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Bhak, Jong
The Genomics Institute of UNIST (TGI)
Research Interests
  • Geromics, genomics, bioinformatics, protein Engineering, OMICS

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PDBWiki: added value through community annotation of the Protein Data Bank

Cited 6 times inthomson ciCited 10 times inthomson ci
Title
PDBWiki: added value through community annotation of the Protein Data Bank
Author
Stehr, HenningDuarte, Jose M.Lappe, MichaelBhak, Jong HwaBolser, Dan M.
Keywords
computer interface; Internet; protein database; structural homology
Issue Date
201007
Publisher
OXFORD UNIV PRESS
Citation
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, v.2010, no., pp.baq009 -
Abstract
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.or
URI
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DOI
http://dx.doi.org/10.1093/database/baq009
ISSN
1758-0463
Appears in Collections:
SLS_Journal Papers
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