EcoliWiki
You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts. <protect>
| Link/URL: | |
|---|---|
| What: |
Wiki-based community annotation for E. coli K-12, as part of PortEco |
| Who: |
Jim Hu, Texas A&M University |
| Updates: |
As edited |
| Upcoming events: | |
| Web Services: |
REST services available |
| edit table |
</protect>
Contents
About EcoliWiki
EcoliWiki[1] 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.
Content
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
Quickview
Gene Product Page
Expression Pages
Using EcoliWiki
View a list of all pages in the "Help" namespace.
Browsing
Searching
Technology
EcoliWiki is run off of Mediawiki version 1.31.1 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.
Statistics
EcoliWiki currently has 166,330 pages. You can view other statistics on Special:Statistics.
Web Services/API
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.
