Linkages between animal models of diseases and human data enable the development of translational research hypotheses. The objective of this study is to investigate two approaches to integrating phenotype and clinical information. On the one hand, we develop a terminology mapping between phenotypes from the Mammalian Phenotype Ontology (MPO) and Online Mendelian Inheritance in Man (OMIM) through the Unified Medical Language System (UMLS). On the other, we associate MPO phenotypes with OMIM manifestations through annotations made to orthologous genes. 1,469 MPO concepts (22%) were mapped successfully to some disease concept in the UMLS, of which 869 were present in OMIM. Among the 16,764 distinct MGI genes associated with human orthologs, 1,968 distinct genes were associated with both MPO and OMIM annotations. The UMLS is a valuable resource for linking phenotype terms to clinical terminologies, and these mappings between terminologies can help enrich gene annotation databases and unify phenotype representation.