http://www.ebi.ac.uk/ontology-lookup/
Having a central repository of Ontologies is great idea and I give them kudos for all the hard work.
They advertise a web service for looking up various Ontologies using the SOAP protocol, which can be found here:
http://www.ebi.ac.uk/ontology-lookup/WSDLDocumentation.do#Link0332BDE0
However, as of today, they have issues with their web service.
I used the wsdl2java utility found with Apache CXF and that generated the stub code successfully.
Using the stub code I threw together some client code to invoke a service. An example is shown below:
package au.edu.apf.phenomebank.ontology;
import java.util.List;
import org.apache.cxf.endpoint.Client;
import org.apache.cxf.frontend.ClientProxy;
import org.apache.cxf.interceptor.LoggingInInterceptor;
import org.apache.cxf.interceptor.LoggingOutInterceptor;
import org.apache.xml.xml_soap.Map;
import org.apache.xml.xml_soap.MapItem;
import uk.ac.ebi.ontology_lookup.ontologyquery.Query;
import uk.ac.ebi.ontology_lookup.ontologyquery.QueryService;
public class OLSTest {
public static void main (String[] args) {
QueryService ss = new QueryService();
Query ontQuery = ss.getOntologyQuery();
Client client = ClientProxy.getClient(ontQuery);
client.getInInterceptors().add(new LoggingInInterceptor());
//client.getInInterceptors().add(new FixInterceptor());
client.getOutInterceptors().add(new LoggingOutInterceptor());
System.out.println("Getting ontology names");
Map ontologyNames = ontQuery.getOntologyNames();
List<MapItem> mapItems = ontologyNames.getItem();
for (MapItem mapItem : mapItems) {
Object mapValue = mapItem.getValue();
System.out.println("mapValue="+mapValue);
}
}
}
The errors started to happen when I invoked a service call on the stub API:
ontQuery.getOntologyNames();
The following errors were dumped in Eclipse:
DefaultValidationEventHandler: [ERROR]: unexpected element (uri:"", local:"item"). Expected elements are <{http://xml.apache.org/xml-soap}item>
Location: line 1
28/01/2010 5:09:52 PM org.apache.cxf.phase.PhaseInterceptorChain doIntercept
WARNING: Interceptor has thrown exception, unwinding now
org.apache.cxf.interceptor.Fault: Unmarshalling Error: unexpected element (uri:"", local:"item"). Expected elements are <{http://xml.apache.org/xml-soap}item>
Bascially, it's complaning that the <item>> element is missing the namespace of
http://xml.apache.org/xml-soap
To verify was wrong I needed to look at the actual SOAP message being sent to me:
<?xml version="1.0" encoding="UTF-8" ?>
- <soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
- <soapenv:Body>
- <getOntologyNamesResponse xmlns="http://www.ebi.ac.uk/ontology-lookup/OntologyQuery">
- <getOntologyNamesReturn>
- <item xmlns:ns1="http://xml.apache.org/xml-soap" xmlns="">
<key xsi:type="xsd:string">LSM</key>
<value xsi:type="xsd:string">Leukocyte Surface Markers</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">TADS</key>
<value xsi:type="xsd:string">Tick Gross Anatomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">FBsp</key>
<value xsi:type="xsd:string">Fly taxonomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">FIX</key>
<value xsi:type="xsd:string">Physico-Chemical Methods and Properties</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">HOM</key>
<value xsi:type="xsd:string">Homology Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">SPD</key>
<value xsi:type="xsd:string">Spider Comparative Biology Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">RO</key>
<value xsi:type="xsd:string">Multiple Alignment</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">HP</key>
<value xsi:type="xsd:string">Human phenotype ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MOD</key>
<value xsi:type="xsd:string">Protein Modifications (PSI-MOD)</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">BTO</key>
<value xsi:type="xsd:string">BRENDA tissue / enzyme source</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MFO</key>
<value xsi:type="xsd:string">Medaka Fish Anatomy and Development</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">TTO</key>
<value xsi:type="xsd:string">Teleost taxonomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">WBls</key>
<value xsi:type="xsd:string">C. elegans Development</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">APO</key>
<value xsi:type="xsd:string">Yeast phenotypes</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MAT</key>
<value xsi:type="xsd:string">Minimal Information About Anatomy ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">NEWT</key>
<value xsi:type="xsd:string">NEWT UniProt Taxonomy Database</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MI</key>
