ABSTRACT
At the time the Gene Ontology (GO) was originally introduced in 2000 [14], inference in GO was for the most part limited to exploiting subclass and parthood relations to infer that a gene annotated to a term is also annotated to ancestors of that term connected by is_a and part_of relations on the basis of the annotation propagation rule (see Chapter 5, page 130). Gene Ontology and the OBO ontology language have matured substantially since then. New relations and specifications as to the types of inference that are allowed have been added. This has not only improved the representation of biology in GO, but also facilitates querying and allows GO developers to systematically check for and correct inconsistencies within the GO [86]. This chapter will provide a brief review of inference in the GO ontology and will explain how inferences based on cross-product logical definitions are being used to correct inconsistencies or to add missing links in the GO. We will conclude the chapter with a description of how cross-product logical definitions are being used in the Human Phenotype Ontology (HPO) to link human disease phenotypes with GO and other ontologies such as the Foundational Model of Anatomy ontology of human anatomy.
