- The Rat Genome Database (RGD) has been annotating genes, QTLs, and strains to disease terms for over 15 years. During that time the controlled vocabulary used for disease curation has changed a few times. The changes were necessitated because no single vocabulary or ontology was freely accessible and complete enough to cover all of the disease states described in the biomedical literature.
Meanwhile, the human disease ontology (DO) had slowly been developing and expanding. As early as 2010, members of RGD were contributing to the development of DO. However, five years went by before MGD (mouse genome database) and RGD joined with DO in an organized attempt to make DO useful for the model organism community. From that collaboration came a large addition of OMIM-based terms, expansion of multiparentage of terms through axiomatic extension, and expansion of cross-references to clinical vocabularies. Based on the promise of those improvements, it was determined that the Alliance of Genome Resources could use the DO as a unifying disease vocabulary across model organism databases.
Despite the improvements in DO, RGD still had more than 1000 custom terms and 3800 MEDIC terms with annotations to deal with if RGD would convert to the use of DO. Those extra terms originated from OMIM, MeSH, and the biomedical literature. If RGD mapped those non-DO disease terms to DO, much granularity of meaning would be lost. For instance the term “osteoarthritis” in DO has no children terms, but the RGD version of DO has 11 children terms or variations of “osteoarthritis” (Figure 1). The extra details of those terms is lost to users of DO. To avoid the loss of granularity it was decided to extend the DO beyond the merged, axiomized DO file. After mapping/adding DO terms completely to the RGD version of MEDIC, a broader, deeper disease vocabulary has been achieved, by providing more term branches throughout the ontology and more child terms within those branches.