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The integration with external ontologies.

BioSWR uses Semantic Annotations for WSDL and XML Schema (SAWSDL) specification to annotate Web services' components. The integration of external ontologies is implemented via intermediate ontology that defines available annotations for essential WSDL 2.0 components (figure 1.). BioSWR uses EMBRACE Data and Methods (EDAM) ontology as a most complete source of bilogical definitions available.

Prefix: : <http://edamontology.org/>
Prefix: wsdl: <http://www.w3.org/ns/wsdl-rdf#>
Prefix: sawsdl: <http://www.w3.org/ns/sawsdl#>
Class: wsdl:Interface SubClassOf: sawsdl:modelReference only topic_0003
Class: wsdl:InterfaceOperation SubClassOf: sawsdl:modelReference only topic_0003
Class: wsdl:InputMessage SubClassOf: sawsdl:modelReference only topic_0006
Class: wsdl:OutputMessage SubClassOf: sawsdl:modelReference only topic_0006
Figure 1. SAWSDL intermediate ontology that links wsdl-rdf ontology components to EDAM ontological definitions.

This very simple ontology allows to decide whether some term may be used as a annotation. For this purpose BioSWR uses a HermiT reasoner.

Once a user annotate some WSDL component with EDAM annotations, both WSDL and OWL Web service descriptions become annotated with sawsdl:modelReference reference (figures 2,3).

<wsdl:description>
  ...
  <wsdl:interface name="describePDB">
    <wsdl:operation name="describePDB">
      <wsdl:input xmlns:sawsdl="http://www.w3.org/ns/sawsdl" sawsdl:modelReference="http://edamontology.org/data_1127" element="request"/>
      <wsdl:output element="PDBdescription"/>
    </wsdl:operation>
  </wsdl:interface>
  ...
</wsdl:description>
Figure 2. WSDL 2.0 Web service's input annotated with "PDB ID" EDAM ontology term.
<owl:NamedIndividual rdf:about="http://www.rcsb.org/pdb/rest/#wsdl.interfaceMessageReference(describePDB/describePDB/In)">
  <rdf:type rdf:resource="http://www.w3.org/ns/wsdl-rdf#InputMessage"/>
  <rdf:type rdf:resource="http://www.w3.org/ns/wsdl-rdf#InterfaceMessageReference"/>
  <sawsdl:modelReference rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://edamontology.org/data_1127</sawsdl:modelReference>
  ...
</owl:NamedIndividual>
Figure 3. OWL 2 Web service's input message reference annotated with "PDB ID" EDAM ontology term.