An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations

Abstract

Gene Ontology (GO) is widely used in the biological domain. It is the most comprehensive ontology providing formal representation of gene functions (GO concepts) and relations between them. However, unintentional quality defects (e.g. missing or erroneous relations) in GO may exist due to the large size of GO concepts and complexity of GO structures. Such quality defects would impact the results of GO-based analyses and applications. In this work, we introduce a novel evidence-based lexical pattern approach for quality assurance of GO relations. We leverage two layers of evidence to suggest potentially missing relations in GO as follows. We first utilize related concept pairs (i.e. existing relations) in GO to extract relationship-specific lexical patterns, which serve as the first layer evidence to automatically suggest potentially missing relations between unrelated concept pairs. For each suggested missing relation, we further identify two other existing relations as the second layer of evidence that resemble the difference between the missing relation and the existing relation based on which the missing relation is suggested. Applied to the 15 December 2021 release of GO, this approach suggested a total of 866 potentially missing relations. Local domain experts evaluated the entire set of potentially missing relations, and identified 821 as missing relations and 45 indicate erroneous existing relations. We submitted these findings to the GO consortium for further validation and received encouraging feedback. These indicate that our evidence-based approach can be utilized to uncover missing relations and erroneous existing relations in GO.

Leveraging logical definitions and lexical features to detect missing IS-A relations in biomedical terminologies

“…A cross-validation-inspired approach was used to apply the model to all hierarchically unrelated concept pairs. In previous work, we have also proposed several approaches that uncover missing IS-A relations purely utilizing lexical features of concepts [ 23 – 29 ], and approaches that combine lexical and structural features [ 23 , 24 , 30 ]. A more detailed comparison with such approaches that are related to this work is provided later in the paper in the Discussion section.…”