<value xsi:type="xsd:string">Molecular Interaction (PSI MI 2.5)</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">FAO</key>
<value xsi:type="xsd:string">Fungal Gross Anatomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">TAIR</key>
<value xsi:type="xsd:string">Arabidopsis Development</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">IDO</key>
<value xsi:type="xsd:string">Infectious Disease Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">EMAP</key>
<value xsi:type="xsd:string">Mouse Gross Anatomy and Development</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">AAO</key>
<value xsi:type="xsd:string">Amphibian Gross Anatomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">PRO</key>
<value xsi:type="xsd:string">Protein Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">OBO_REL</key>
<value xsi:type="xsd:string">OBO Relationship Types</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">ZFA</key>
<value xsi:type="xsd:string">Zebrafish Anatomy and Development</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MA</key>
<value xsi:type="xsd:string">Mouse Adult Gross Anatomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">XAO</key>
<value xsi:type="xsd:string">Xenopus anatomy and development</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">TRANS</key>
<value xsi:type="xsd:string">Pathogen transmission</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">PATO</key>
<value xsi:type="xsd:string">Phenotypic qualities (properties)</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">TGMA</key>
<value xsi:type="xsd:string">Mosquito Gross Anatomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">PRIDE</key>
<value xsi:type="xsd:string">PRIDE Controlled Vocabulary</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">REX</key>
<value xsi:type="xsd:string">Physico-Chemical Process</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">UO</key>
<value xsi:type="xsd:string">Unit Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">CARO</key>
<value xsi:type="xsd:string">Common Anatomy Reference Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">SEP</key>
<value xsi:type="xsd:string">Separation Methods</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">TAO</key>
<value xsi:type="xsd:string">Teleost Anatomy and Development Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MP</key>
<value xsi:type="xsd:string">Mammalian Phenotype</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">EV</key>
<value xsi:type="xsd:string">eVOC (Expressed Sequence Annotation for Humans)</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">FBdv</key>
<value xsi:type="xsd:string">Drosophila Development</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">HAO</key>
<value xsi:type="xsd:string">Hymenoptera Anatomy Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MS</key>
<value xsi:type="xsd:string">PSI Mass Spectrometry Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">GRO</key>
<value xsi:type="xsd:string">Cereal Plant Development</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">EO</key>
<value xsi:type="xsd:string">Plant Environmental Conditions</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">PAR</key>
<value xsi:type="xsd:string">Protein Affinity Reagents</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">IMR</key>
<value xsi:type="xsd:string">Molecule Role (INOH)</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">PSI</key>
<value xsi:type="xsd:string">Mass Spectroscopy CV (PSI-MS)</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">PW</key>
<value xsi:type="xsd:string">Pathway Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">IEV</key>
<value xsi:type="xsd:string">Event (INOH)</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">ECO</key>
<value xsi:type="xsd:string">Evidence Codes</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MIAA</key>
<value xsi:type="xsd:string">Minimal Information About Anatomy ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">ENVO</key>
<value xsi:type="xsd:string">Environmental Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">BS</key>
<value xsi:type="xsd:string">Biosapiens Annotations</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">CCO</key>
<value xsi:type="xsd:string">Cell Cycle Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">TO</key>
<value xsi:type="xsd:string">Cereal Plant Trait</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">FBcv</key>
<value xsi:type="xsd:string">Flybase Controlled Vocabulary</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MIRO</key>
