HINO: BFO-aligned ontology representation of human molecular interactions and pathways

Reactome is a manually-curated, peer-reviewed knowledgebase of human pathways and processes. As a standard pathway data exchange format, BioPAX represents individual interactors (e.g., a protein), interactions, and pathways as instances instead of classes. This study aims to represent various human interaction pathways and networks as classes via a formal ontology aligned with the Basic Formal Ontology (BFO). Towards this goal, the Human Interaction Network Ontology (HINO) was generated by extending the BFO-aligned Interaction Network Ontology (INO). All human pathways and associated processes and interactors listed in the Reactome database were first converted to ontology classes by aligning them within the framework of the INO ontology. Related terms and associated relations and hierarchies from external ontologies (e.g., CHEBI and GO) were retrieved and imported into HINO. Resulting HINO OWL file was transferred to a RDF triple store. Detailed information about individual HINO ontology terms can be displayed using the linked ontology data server Ontobee. The RDF triples stored in the RDF triple store are queryable through a SPARQL program. Such an ontology system supports advanced pathway data integration and applications.