EcoliWiki: Difference between revisions
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[[Category:Databases]] | [[Category:Databases]] | ||
[[Category:Biology wikis]] | [[Category:Biology wikis]] | ||
[[Category: | [[Category:PortEco Partner]] | ||
[[Category:E. coli Databases]] | [[Category:E. coli Databases]] | ||
[[Category:IECA Portal]] | [[Category:IECA Portal]] | ||
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{| id="P480cc92777450" class=" tableEdit Database_table" | {| {{Prettytable}} width='30%' align="right" id="P480cc92777450" class=" tableEdit Database_table" | ||
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!align=left | !align=left {{table heading style}} |Link/URL: | ||
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[http://ecoliwiki.net/colipedia EcoliWiki] | [http://ecoliwiki.net/colipedia EcoliWiki] | ||
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!align=left | !align=left {{table heading style}} |What: | ||
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Wiki-based community annotation for ''E. coli'' K-12, as part of [http:// | Wiki-based community annotation for ''E. coli'' K-12, as part of [http://PortEco.org PortEco] | ||
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!align=left | !align=left {{table heading style}} |Who: | ||
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Jim Hu, Texas A&M University | Jim Hu, Texas A&M University | ||
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!align=left | !align=left {{table heading style}} |Updates: | ||
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As edited | As edited | ||
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!align=left | !align=left {{table heading style}} |Upcoming events: | ||
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!align=left | !align=left {{table heading style}} |Web Services: | ||
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REST services available | REST services available | ||
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==About {{PAGENAME}}== | ==About {{PAGENAME}}== | ||
[http://ecoliwiki.org {{PAGENAME}}] 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. | [http://ecoliwiki.org {{PAGENAME}}]<ref name='PMID:22064863'/> 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== | ==Content== | ||
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==Other sites with related content== | ==Other sites with related content== | ||
==Technology== | ==Technology== | ||
EcoliWiki is run off of [http://www.mediawiki.org Mediawiki] version {{CURRENTVERSION}} 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=== | ===Statistics=== | ||
EcoliWiki currently has {{NUMBEROFPAGES}} pages. You can view other statistics on [[Special:Statistics]]. | |||
===Web Services/API=== | ===Web Services/API=== | ||
EcoliWiki provides REST web services as part of the | EcoliWiki provides REST web services as part of the PortEco Web Services infrastructure project | ||
*keyword - currently searches based on a single keyword | *keyword - currently searches based on a single keyword | ||
*gene - prototype to extract gene details from the wiki | *gene - prototype to extract gene details from the wiki | ||
Latest revision as of 17:27, 20 August 2013
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.
| 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 |
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 1.43.11 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 167,218 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.