On the Application of Formal Principles to Life Science Data: a Case Study in the Gene Ontology

Abstract

Abstract. Formal principles governing best practices in classification and definition have for too long been neglected in the construction of biomedical ontologies, in ways which have important negative consequences for data integration and ontology alignment. We argue that the use of such principles in ontology construction can serve as a valuable tool in error-detection and also in supporting reliable manual curation. We argue also that such principles are a prerequisite for the successful application of advanced data integration techniques such as ontology-based multi-database querying, automated ontology alignment and ontology-based text-mining. These theses are illustrated by means of a case study of the Gene Ontology, a project of increasing importance within the field of biomedical data integration.

The Ecology of Ontologies in the Public Domain

“…Philosophical rules of thumb should not be violated, though frequently they are, especially the rules of univocity, positivity, objectivity, single inheritance, exhaustiveness, and intelligibility [13]. These rules provide important guidelines to ensure that conceptualizations have clarity and avoid ambiguity.…”

“…Multiple-inheritance, the presence in an ontology of terms with multiple parents, is sometimes considered the result of poor conceptualization of domain knowledge. It can also present obstacles to ontology integration, since in such cases is_a relations are permitted to mean different things in different contexts [13]. Consider: dog is_a mammal; dog is_a pet; nurse is_a person, nurse is_a hospital role.…”

A Cell-Cycle Knowledge Integration Framework

“…Thus reasoning environments as RACER can be employed for checking the validity of some of the design principles of CCO, mentioned in Section 3.1. For instance, as already indicated in [23], the way GO uses the is a relation may lead to a violation of the single inheritance principle. After loading the CCO into Protégé (with the Protégé OWL plugin [16]) and adding simple disjointness constraints to some of the CCO classes a certain number of this type of inconsistencies (32 in total which represents 10% of the entire CCO) have been detected by RACER.…”

“…The following rules, summarized from [23], have been taken into account while engineering the CCO: Table 1. Some CCO motivating scenarios 1.…”

“…Furthermore, as stated in [23], the part of relation should be specialized using spatial and temporal relations [24] to solve this type of inconsistencies.…”