Bottom-up ontology development reusing semi-structured life sciences diagrams

Bio-ontology development is a resource-consuming task despite the many open source ontologies available for reuse. Various strategies and tools for bottom-up ontology development have been proposed from a computing angle, yet the most obvious one from a domain expert perspective is unexplored: the abundant diagrams. To speed up and simplify bio-ontology development, we propose guidelines to formalise such diagrams in several logic languages availing also of a foundational ontology to achieve a more precise representation of the subject domain semantics and increase interoperability. The guidelines are demonstrated with a transformation of the Pathway Studio diagrams into an OWLized bio-ontology with BFO and RO.