ECOLIWIKI CONTENT EcoliWiki houses information in >64 000 content pages. As in other MediaWiki-based wikis, EcoliWiki content pages are paired with talk pages where users can discuss or debate content. EcoliWiki also extensively uses MediaWiki’s system of placing pages in Categories, and the ability to nest Categories and Subcategories. Category terms increase the usability of the wiki for both users and automated processes. Gene-centric pages EcoliWiki contains groups of pages for genes from the E. coli lab strains MG1655 (11,12), W3110 (11), DH10B (13), BW2952 (14) and REL606 (15). Where a canonical gene name is available from EcoGene (5), it is used as the basis for the page names. Identiﬁers and non-canonical gene names are treated as synonyms that redirect to the gene, or to a disambiguation page when the same synonym is used for more than one gene. Orthologs from different strains are grouped together so that their annotations are made in a shared location. We used BLAST (16) to identify orthologs based on homology within the gene and in its ﬂanking sequences. Note, however, that this method relies on orthologs being annotated as features in the GenBank or RefSeq ﬁles we use as sources. Orthologs that are present in a genome, but not annotated, will be missed. Improved projection of annotations between genomes is needed and is planned for the future. Some genes from the E. coli B strain REL606 share gene names with non- homologous genes in MG1655 (15). For example, two blocks of genes involved in LPS synthesis in MG1655 and REL606 are in similar locations. Several of these have common waa and wbb names although they do not have signiﬁcant sequence similarity. To distinguish these from the K-12 genes, we give these genes from E. coli B their own sets of gene pages with page titles preﬁxed with E_coli_B. Other genes from REL606 that are not present in the K-12 strains do not have canonical gene names based on the Demerec system (17). In these cases, we base the gene names on the ECB locus tags (15). In addition to E. coli genomes, we have gene-centric pages for the F plasmid, 21 different bacteriophage gen- omes and eight transposons (Table 1). These genes were imported from GenBank and RefSeq records, where avail- able. The genome of bacteriophage phi80 and some of the transposon sequences were extracted from other sequence records. These pages are named with preﬁxes indicating the source genome, e.g. Phage_lambda_cI:Quickview. Every gene in EcoliWiki is associated with six wiki pages linked by formatting that mimics tabs: Quickview, Gene, Gene Product(s), Expression, Evolution and On One Page. Each of the ﬁrst ﬁve contains pertinent information about that aspect of the gene, and they all contain editable tables and notes. Each of these pages has a references section and a list of categories the page belongs to. EcoliWiki pages include links to other databases including EcoCyc (3), EcoGene (5), EchoBase (4), ASAP (2), EcoliGenExpDB (http://genexpdb.ou.edu/main/), RefSeq (18), UniProt (19), Pfam (20), Brenda (21), SwissModel (22), and ModBase (23). References are automatically Nucleic Acids Research, 2012, Vol. 40, Database issue D1271 Table 1. Sources of genes listed on EcoliWiki NCBI accession Name Notes NC_000913 AC_000091 NC_010473 NC_012759 NC_012967 NC_002483 NC_003298 NC_000866 NC_005859 NC_001604 NC_001416 NC_002166 NC_002167 NC_001901 NC_008720 NC_005856 NC_001895 NC_001609 NC_001421 NC_000929 NC_001422 NC_003287 J02448 NC_001417 NC_001890 V00613 U00004 NC_002525 V00622 AF162223 V00359 V00612 D16449 E. coli K-12 MG1655 E. coli K-12 W3110 E. coli K-12 DH10B E. coli K-12 BW2952 E. coli B REL606 Plasmid F Bacteriophage T3 Bacteriophage T4 Bacteriophage T5 Bacteriophage T7 Bacteriophage lambda Bacteriophage HK022 Bacteriophage HK97 Bacteriophage N15 Bacteriophage N4 Bacteriophage P1 Bacteriophage P2 Bacteriophage P4 Bacteriophage phi80 Bacteriophage PRD1 Bacteriophage Mu Bacteriophage phiX174 Bacteriophage M13 Bacteriophage f1 Bacteriophage MS2 Bacteriophage Qbeta Transposon Tn3 Transposon Tn5 Transposon Tn7 Transposon Tn9 Transposon Tn10 Transposon Tn903 Transposon Tn1681 Transposon gamma-delta Extracted from a ﬁle (reannotated version of NC_001604) gen- erously provided by Dr. Drew Endy Extracted from NC_010473 Extracted from NC_002525 generated using a modiﬁed version of the Cite extension (see below). The On One Page view catenates content from the other ﬁve for users who prefer scrolling to clicking between tabs. Figure 1 shows some of the elements of one of the gene-centric pages. The Quickview page provides users with a brief summary of data in the form of a table that dynamically updates from tables on the other associated pages for the gene. The Quickview table also contains links to the DNA and pro- tein sequences for the gene, literature searches and other database searches. Below the table, a Notes area is pro- vided for general information. The Gene, Gene Product(s), Expression and Evolution pages consist of multiple sections containing tables and Notes ﬁelds to allow capture of much more detailed information. Information on the Gene page includes gene synonyms, mutant alleles and their availability, genetic interactions, and a set of images from GBrowse (25) showing the gen- omic context of the gene in each strain where it is found.