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Nucleic Acids Research 2004 32(18):5539-5545; doi:10.1093/nar/gkh894
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Published online 14 October 2004

Nucleic Acids Research, Vol. 32 No. 18 © Oxford University Press 2004; all rights reserved

The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes

Andreas Ruepp1,*, Alfred Zollner2, Dieter Maier2, Kaj Albermann2, Jean Hani2, Martin Mokrejs1,3, Igor Tetko1, Ulrich Güldener1, Gertrud Mannhaupt4, Martin Münsterkötter1 and H. Werner Mewes1,4

1 Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany, 2 Biomax Informatics AG, Lochhamerstr. 11, D-82152 Martinsried, Germany, 3 Faculty of Science, Charles University, Vinicna 5, 128 42 Prague, Czech Republic and 4 Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany

* To whom correspondence should be addressed. Tel: +49 89 3187 3189; Fax: +49 89 3187 3585; Email: andreas.ruepp{at}gsf.de

Received July 30, 2004; Revised September 9, 2004; Accepted September 28, 2004

In this paper, we present the Functional Catalogue (FunCat), a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism. FunCat has been applied for the manual annotation of prokaryotes, fungi, plants and animals. We describe how FunCat is implemented as a highly efficient and robust tool for the manual and automatic annotation of genomic sequences. Owing to its hierarchical architecture, FunCat has also proved to be useful for many subsequent downstream bioinformatic applications. This is illustrated by the analysis of large-scale experiments from various investigations in transcriptomics and proteomics, where FunCat was used to project experimental data into functional units, as ‘gold standard’ for functional classification methods, and also served to compare the significance of different experimental methods. Over the last decade, the FunCat has been established as a robust and stable annotation scheme that offers both, meaningful and manageable functional classification as well as ease of perception.


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