Ontologies have traditionally been used in biomedicine for representing relationships among biological concepts, and as a result, large knowledge-bases like Gene Ontology (GO) have emerged. We believe use of Semantic Web technologies can allow better querying and collaboration of biomedical ontologies.
As a migration path for biomedical ontologies, we have developed a mechanism for lossless roundtrip transformations between Open Biomedical Ontologies (OBO) format and OWL. We have methodically examined each of the constructs of OBO and grouped them to form a layer cake for OBO, similar to the Semantic Web stack.
We have also enumerated constructs in each system that do not have simple syntactic equivalent in the other, important ones being GUIDs, various kinds of synonyms and subsets. We have implemented a tool that uses our transformation rules to translate OBO ontologies into OWL, and back, without loss of knowledge.
Translated Ontologies
In order to test our mapping and tool, we have translated the following ontologies from OBO to OWL and back to OBO.
- Gene Ontology (GO): Original OBO Translated OWL Roundtrip OBO
- Zebrafish Ontology (ZFIN): Original OBO Translated OWL Roundtrip OBO
- Mouse Anatomy (EMAP): Original OBO Translated OWL Roundtrip OBO