EcoliWiki: Difference between revisions

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[[Category:Databases]]
[[Category:Databases]]
[[Category:Biology wikis]]
[[Category:Biology wikis]]
[[Category:EcoliHub Partner]]
[[Category:PortEco Partner]]
[[Category:E. coli Databases]]
[[Category:E. coli Databases]]
[[Category:IECA Portal]]
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{| {{Prettytable}} width='30%' align="right"  id="P480cc92777450"  class=" tableEdit Database_table" 
 
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!{{table heading style}} |Link/URL:
!align=left {{table heading style}} |Link/URL:
|
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[http://ecoliwiki.net/colipedia EcoliWiki]
[http://ecoliwiki.net/colipedia EcoliWiki]
|-
|-
!{{table heading style}} |What:
!align=left {{table heading style}} |What:
|
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Wiki-based community annotation for ''E. coli'' K-12, as part of [http://ecolihub.org EcoliHub]
Wiki-based community annotation for ''E. coli'' K-12, as part of [http://PortEco.org PortEco]
|-
|-
!{{table heading style}} |Who:
!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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!{{table heading style}} |Updates:
!align=left {{table heading style}} |Updates:
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As edited
As edited
|-
|-
!{{table heading style}} |Upcoming events:
!align=left {{table heading style}} |Upcoming events:
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|-
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!{{table heading style}} |Web Services:
!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}}==
''Add general information here''
[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.
[http://ecoliwiki.org {{PAGENAME}}] is...
 
==Content==
==Content==
Most of the ''E. coli'' information was initially seeded with a subset of information from parsing [[EcoCyc]] data dumps. For phage &lambda; and the F plasmid, [[Genbank]] accessions were converted to [http://www.sanger.ac.uk/Software/formats/GFF/ 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===
[[Image:EW_quickview.jpg|center|400px|thumb]]
===Gene Product Page===
[[Image:EW_jmol.jpg|right|thumb|150px]]
<BR><br clear='all'>
===Expression Pages===
[[Image:EW_expression.jpg|right|thumb|250px]]
<BR><br clear='all'>
==Using {{PAGENAME}}==
==Using {{PAGENAME}}==
View a list of all pages in the  [http://ecoliwiki.net/colipedia/index.php?title=Special%3AAllpages&from=&namespace=4 "Help" namespace].
===Browsing===
===Browsing===
===Searching===
===Searching===
===Usage examples===
''Add links to additional pages describing success stories here.''


==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===
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 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==
==Discussion==


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:

EcoliWiki

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:

Quickview

Gene Product Page



Expression Pages



Using EcoliWiki

View a list of all pages in the "Help" namespace.

Browsing

Searching

Other sites with related content

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 167,280 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.

Discussion

References

External Links

EcoliWiki

Discussion of EcoliWiki on other websites

  1. ↑ McIntosh, BK et al. (2012) EcoliWiki: a wiki-based community resource for Escherichia coli. Nucleic Acids Res. 40 D1270-7 PubMed
Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=EcoliWiki&oldid=1400750"