Difference between revisions of "PDBwiki"
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| − | <p><strong>PDBWiki</strong> is a prototype for a community annotated knowledge base of biological molecular structures and related information. It was created in August 2007 by members of the <a | + | <p><strong>PDBWiki</strong> is a prototype for a community annotated knowledge base of biological molecular structures and related information. It was created in August 2007 by members of the <a href="http://www.molgen.mpg.de/%7Elappe/" class="external text" title="http://www.molgen.mpg.de/~lappe/" rel="nofollow">Structural Proteomics Group</a> at the <a href="http://www.molgen.mpg.de/" class="external text" title="http://www.molgen.mpg.de/" rel="nofollow">Max-Planck-Institute for Molecular Genetics</a> and is currently under development. <a href="http://pdbwiki.org/index.php/Feedback_and_suggestions" title="Feedback and suggestions">Feedback and suggestions</a> are very welcome. </p> |
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<h2><span class="editsection"></span><span class="mw-headline">Project purpose</span></h2> | <h2><span class="editsection"></span><span class="mw-headline">Project purpose</span></h2> | ||
| − | <p>The purpose of the project is to create a community driven resource for basic protein structure annotation. Starting with data from the <a | + | <p>The purpose of the project is to create a community driven resource for basic protein structure annotation. Starting with data from the <a href="http://pdbwiki.org/index.php/Protein_Data_Bank" title="Protein Data Bank">Protein Data Bank</a> (PDB), we allow users to contribute comments, classification, and other information to the archive. By this mechanism we aim to create a forum for discussion, improve data quality and minimize duplication of effort. </p> |
<p>Our hope is that community driven feedback can produce a high standard of quality feedback leading to standardised datasets for protein structure analysis. Ultimately we aim to provide a hub for information related to the PDB, highlighting the diverse range of decentralised data related to protein structure. </p> | <p>Our hope is that community driven feedback can produce a high standard of quality feedback leading to standardised datasets for protein structure analysis. Ultimately we aim to provide a hub for information related to the PDB, highlighting the diverse range of decentralised data related to protein structure. </p> | ||
<a name="Future_development"></a> | <a name="Future_development"></a> | ||
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<li> Information about non-polymeric structural entities (ligands, metal ions, etc.) </li> | <li> Information about non-polymeric structural entities (ligands, metal ions, etc.) </li> | ||
| − | <li> More external annotations (<a | + | <li> More external annotations (<a href="http://pdbwiki.org/index.php/SCOP" title="SCOP">SCOP</a>, <a href="http://pdbwiki.org/index.php?title=Bind&action=edit" class="new" title="Bind">Bind</a>, <a href="http://pdbwiki.org/index.php?title=Kegg&action=edit" class="new" title="Kegg">Kegg</a>, <a href="http://pdbwiki.org/index.php?title=Pfam&action=edit" class="new" title="Pfam">Pfam</a>, etc.) </li> |
<li> Facilities to upload and share user contributed sets of proteins </li> | <li> Facilities to upload and share user contributed sets of proteins </li> | ||
<li> Threaded discussions </li> | <li> Threaded discussions </li> | ||
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<h2><span class="editsection"></span><span class="mw-headline">Similar projects</span></h2> | <h2><span class="editsection"></span><span class="mw-headline">Similar projects</span></h2> | ||
<ul> | <ul> | ||
| − | <li> <a | + | <li> <a href="http://www.wikiprofessional.info/" class="external free" title="http://www.wikiprofessional.info/" rel="nofollow">http://www.wikiprofessional.info/</a> </li> |
| − | <li> <a | + | <li> <a href="http://www.humanproteinpedia.org/" class="external free" title="http://www.humanproteinpedia.org/" rel="nofollow">http://www.humanproteinpedia.org/</a> </li> |
| − | <li> <a | + | <li> <a href="http://www.proteopedia.org/" class="external free" title="http://www.proteopedia.org/" rel="nofollow">http://www.proteopedia.org/</a> </li> |
| − | <li> <a | + | <li> <a href="http://openwetware.org/" class="external free" title="http://openwetware.org/" rel="nofollow">http://openwetware.org/</a> </li> |
| − | <li> <a | + | <li> <a href="http://www.ncbi.nlm.nih.gov/projects/GeneRIF" class="external free" title="http://www.ncbi.nlm.nih.gov/projects/GeneRIF" rel="nofollow">http://www.ncbi.nlm.nih.gov/projects/GeneRIF</a> </li> |
| − | <li> <a | + | <li> <a href="http://biowiki.net/" class="external free" title="http://biowiki.net/" rel="nofollow">http://biowiki.net/</a> </li> |
| − | <li> <a | + | <li> <a href="http://thebiologistonline.com/" class="external free" title="http://thebiologistonline.com" rel="nofollow">http://thebiologistonline.com</a> </li> |
| − | <li> <a | + | <li> <a href="../../" class="external free" title="http://biopedia.org" rel="nofollow">http://biopedia.org</a> </li> |
| − | <li> <a | + | <li> <a href="http://bio.cc/" class="external free" title="http://bio.cc/" rel="nofollow">http://bio.cc/</a> </li> |
| − | <li> <a | + | <li> <a href="http://www.topsan.org/" class="external free" title="http://www.topsan.org/" rel="nofollow">http://www.topsan.org/</a> </li> |
</ul> | </ul> | ||
Revision as of 18:08, 13 April 2008
PDBWiki is a prototype for a community annotated knowledge base of biological molecular structures and related information. It was created in August 2007 by members of the Structural Proteomics Group at the Max-Planck-Institute for Molecular Genetics and is currently under development. Feedback and suggestions are very welcome.
Project purpose
The purpose of the project is to create a community driven resource for basic protein structure annotation. Starting with data from the Protein Data Bank (PDB), we allow users to contribute comments, classification, and other information to the archive. By this mechanism we aim to create a forum for discussion, improve data quality and minimize duplication of effort.
Our hope is that community driven feedback can produce a high standard of quality feedback leading to standardised datasets for protein structure analysis. Ultimately we aim to provide a hub for information related to the PDB, highlighting the diverse range of decentralised data related to protein structure.
Future development
Features which may be incorporated in the future include
- Information about non-polymeric structural entities (ligands, metal ions, etc.)
- More external annotations (SCOP, Bind, Kegg, Pfam, etc.)
- Facilities to upload and share user contributed sets of proteins
- Threaded discussions
References
- J. Giles: Key biology databases go wiki. Nature 445, 691 - 691 (2007)
- J.D. Osborne, S. Lin, W.A. Kibbe: Other riffs on cooperation are already showing how well a wiki could work. Nature 446, 856 - 856 (2007)
- K. Wang: Gene-function wiki would let biologists pool worldwide resources. Nature 439, 534 (2006).
- K. Yager: Wiki ware could harness the Internet for science. Nature 440, 278 (2006).
- S. Gong, T. Kim, J. Oh, J. Kwon, S. Cho, D. Bolser & J. Bhak, BioCC: An Openfree Hypertext Bio Community Cluster for Biology. Genomics & Informatics, 4(3) 125 - 128, (2006)
