There is an increasing accumulation of data on disease-related mutations and associated phenotypes in a wide variety of databases worldwide. Exploiting these data in the context of whole genome sequencing is inhibited because the phenotype information in these databases is often difficult to search meaningfully or relate between data sets, and automated computational integration is not possible. Key to this integration is the development of ontology-based methods for describing diseases in terms of their component phenotypes. This would allow analysis of variation in disease manifestation, relationships between diseases and phenotypes in model organisms, and linking diseases to gene mutations, pathways, and phenotypes. Building a systematic link to phenotypes manifested in model organisms will be of particular importance with the advent of new, large-scale phenotyping projects such as the International Mouse Phenotyping Consortium. In addition to improved semantic description, funding and organizational innovations are required to support this integration. In particular, a series of national or international hubs to hold genotype and phenotype data are needed which could feed data to a central database. In addition, better coordination of clinical and bioinformatics experts and, crucially, development of a transnational funding and international coordination infrastructure will be required. Hum Mutat 33813-816, 2012. © 2012 Wiley Periodicals, Inc.