HINO: a BFO-aligned ontology representing human molecular interactions and pathways

TL;DR

This paper introduces HINO, an ontology aligned with BFO, that models human molecular interactions and pathways as classes, enhancing data integration and querying capabilities over traditional instance-based representations.

Contribution

The study presents HINO, a novel BFO-aligned ontology that represents human molecular pathways as classes, improving upon existing instance-based models for better data integration.

Findings

HINO effectively models human pathways as classes.

HINO enables advanced querying via SPARQL.

Integration with external ontologies enhances data richness.

Abstract

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.