Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning

Abstract

Researchers design ontologies as a means to accurately annotate and integrate experimental data across heterogeneous and disparate data- and knowledge bases. Formal ontologies make the semantics of terms and relations explicit such that automated reasoning can be used to verify the consistency of knowledge. However, many biomedical ontologies do not sufficiently formalize the semantics of their relations and are therefore limited with respect to automated reasoning for large scale data integration and knowledge discovery. We describe a method to improve automated reasoning over biomedical ontologies and identify several thousand contradictory class definitions. Our approach aligns terms in biomedical ontologies with foundational classes in a top-level ontology and formalizes composite relations as class expressions. We describe the semi-automated repair of contradictions and demonstrate expressive queries over interoperable ontologies. Our work forms an important cornerstone for data integration, automatic inference and knowledge discovery based on formal representations of knowledge. Our results and analysis software are available at http://bioonto.de/pmwiki.php/Main/ReasonableOntologies.

Figure 1. Taxonomy of the upper-level ontology.

The four classes Material object, Process, Quality and Function are mutually disjoint.

Figure 2. Overview of method and results.

Figure 3. Local contradiction in the Cell type Ontology.

The contradictory class definition arises from the assertion that Spore is both a Prokaryotic cell and a Fungal cell. Fungal cell is a kind of Eukaryotic cell which is disjoint from Prokaryotic cell.

Figure 4. Global contradiction in the GO-XP.

The contradiction arises from the inference that Immune system process is a kind of System process. System process is a kind of Multicellular organismal process which is disjoint from Cellular process.

Figure 5. Contradiction in the GO-XP arising from faulty class definition due to homonymy.

Mucus secretion is asserted to be a subclass of Secretion, an anatomical entity in the UBERON ontology which is a kind of Material object. Due to the domain and range restrictions of the relation results-in-release-of, Mucus secretion is inferred to become a kind of Process, which is disjoint from Material object. Use of the class Secretion from GO would have prevented this error.