A Comparison of Exhaustive and Non-lattice-based Methods for Auditing Hierarchical Relations in Gene Ontology

Uncovering and fixing errors in biomedical terminologies is essential so that they provide accurate knowledge to downstream applications that rely on them. Non-lattice-based methods have been applied to identify various kinds of inconsistencies in different biomedical terminologies. In previous work, we have introduced two inference-based approaches that were applied in an exhaustive manner to audit hierarchical relations in the Gene Ontology: (1) Lexical-based inference framework, and (2) Subsumption-based sub-term inference framework. However, it is unclear how effective these exhaustive approaches perform compared with their corresponding non-lattice-based approaches. Therefore, in this paper, we implement the non-lattice versions of these two exhaustive approaches, and perform a comprehensive comparison between non-lattice-based and exhaustive approaches to audit the Gene Ontology. The domain expert evaluations performed for the two exhaustive approaches are leveraged to evaluate the non-lattice versions. The results indicate that the non-lattice versions have increased precision than their exhaustive counterparts even though they do not capture some of the potential inconsistencies that the exhaustive approaches identify.