D1270–D1277 Nucleic Acids Research, 2012, Vol. 40, Database issue doi:10.1093/nar/gkr880 Published online 7 November 2011 EcoliWiki: a wiki-based community resource for Escherichia coli Brenley K. McIntosh 1 , Daniel P. Renfro1, Gwendowlyn S. Knapp 1 , Chanchala R. Lairikyengbam2, Nathan M. Liles 1 , Lili Niu1, Amanda M. Supak 1 , Anand Venkatraman 1 , Adrienne E. Zweifel1, Deborah A. Siegele3 and James C. Hu1,* 1Department of Biochemistry and Biophysics, Texas Agrilife Research, 2Department of Computer Science and Engineering and 3Department of Biology, Texas A&M University College Station, TX 77843, USA Received August 14, 2011; Revised September 28, 2011; Accepted September 29, 2011 ABSTRACT EcoliWiki is the community annotation component of the PortEco (http://porteco.org; formerly EcoliHub) project, an online data resource that integrates in- formation on laboratory strains of Escherichia coli, its phages, plasmids and mobile genetic elements. As one of the early adopters of the wiki approach to model organism databases, EcoliWiki was designed to not only facilitate community-driven sharing of biological knowledge about E. coli as a model organ- ism, but also to be interoperable with other data re- sources. EcoliWiki content currently covers genes from five laboratory E. coli strains, 21 bacteriophage genomes, F plasmid and eight transposons. EcoliWiki integrates the Mediawiki wiki platform with other open-source software tools and in-house soft- ware development to extend how wikis can be used for model organism databases. EcoliWiki can be accessed online at http://ecoliwiki.net. INTRODUCTION Laboratory Escherichia coli strains form the basis of much of our fundamental understanding of the molecular and genetic basis of life. As a central model system, E. coli has been either the primary focus or a key component for many bioinformatics data resources that cover overlapp- ing but distinct aspects of E. coli biology. Many existing re- sources provide encyclopedic information about genes, gene products, transcripts and regulons of E. coli K-12 (1–6). Nevertheless, these resources only cover a fraction of the E. coli knowledge base wanted by biologists working with E. coli, which includes not only those interested in the biology of E. coli per se, but also many more using E. coli as a platform for a wide range of basic research and biotechnology. We designed EcoliWiki (http://ecoliwiki.net) to facili- tate community-driven sharing of biological knowledge of the model organism E. coli. First implemented in 2007, EcoliWiki is one of the early adopters of the wiki approach to model organism databases. Although it has been mentioned and cited in several reports and descrip- tions of other wiki-based projects (7–10), this report is the ﬁrst comprehensive description of EcoliWiki. One of our primary objectives for EcoliWiki is to capture community-contributed information about la- boratory strains, phages, plasmids and so forth. Data about E. coli are being continually generated through bio- informatics, proteomic, genomic, biochemical and genetic research. This massive onslaught of data can be difﬁcult to manage and integrate, though its importance to other scientists cannot be understated. It is crucial that the in- formation being produced is interwoven with exist- ing knowledge in an easily accessible and searchable resource. Linking all of this information to the relevant gene as well as to publications is vital for identifying or predicting the function of the gene product not only in E. coli, but also for orthologous gene products. EcoliWiki is designed with this linking and interoperabil- ity in mind. *To whom correspondence should be addressed. Tel: +1 979 862 4054; Fax: +1 979 845 9274; Email: jimhu@tamu.edu Present addresses: Gwendowlyn S. Knapp, Wadsworth Center, NY State Department of Health, Albany, NY 12208, USA. Lili Niu, Agilent Technologies, Santa Clara, CA 95051, USA. Anand Venkatraman, Monsanto Company, 800 North Lindbergh Boulevard, St Louis, MO 63167, USA. The authors wish it to be known that, in their opinion, the ﬁrst two authors should be regarded as joint First Authors. The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.