<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Ontologies are becoming increasingly important for the efficient storage, retrieval
and mining of biological data. The description of phenotypes using ontologies is a
particularly complex problem. We outline a schema that can be used to describe
phenotypes by combining orthologous axiomatic ontologies. We also describe tools for
storing, browsing and searching such complex ontologies. Central to this approach is
that assays (protocols for measuring phenotypic characters) describe what has been
measured as well as how this was done, allowing assays to link individual organisms to
ontologies describing phenotypes. We have evaluated this approach by automatically
annotating data on 600 000 mutant mice phenotypes using the SHIRPA protocol. We
believe this approach will enable the flexible, extensible and detailed description of
phenotypes from any organism.</p>
[]
Comp Funct Genomics. 2004 Aug-Oct; 5(6-7):545-551