On Controlled Vocabularies in Bioinformatics: A Case Study in the Gene Ontology

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the status of a de facto standard in the field of gene and gene product annotations and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. As the GO Consortium has recognized, however, its controlled vocabulary is as currently constituted marked by a number of problematic features which are characteristic of much recent work in bioinformatics and