The European Bioinformatics Institute (EBI) has announced the successful completion of BioBabel, which includes the development of a controlled vocabulary and common ontology to describe biological attributes in biological databases. The project was funded by the European Union within its Fifth Framework Programme under the 'Quality of Life and Management of Living Resources' priority. BioBabel was coordinated by the EBI (UK), and brought together partners from the Swiss Institute of Bioinformatics (Switzerland), the Institute for Biochemistry of the University of Köln (Germany) and the National Pharmaceutical Biotechnology Centre for Biochemistry of the Trinity College (Ireland). The project ran between December 2001 and November 2004. The complete title of the project was 'Enhanced interoperability of biological databases by standardisation of biochemical terminology and introduction of a shared ontology', and it combined the different strengths of European groups working on various aspects of standardisation for biochemical terminology in databases to develop and implement controlled vocabulary and a common ontology to describe biological attributes in biological databases. Why do scientists need standardised vocabularies? Biological databases describe a wide spectrum of information. Their diversity makes efforts towards database integration difficult. The Biobabel project allowed the development and implementation of common ontologies to describe biological attributes in these databases. Ontologies may be defined as systems for representing knowledge. In this context, this particularly refers to the representation of models and hypothesis in computer-compatible terms. This work will allow users to carry out complex queries across databases in a simpler way. The partners in this project aimed to implement standardised terminology in all the databases they produce and maintain. The project consisted of 12 work packages in six different classes: - research and development of controlled vocabulary for biological and biochemical terminology; - research and development of a structured controlled vocabulary; the Gene Ontology (GO) to describe gene products in terms of their molecular function; biological role and cellular location; - development and implementation of a database system to store the controlled vocabulary for biological and biochemical terminology and the Gene Ontology, enabling the partners to keep the controlled vocabulary up-to-date; - implementation of controlled vocabulary for biological and biochemical terminology in the databases of the BioBabel partners; - rigorous classification of data in protein sequence, protein signature, enzyme and enzyme function databases with GO terms; - development and implementation of new access and retrieval tools that will enable researchers to exploit maximally the data in the databases participating in the project. Biobabel has delivered its objective of enhancing the interoperability of biological databases by improving the standardisation of biochemical terminology, and through the introduction of shared ontologies that will allow users to do complex queries across databases in a much simpler way. The Bio Babel partners introduced the standardised ontology in all the databases they produce and maintain. Accessing these highly interoperable sequence databases, genomic databases, protein motif databases, enzyme databases and nomenclature databases will allow researchers to infer knowledge about the structure and function of genes and proteins, and to relate these to the existing corpus of scientific knowledge.