Inter-database linkage via annotations is one approach to the integration of knowledge in the biomedical domain, which is often fragmented by specialization. This pilot study examined annotations in nine model organism databases and the Gene Ontology (GO) to assess explicit and implicit linkages between organisms. The databases had similar annotation processes, content, and knowledge. While all databases had the potential to be linked to all others via GO, only some databases had non-GO links to others. This may be due in part to a lack of biologically significant relationships among some of the organisms.