Project 3: Ontology Querying

Maximum grade: 15 points

NOTE:   This is an individual project

This project uses an ontology representing knowledge about glycan structures and a triple store called Jena. The ontology is called GlycO-small.owl. Both Jena and the ontology are available on uml: Jena is in /opt/Jena-2.6.0, and the ontology is in my own directory cs8350/ontologies.

Here is what you are asked to do:

1. Write a Sparql query to retrieve all moieties, residues, and links of GlycopeptideN, where N is an integer which you will be given individually in class (you will need to find out the complete URI of the Glycopeptide). In the same query, also retrieve the class of GlycopeptideN. Then, use Jena’s ARQ query processor to execute your query and print out the result.
2. Write a small Java program using Jena API to retrieve and print the same information as above (GlycopeptideN), but using only Jena API (you are not allowed to execute a Sparql query here).

A glycopeptide is usually composed of two moietites and a link connecting them. These two are available as values (objects) of properties has_moiety and has_link, respectively. Furthermore, a moiety is composed of residues and links, which are available as values (objects) of properties has_residue and has_link, respectively. The internal structure of a moiety called representative_asparagine-containing_peptide_moiety is not represented in the ontology (it has no smaller parts).

You will have to write Java programs that use Jena’s functionality to run both programs. Using Jena will require making the jar files in /opt/Jena-2.6.0/lib on your CLASSPATH. You may use a wildcard to do so (remember to quote it, since * is a special character).

Jena documentation is available at http://jena.sourceforge.net/documentation.html (http://jena.sourceforge.net/tutorial/RDF_API/index.html will be really useful).

ARQ documentation is available at http://jena.sourceforge.net/ARQ/documentation.html (http://jena.sourceforge.net/ARQ/app_api.html will be really useful).