2 votes

PDBWiki

Henning Stehr¹, Jose Duarte¹, Michael Lappe¹, Jong Bhak² & Dan Bolser¹

Correspondence: (Login to view email address)

1. Max-Planck-Institute for Molecular Genetics
2. Korean Bio Information Center (KOBIC)

PDF (1.3 MB)

Document Type:

Poster

Date:

Received 22 April 2009 11:07 UTC; Posted 22 April 2009

Subjects:

Bioinformatics

Tags:

• community annotation
• PDB
• wiki
• database
• protein data bank
• community knowledge
• protein structure
• biocuration

Abstract:

Background: The success of community projects such as Wikipedia has recently prompted a discussion about the applicability of such tools in the life sciences. However, there is currently no consensus about how best to achieve this goal.

Methodology/Principal Findings: Here we present a community knowledge base for the annotation of biological molecular structures that addresses some of these issues. This Wiki-style database consists of one structured page for each entry in the the Protein Data Bank (PDB) and allows users to attach categorised comments and discussions to the entries. The core data for each entry is shown as a summary and can be used for searching and navigation via categories. A user-editable list of database cross references is automatically included in each page. Like in a database, it is possible to produce tabular reports and ‘structure galleries’ based on user defined queries. PDBWiki runs in parallel to the PDB and is automatically synchronised every week.

Conclusions/Significance: PDBWiki is a simple but usable system that serves as a bug-tracker, discussion forum and community annotation system for the structures in the PDB. We believe that PDBWiki can serve as a model for better understanding how to capture community knowledge in the biological sciences.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

Discussion

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1 comment

Dan Bolser on 22 April 2009 22:15 UTC

Thanks for uploading this Henning. Its great to have a formalized system for recognition of poster submissions.

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Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Stehr, Henning, Duarte, Jose, Lappe, Michael, Bhak, Jong, and Bolser, Dan. PDBWiki. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3123.1> (2009)

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