Semantic Web Services with the SADI Framework: my notebook.

At Biohackathon2010 , Mark Wilkinson and Luke McCarthy introduced The SADI Framework. From sadiframework.org:SADI is a framework for discovery of, and interoperability between, distributed data and analytical resources. It combines simple, stateless, GET/POST-based Web Services with standards from the W3C Semantic Web initiative. The objective of SADI is to make it easy for data and analytical tool providers to quickly make their resources available on the Semantic Web with minimal disruption to their usual practices.(...)

• SADI Services consume and provide data via simple HTTP POST and GET
• SADI Services consume and produce data in RDF format. This allows SADI Services to exploit existing OWL reasoners and SPARQL query engines to enhance interoperability between Services and the interpretation of the data being passed between them
• Service interfaces (i.e., Inputs and Outputs) are defined in terms of OWL-DL classes; the property restrictions on these OWL classes define what specific data elements are required by the Service and what data will be provided by the Service, respectively
• Input RDF data - data that is compliant with the Input OWL Class - is “decorated” or “annotated” by the service provider to include new properties. These properties will (of course) be a function of the lookup/analytical operations performed by the Web Service.
• Importantly, discovery of SADI Services can include searches for the properties the user wants to add to their data. This contrasts with other Semantic Web Service standards which attempt only to define the computational process by which input data is analysed, rather than the properties that process generates between the input and output data. This is KEY to the semantic behaviours of SADI.
  
• SADI Web Services are stateless and atomic.

In the current post, I just want to understand how SADI invokes the services.

The classical Web Services are described using WSDL (Web Services Description Language) and the messages are transported with SOAP.

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In Sadi, as far as I understand it, the description of the services, the operations, the inputs, the ouputs and the transport of the messages use a RDF/OWL format.

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http://sadiframework.org/registry/ contains all the services handled by the SADI framework. For example calling http://sadiframework.org/services/getPubMedReferencesForPDB returns the following XML document describing the service:

<rdf:RDF
xmlns="http://www.w3.org/2002/07/owl#"
xmlns:a="http://www.mygrid.org.uk/mygrid-moby-service#"
xmlns:b="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl#"
xml:base="http://bioinfo.icapture.ubc.ca/SADI"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:databases="http://sadiframework.org/ontologies/Databases.owl#"
xmlns:misc="http://sadiframework.org/ontologies/miscellaneousObjects.owl#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="http://sadiframework.org/services/getPubMedReferencesForPDB">
<rdf:type rdf:resource="http://www.mygrid.org.uk/mygrid-moby-service#serviceDescription"/>
<b:format>sadi</b:format>
<b:identifier>urn:lsid:myservices:getPubMedReferencesForPDB</b:identifier>
<a:locationURI>http://sadiframework.org/services/getPubMedReferencesForPDB</a:locationURI>
<a:hasServiceDescriptionText>A implementation of the 'getPubMedReferencesForPDB' service</a:hasServiceDescriptionText>
<a:hasServiceDescriptionLocation>http://sadiframework.org/services/getPubMedReferencesForPDB</a:hasServiceDescriptionLocation>
<a:hasServiceNameText>getPubMedReferencesForPDB</a:hasServiceNameText>
<a:providedBy>
<rdf:Description rdf:about="getPubMedReferencesForPDB_mark.ubic.ca_0">
<a:authoritative>0</a:authoritative>
<b:creator>markw@illuminae.com</b:creator>
<b:publisher>mark.ubic.ca</b:publisher>
<rdf:type rdf:resource="http://www.mygrid.org.uk/mygrid-moby-service#organisation"/>
</rdf:Description>
</a:providedBy>
<a:hasOperation>
<rdf:Description rdf:about="getPubMedReferencesForPDB_mark.ubic.ca_1">
<a:hasOperationNameText>getPubMedReferencesForPDB</a:hasOperationNameText>
<rdf:type rdf:resource="http://www.mygrid.org.uk/mygrid-moby-service#operation"/>
<a:performsTask>
<rdf:Description rdf:about="getPubMedReferencesForPDB_mark.ubic.ca_2">
<rdf:type rdf:resource="http://www.mygrid.org.uk/mygrid-moby-service#operationTask"/>
<rdf:type rdf:resource="http://mygrid.org.uk/sometype"/>
</rdf:Description>
</a:performsTask>
<a:inputParameter>
<rdf:Description rdf:about="getPubMedReferencesForPDB_mark.ubic.ca_3">
<rdf:type rdf:resource="http://www.mygrid.org.uk/mygrid-moby-service#parameter"/>
<a:objectType>
<rdf:Description rdf:about="http://purl.oclc.org/SADI/LSRN/PDB_Thing"/>
</a:objectType>
</rdf:Description>
</a:inputParameter>
<a:outputParameter>
<rdf:Description rdf:about="getPubMedReferencesForPDB_mark.ubic.ca_4">
<rdf:type rdf:resource="http://www.mygrid.org.uk/mygrid-moby-service#parameter"/>
<a:objectType>
<rdf:Description rdf:about="http://sadiframework.org/ontologies/pdb_2_pmid.owl#getPubMedReferencesForPDB_Output"/>
</a:objectType>
</rdf:Description>
</a:outputParameter>
</rdf:Description>
</a:hasOperation>
</rdf:Description>
</rdf:RDF>

A part of this service can be visualized as a graph:

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So, the service getPubMedReferencesForPDB takes as input a parameter of type http://purl.oclc.org/SADI/LSRN/PDB_Thing and returns an object of type http://sadiframework.org/ontologies/pdb_2_pmid.owl#getPubMedReferencesForPDB_Output. Ok, let's try this service: I'm going to invoke the service getPubMedReferencesForPDB with two structures of type http://purl.oclc.org/SADI/LSRN/PDB_Thing (Many thanks to Mark for helping me via Twitter ...:-P ): 1KNZ and 1LJ2.

File: input.rdf

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:lsrn="http://purl.oclc.org/SADI/LSRN/">
<lsrn:PDB_Thing rdf:about="http://lsrn.org/PDB:1KNZ"/>
<lsrn:PDB_Thing rdf:about="http://lsrn.org/PDB:1LJ2"/>
</rdf:RDF>

Calling curl with this file for the service getPubMedReferencesForPDB:

curl -d @input.rdf http://sadiframework.org/services/getPubMedReferencesForPDB

Result:

<rdf:RDF>
<rdf:Description rdf:about="http://lsrn.org/PDB:1LJ2">
<a:hasReference>
<rdf:Description rdf:about="http://lsrn.org/PMID:12086624">
<rdf:type rdf:resource="http://purl.oclc.org/SADI/LSRN/PMID_Thing"/>
</rdf:Description>
</a:hasReference>
<rdf:type rdf:resource="http://sadiframework.org/ontologies/pdb_2_pmid.owl#getPubMedReferencesForPDB_Output"/>
</rdf:Description>
<rdf:Description rdf:about="http://lsrn.org/PDB:1KNZ">
<a:hasReference>
<rdf:Description rdf:about="http://lsrn.org/PMID:11792322">
<rdf:type rdf:resource="http://purl.oclc.org/SADI/LSRN/PMID_Thing"/>
</rdf:Description>
</a:hasReference>
<rdf:type rdf:resource="http://sadiframework.org/ontologies/pdb_2_pmid.owl#getPubMedReferencesForPDB_Output"/>
</rdf:Description>
</rdf:RDF>

Here, for each PDB entry (input), we were returned a Pubmed Identifier (output).


That's it !
Pierre