The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

An ontology is a domain of knowledge structured through formal rules so that it can be interpreted and used by computers. Ontologies are becoming increasingly important in bioinformatics because they can be linked to the information in databases and their knowledge then used to query the databases. Typical examples in current use are the Gene Ontology, which incorporates much of our knowledge about gene products, and ontologies of developmental anatomy, which, for example, facilitate tissue‐based queries to gene expression databases both (...) textually and spatially. This article considers the production, formulation and types of bio‐ontologies together with the reasons why they are so useful. © BioEssays 25:501–506, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

New observations by Hatini et al.(1) on the ‘winged helix’ transcription factor BF‐2 will make us change our views about kiney development. This gene is only expressed in stromal cells associated with the kidney medulla and cortex, but the BF‐2 knockout has unexpected abnormalities. Although the stromal cells appear normal, the kidney is small, the ducts have limited branching and, instead of the many normal nephrogenic aggregates, there are relatively few large mesenchymal aggregates that fail to differentiate. The stromal cells (...) thus seem to produce factors regulating other aspects of kidney development, while the abnormalities highlight a series of unsolved problems in kidney morphogenesis. (shrink)