Nucleic Acids Research, 2012, Vol. 40, Database issue D1273 Figure 2. Progress toward annotation of E. coli genes. EcoliWiki and EcoCyc are collaborating to improve how the experimental literature is captured in GO annotations (8). Complete annotation of a gene is deﬁned as at least one literature-based annotation to each of the three ontologies: molecular function, cellular component and biological process; unreviewed computational annotations (those with the IEA evidence code) are omitted. The gene association ﬁle with current annotations is available at http://www.geneontology.org/GO.downloads.annotations.shtml. properties and links to information at other sites. Each of these is seeded and updated with information that users can elaborate via community annotation. A section is provided to allow users to place a Jmol structure viewer (http://www.jmol.org/) on the product page. EcoliWiki includes instructions for how to use Jmol to make Proteopedia-style (27) links that launch scripts to custom- ize the structure image. The Expression page contains information about gene expression and regulation. Transcription units are shown with an image of the operon provided by RegulonDB (1). The Expression page includes a table for quantitative data about the level, synthesis and degradation of the gene product and/or its mRNA. The Evolution page has infor- mation about homologs and includes links to sequence comparison and ortholog databases such as BLAST (16), InParanoid (28), CDD (29) and YOGY (30). Literature A common concern about wiki-based content is its cred- ibility. An important way of improving the credibility of community-provided content is to provide a robust system for linking assertions to the peer-reviewed primary literature. EcoliWiki uses a modiﬁed version of the Cite extension used by Wikipedia. Our modiﬁed version recog- nizes ‘ref’ tags containing PubMed identifers in the format ‘<ref name=’PMID:#’/>’. EcoliWiki uses these tags to generate in-place numbered citation links and a refer- ence list with bibliographic information provided by NCBI’s E-Utilities (31). The reference also generates a link to create a page about the cited article in EcoliWiki. This reference page is named for the PMID and is seeded with information from PubMed including the abstract, links to the full-text article (if available) and a table for GO annotations relevant to that publication. Reference pages allow for a community-driven equivalent of the curated papers functionality of other model organism databases. Other page types Table 2 lists major page types in EcoliWiki. EcoliWiki aims to provide information about any topic of interest to scientists working with laboratory E. coli, its phage, plasmids and mobile elements, either from interest in the E. coli’s fundamental biology or simply as a biotechnology tool. Thus, we have pages for cloning vectors, strains, methods and other online resources. EcoliWiki generates pages for any GO term used in an annotation; these can be used for information about how a particular process or complex is used in the organisms covered by EcoliWiki. One of the most important aspects of wikis is how they allow users to create new pages. EcoliWiki has a system of form-based entry that will create several page types based on internal templates. Users can also create pages that do not necessarily ﬁt into any predeﬁned type. INTEGRATION WITH INTERNAL AND EXTERNAL TOOLS One of the early design decisions for EcoliWiki was whether or not to build an independent website or incorp- orate the desired E. coli content into Wikipedia, as has been done by the GeneWiki project (32). Although other factors contributed to our decision to build a stand-alone website, a major beneﬁt is in how it allows us to customize the wiki to handle complex data in structured tables. The