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.org
Highlights
The number of protein structures deposited in the Protein Data Bank (PDB) [1] has recently surpassed 60 000 and continues to grow at an increasing rate [2, 3]
The atomic resolution data in the PDB is the basis for the analysis of enzyme catalysis [4,5,6], the study of protein folding [7] and the evolution of protein structure [8,9,10]
To provide an additional resource for the structural biology community, we have summarized over 2 years worth of posts to a popular community mailing list http://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l
Summary
The number of protein structures deposited in the Protein Data Bank (PDB) [1] has recently surpassed 60 000 and continues to grow at an increasing rate [2, 3]. The atomic resolution data in the PDB is the basis for the analysis of enzyme catalysis [4,5,6], the study of protein folding [7] and the evolution of protein structure [8,9,10]. The PDB provides a primary source of protein structure reference data for the community. The results of most studies are typically only found in the literature For this reason, much of the information about the structures in the PDB cannot be integrated back into the central archive
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