HINO: a BFO-aligned ontology representing human molecular interactions and pathways
This work addresses the need for formal ontological representation in bioinformatics to improve data integration and applications for researchers in molecular biology and systems biology, though it is incremental as it builds on existing ontologies.
The study tackled the problem of representing human molecular interactions and pathways as classes rather than instances by developing HINO, a BFO-aligned ontology, which successfully integrated data from Reactome and external sources to support advanced pathway data integration and querying.
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.