Formalization of Syntax and Semantics of Ontology Languages in Biology

The use of ontologies in the biomedical field has been increasing exponentially for the two last decades. For historical and technical reasons however, two languages have been coexisting: OWL, a specification of the W3C part of the Semantic Web technologies, and OBO, a provisional standard put together by the OBO consortium out of already existing ontologies. The lack of specification of the OBO language is a source of conversion issues, and reduces the integration of ontologies based on the language they were developed in: OBO ontologies are harder to reason with, while OWL ontologies are more complicated to use for simple analyses. We developed the fastobo library as an implementation of the OBO format version 1.4, which restricts the OBO syntax to improve compatibility with OWL. Using a strict parser allowed us to find issues in existing ontologies such as the Environment Ontology or the Plant Ontology, and helped amending the currently unreleased specification of the format. We also developed Python bindings with the goal of enabling developers and data analysts to use OBO ontologies in their work more easily. Finally, provisional mappings were established from scratch with the OWL language as well as with the OBO Graphs specification, which is an ongoing development format for ontological graphs