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PDBWiki: added value through community annotation of the Protein Data Bank
Abstract The success of community projects such as The success of community projects such as Wikipedia has recently prompted a discussion about the applicability of such tools in the life sciences. Currently, there are several such science-wikis' that aim to collect specialist knowledge from the community into centralized resources. However, there is no consensus about how to achieve this goal. For example, it is not clear how to best integrate data from established, centralized databases with that provided by community annotation'. We created {PDBWiki,} a scientific wiki for the community annotation of protein structures. The wiki consists of one structured page for each entry in the the Protein Data Bank {(PDB)} and allows the user to attach categorized comments to the entries. Additionally, each page includes a user editable list of cross-references to external resources. As in a database, it is possible to produce tabular reports and structure galleries' based on user-defined queries or lists of entries. {PDBWiki} runs in parallel to the {PDB,} separating original database content from user annotations. {PDBWiki} demonstrates how collaboration features can be integrated with primary data from a biological database. It can be used as a system for better understanding how to capture community knowledge in the biological sciences. For users of the {PDB,} {PDBWiki} provides a bug-tracker, discussion forum and community annotation system. To date, user participation has been modest, but is increasing. The user editable cross-references section has proven popular, with the number of linked resources more than doubling from 17 originally to 39 today. Database {URL:} http://www.pdbwiki.orgay. Database {URL:} http://www.pdbwiki.org
Abstractsub The success of community projects such as The success of community projects such as Wikipedia has recently prompted a discussion about the applicability of such tools in the life sciences. Currently, there are several such science-wikis' that aim to collect specialist knowledge from the community into centralized resources. However, there is no consensus about how to achieve this goal. For example, it is not clear how to best integrate data from established, centralized databases with that provided by community annotation'. We created {PDBWiki,} a scientific wiki for the community annotation of protein structures. The wiki consists of one structured page for each entry in the the Protein Data Bank {(PDB)} and allows the user to attach categorized comments to the entries. Additionally, each page includes a user editable list of cross-references to external resources. As in a database, it is possible to produce tabular reports and structure galleries' based on user-defined queries or lists of entries. {PDBWiki} runs in parallel to the {PDB,} separating original database content from user annotations. {PDBWiki} demonstrates how collaboration features can be integrated with primary data from a biological database. It can be used as a system for better understanding how to capture community knowledge in the biological sciences. For users of the {PDB,} {PDBWiki} provides a bug-tracker, discussion forum and community annotation system. To date, user participation has been modest, but is increasing. The user editable cross-references section has proven popular, with the number of linked resources more than doubling from 17 originally to 39 today. Database {URL:} http://www.pdbwiki.orgay. Database {URL:} http://www.pdbwiki.org
Bibtextype article  +
Has author Henning Stehr + , Jose M. Duarte + , Michael Lappe + , Jong Bhak + , Dan M. Bolser +
Has remote mirror http://database.oxfordjournals.org/cgi/content/abstract/2010/0/baq009  +
Number of citations by publication 0  +
Number of references by publication 0  +
Peer-reviewed Yes  +
Published in Database +
Title PDBWiki: added value through community annotation of the Protein Data Bank +
Type journal article  +
Year 2010 +
Creation dateThis property is a special property in this wiki. 20 September 2014 16:55:27  +
Categories Publications without keywords parameter  + , Publications without language parameter  + , Publications without license parameter  + , Publications without DOI parameter  + , Publications without archive mirror parameter  + , Publications without paywall mirror parameter  + , Journal articles  + , Publications without references parameter  + , Publications  +
Modification dateThis property is a special property in this wiki. 20 September 2014 16:55:27  +
DateThis property is a special property in this wiki. 2010  +
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PDBWiki: added value through community annotation of the Protein Data Bank + Title
 

 

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