  Many database resources, such as Reactome, collect manually annotated
reactions, interactions, and pathways from peer-reviewed publications. The
interactors (e.g., a protein), interactions, and pathways in these data
resources are often represented as instances in using BioPAX, a standard
pathway data exchange format. However, these interactions are better
represented as classes (or universals) since they always occur given
appropriate conditions. 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 Reactome and represented in BioPAX were first converted to ontology
classes by aligning them under INO. Related terms and associated relations and
hierarchies from external ontologies (e.g., CHEBI and GO) were also retrieved
and imported into HINO. HINO ontology terms were resolved in 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.
