EcoliWiki: a wiki-based community resource for Escherichia coli

Abstract

EcoliWiki is the community annotation component of the PortEco (http://porteco.org; formerly EcoliHub) project, an online data resource that integrates information 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 organism, but also to be interoperable with other data resources. 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 software development to extend how wikis can be used for model organism databases. EcoliWiki can be accessed online at http://ecoliwiki.net.

Figure 1.

Example Gene-centric page for PhoQ product(s). (A) Overall page, showing the structure of coliWiki pages with tables (red arrows), figures, jmol viewer (blue arrow) and text notes (yellow arrows). (B–E) Show expanded views of page areas. (B) Simulated tabs for navigation between pages related to PhoQ, and links to page sections. (C) User-editable table for GO annotations for PhoQ. This table is periodically repopulated with annotations from EcoCyc. (D) Domains and motifs table and associated figures. The motifs diagram is generated from the content of the domains table to its left, and from the alleles and phenotypes table on the PhoQ:Gene page. The TMHMM (24) diagram is automatically generated for all genes. (E) References and categories. References are automatically generated from a software extension that recognizes PMIDs in the tables and embedded via markup in the text notes sections.

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.

Figure 3.

(A) Visitor statistics from Google Analytics for 11 August 2010–10 August 2011. The numbers of visits that are the n-th visit for a given user indicate users who return to EcoliWiki multiple times. Note that the number of users who visited n times is included in the count for users who visited fewer than n times. Thus, each bar is for the number of users who visited n times or more. (B) Distribution of user contributions to EcoliWiki, excluding project employees.