Published online 16 October 2007 SURVEY AND SUMMARY Multidimensional annotation of the Escherichia coli K-12 genome Peter D. Karp1,*, Ingrid M. Keseler1, Alexander Shearer1, Mario Latendresse1, Markus Krummenacker1, Suzanne M. Paley1, Ian Paulsen2,3, Julio Collado-Vides4, Socorro Gama-Castro4, Martin Peralta-Gil4, Alberto Santos-Zavaleta4, Mo´ nica I. Pen˜ aloza-Spı´nola4, C e´sar Bonavides-Martinez4 and John Ingraham5 1SRI International, 333 Ravenswood Ave EK207, Menlo Park CA 94025, 2J. Craig Venter Institute, Rockville, MD 20850, USA, 3Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia, 2109, 4Centro de Ciencias Geno´ micas, Universidad Nacional Aut o´noma de Me´ xico and 5University of California, Davis, USA Received June 8, 2007; Revised August 9, 2007; Accepted September 6, 2007 Nucleic Acids Research, 2007, Vol. 35, No. 22 7577–7590 doi:10.1093/nar/gkm740 ABSTRACT The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annota- tions. Of the 4460 E. coli genes, EcoCyc assigns biochemical functions to 76%, and 66% of all genes had their functions determined experimentally. EcoCyc assigns E. coli genes to Gene Ontology and to MultiFun. Seventy-five percent of gene products contain reviews authored by the EcoCyc project that summarize the experimental literature about the gene product. EcoCyc information was derived from 15 000 publications. The database contains extensive descriptions of E. coli cellular networks, describing its metabolic, transport and transcriptional regulatory processes. A comparison to genome annotations for other model organisms shows that the E. coli genome contains the most experimentally determined gene functions in both relative and absolute terms: 2941 (66%) for E. coli, 2319 (37%) for Saccharomyces cerevisiae, 1816 (5%) for Arabidopsis thaliana, 1456 (4%) for Mus musculus and 614 (4%) for Drosophila melanoga- ster. Database queries to EcoCyc survey the global properties of E. coli cellular networks and illuminate the extent of information gaps for E. coli, such as dead-end metabolites. EcoCyc provides a genome browser with novel properties, and a novel interactive display of transcriptional regulatory networks. INTRODUCTION This article presents the state of the annotation of the Escherichia coli K-12 genome as deﬁned by the EcoCyc (1–3) database (DB). We use database queries to EcoCyc to ﬁnd the gaps in our knowledge of E. coli, thus deﬁning opportunities for future research, such as dead-end metabolites within the E. coli metabolic network. Without computable descriptions of the genome and cellular networks of E. coli, it would be diﬃcult if not impossible to perform the analyses described here. Reed et al. (4) developed the notion that genome annotations have the potential to be multidimensional. They deﬁne a one-dimensional genome annotation as consisting of a list of cellular components; a two- dimensional annotation adds descriptions of cellular networks. A three-dimensional annotation describes spatial orientations of the network components, and a four-dimensional annotation describes genome changes that occur during evolution (Note that EcoCyc does not provide the third or fourth dimensions deﬁned by Reed et al.). Adding to this concept, several additional aspects of genome annotations should be considered. To what degree does the genome annotation incorporate experimental versus computational information, and does it clearly diﬀerentiate them? What fraction of the annotations has been validated experimentally? Does the genome annotation include comprehensive written reviews of the gene products and cellular interactions? Does the annotation include citations that support written statements and other information in the annotation? Does the annotation include assertions made with *To whom correspondence should be addressed. Tel: +1 650 859 4358; Fax: +1 650 859 3735; Email: pkarp@ai.sri.com 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.