
where {
{?algorithm  rdf:type ot:Algorithm}
{?algorithm  owl:sameAs ?algorithm_type}
{?algorithm_type rdf:type ota:Classification}
}

Results:

Retrieve all Features

SPARQL

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX dc:<http://purl.org/dc/elements/1.1/>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>

select ?feature ?id ?name ?source 
where 
{
{?feature  rdf:type ot:Feature}
{?feature dc:title ?name}
{?feature dc:identifier ?id}
{?feature ot:hasSource ?source}
}

 Results:

Retrieve all Models

SPARQL

select ?model 
where 
{?model rdf:type ot:Model}

Results:

Retrieve all Models, created by eager classification algorithms, single target variable:

SPARQL

PREFIX ot:<http://www.opentox.org/api/1.1#>
PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX owl:<http://www.w3.org/2002/07/owl#>

select ?model ?algorithm 
where 
{
{?model rdf:type ot:Model}
{?model ot:algorithm ?algorithm}
{?algorithm owl:sameAs ota:ClassificationEagerSingleTarget}
}

Results