1 Linking the Gene Ontology to other biological ontologies

The entities described in the Gene Ontology, (i.e., molecular functions, cellular components and biological processes), often make reference (in their names) to other entities, either from GO or from other ontologies, such as ontologies of chemical entities, cell types and organisms. We developed a method for mapping terms from the Open Biomedical Ontol-ogy (OBO) family to GO. We show that 55 % of the 17,250 GO terms include in their names the name of some chemical entity (ChEBI). Our findings are consistent with that of other studies. Additionally, our study provides a quantification of the relations between GO terms and terms from other on-tologies.