<value xsi:type="xsd:string">Mosquito Insecticide Resistance</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">WBPhenotype</key>
<value xsi:type="xsd:string">C. elegans phenotype</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">CHEBI</key>
<value xsi:type="xsd:string">Chemical Entities of Biological Interest</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">DOID</key>
<value xsi:type="xsd:string">Human Disease</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">BSPO</key>
<value xsi:type="xsd:string">Spatial Reference Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">ZDB</key>
<value xsi:type="xsd:string">Zebrafish Anatomy and Development</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">WBbt</key>
<value xsi:type="xsd:string">C. elegans gross anatomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">FBbi</key>
<value xsi:type="xsd:string">Biological Imaging Methods</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">ATO</key>
<value xsi:type="xsd:string">Amphibian Taxonomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">FBbt</key>
<value xsi:type="xsd:string">Drosophila Gross Anatomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">SO</key>
<value xsi:type="xsd:string">Sequence Types and Features</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">FMA</key>
<value xsi:type="xsd:string">Foundational Model of Anatomy Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">EHDA</key>
<value xsi:type="xsd:string">Human Developmental Anatomy, timed version</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">ZEA</key>
<value xsi:type="xsd:string">Maize Gross Anatomy</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">PM</key>
<value xsi:type="xsd:string">Phenotypic manifestation (genetic context)</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">PO</key>
<value xsi:type="xsd:string">Plant Ontology (Structure, Growth and Developmental Stage)</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">EFO</key>
<value xsi:type="xsd:string">ArrayExpress Experimental Factor Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">GO</key>
<value xsi:type="xsd:string">Gene Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">ENA</key>
<value xsi:type="xsd:string">European Nucleotide Archive Submission Ontology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">MPATH</key>
<value xsi:type="xsd:string">Mouse Pathology</value>
</item>
- <item xmlns="">
<key xsi:type="xsd:string">CL</key>
<value xsi:type="xsd:string">Cell Type</value>
</item>
</getOntologyNamesReturn>
</getOntologyNamesResponse>
</soapenv:Body>
</soapenv:Envelope>
The main problem is that nearly all the<item> elements don't have a declared namespace. Here's an example:
<item xmlns="">
<key xsi:type="xsd:string">HOM</key>
<value xsi:type="xsd:string">Homology Ontology</value>
</item>
And yet in the WSDL file the schema requires that the namespaces be fully qualified:
<schema elementFormDefault="qualified" targetNamespace="http://xml.apache.org/xml-soap" xmlns="http://www.w3.org/2001/XMLSchema">
<import namespace="http://model.web.ook.ebi.ac.uk"/>
<complexType name="mapItem">
<sequence>
<element name="key" nillable="true" type="xsd:anyType"/>
<element name="value" nillable="true" type="xsd:anyType"/>
</sequence>
</complexType>
<complexType name="Map">
<sequence>
<element maxOccurs="unbounded" minOccurs="0" name="item" type="apachesoap:mapItem"/>
</sequence>
</complexType>
<complexType name="Vector">
<sequence>
<element maxOccurs="unbounded" minOccurs="0" name="item" type="xsd:anyType"/>
</sequence>
</complexType>
</schema>
The workaround for this problem was to download the WSDL file and manually change it from qualified to unqualified as follows:
<schema elementFormDefault="unqualified" targetNamespace="http://xml.apache.org/xml-soap" xmlns="http://www.w3.org/2001/XMLSchema">
<import namespace="http://model.web.ook.ebi.ac.uk"/>
<complexType name="mapItem">
<sequence>
<element name="key" nillable="true" type="xsd:anyType"/>
<element name="value" nillable="true" type="xsd:anyType"/>
</sequence>
</complexType>
<complexType name="Map">
<sequence>
<element maxOccurs="unbounded" minOccurs="0" name="item" type="apachesoap:mapItem"/>
</sequence>
</complexType>
<complexType name="Vector">
<sequence>
<element maxOccurs="unbounded" minOccurs="0" name="item" type="xsd:anyType"/>
</sequence>
</complexType>
</schema>
More details about this issue can be followed up here:
http://code.google.com/p/ols-ebi/issues/detail?id=6
Hope this helps somebody from the headaches i had to go through to get this working!!
Yep sounds like the ebi
ReplyDeleteRegards dears
ReplyDelete