#GADES

Extension of the similarity measure ICOnSim with Information Content. A Similarity Measure for Determining Relatedness Between Ontology Terms.

[1] Ignacio Traverso-Ribón, Maria-Esther Vidal, Benedikt Kämpgen and York Sure-Vetter. GADES: A Graph-based Semantic Similarity Measure. Semantics 2016, Leipzig.

[2] Ignacio Traverso-Ribón, Maria-Esther Vidal and Guillermo Palma. A Similarity Measure for Determining Relatedness Between Ontology Terms. 11th International Conference on Data Integration in the Life Sciences 2015 (DILS2015).

[3] Ignacio Traverso-Ribón, Maria-Esther Vidal. Exploiting Information Content and Semantics to Accurately Computing Similarity of GO-based Annotated Entities. 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology

[4] Palma, G.; Vidal, M. E.; Haag, E.; Raschid, L.; Thor, A. Measuring Relatedness Between Scientific Entities in Annotation Datasets. ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (BCB), 2013

Setting up GADES

Once you have downloaded the code from GitHub you only need to modify the file src/main/java/test/DatasetTestPhase.java to run GADES.

GADES need as inputs:

• A knowledge graph in OWL format.
• Two knowledge graph entities to be compared.

Main example

In this example we compare the entities http://purl.org/obo/owl/GO#GO_0006355 and http://purl.org/obo/owl/GO#GO_0006342, which are two classes from the Gene Ontology.

		String ontFile = prefix + "goProtein/go.owl";
	MyOWLOntology o = new MyOWLOntology(ontFile, ontPrefix.get(prefix), "HermiT");
	
	
	OWLConcept a = o.getOWLConcept("http://purl.org/obo/owl/GO#GO_0006355");
	OWLConcept b = o.getOWLConcept("http://purl.org/obo/owl/GO#GO_0006342");
	Set<MyOWLLogicalEntity> anns = new HashSet<MyOWLLogicalEntity>();
	anns.add(a);
	anns.add(b);
	o.setOWLLinks(anns);
	Set<OWLLink> neighA = a.getNeighbors();
	Set<OWLLink> neighB = b.getNeighbors();
	System.out.println(b.similarityIC(a));//.taxonomicSimilarity(a));
	
	OWLRelation r1 = o.getOWLRelation("http://purl.obolibrary.org/obo/RO_0002213");
	System.out.println(o.getPropertyChains(r1));
	OWLRelation r2 = o.getOWLRelation("http://purl.obolibrary.org/obo/RO_0002211");
	System.out.println(o.getPropertyChains(r2));
	System.out.println(r1.similarity(r2));

License

This work is licensed under GNU/GPL v2.