Computational protocol: Mapping between the OBO and OWL ontology languages

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Protocol publication

[…] Based on the mapping rules, we have implemented a Java implementation of the OBO to OWL transformation. Our implementation is part of the official Gene Ontology project source []. Gene Ontology project is an open source project on, and is home to the OBO ontology editor OBO-Edit. Our implementation is part of the OBO API that provides data structures for storing OBO ontologies, as well as read and write capabilities for OBO and OWL, among other operations. The source code for our transformation tool is available at [].Finally, we have deployed our transformation as a web service for general use: the OBO API, we have created NCBOOboInOWLMetadataMapping class in the package org.obo.owl.datamodel.impl. This class implements the roundtrip mapping between OBO and OWL. In order to provide console-based use of the transformation tool, we have created Obo2Owl and Owl2Obo classes in org.obo.owl.test package.In order to evaluate the OWL output of our implementation, we have tested our tool on Gene Ontology, Zebrafish Anatomical Ontology, Spider Ontology and Adult Mouse Gross Anatomy, obtained from NCBO BioPortal. After transformation of these ontologies into OWL, we have successfully loaded the OWL files into Protégé [], an ontology development tool for the Semantic Web. Using the ‘summary’ feature of Protégé, we have compared the overall class and object property count with the term and typedef count obtained for the original OBO file, using OBO-Edit’s ‘extended information’ feature. The results of the comparison (Table ) show equal values for both versions of the ontologies. Similarly, for testing the roundtrip, we compared the original OBO file with the roundtrip version, again using OBO-Edit’s ‘extended information’ feature. Our evaluation showed that the two OBO ontologies had the same term and typedef counts (Table ). […]

Pipeline specifications

Software tools OBO-Edit, Protégé
Application Ontology generation