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Wiki-based community annotation for E. coli K-12, as part of PortEco
Jim Hu, Texas A&M University
REST services available
EcoliWiki is a wiki-based system for finding, editing, and adding information about E. coli K-12 and other model organism strains of E. coli. EcoliWiki is being constructed to include information about bacteriophage, plasmids, and mobile genetic elements.
Most of the E. coli information was initially seeded with a subset of information from parsing EcoCyc data dumps. For phage λ and the F plasmid, Genbank accessions were converted to GFF, which was parsed into the appropriate tables. Other sources of content include:
- user additions
- monthly addition of annotations from EcoCyc
- structural data from the PDB
- domains and motif information from InterPro
- various databases including EcoGene, RegulonDB, Genbank, GenoBase, ASAP
- many many scientific papers
Gene Product Page
View a list of all pages in the "Help" namespace.
EcoliWiki is run off of Mediawiki version 1.21.9 modified with a mix of open source extensions. Many of these are from other publicly available sources, while others were created for this project. Notable custom extensions include:
- TableEdit: provides structured data in the wiki format, allowing easier data reuse.
- PagesOnDemand: Automated seeding of content for various kinds of pages. PagesOnDemand is extensible to support new page types.
EcoliWiki currently has 165,374 pages. You can view other statistics on Special:Statistics.
EcoliWiki provides REST web services as part of the PortEco Web Services infrastructure project
- keyword - currently searches based on a single keyword
- gene - prototype to extract gene details from the wiki
- is_edited - shows numbers of human revisions to EcoliWiki pages.
For more detail about the EcoliWiki web services, see Help:Web Services.
Discussion of EcoliWiki on other websites
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