PDBWiki was a
wiki
A wiki ( ) is an online hypertext publication collaboratively edited and managed by its own audience, using a web browser. A typical wiki contains multiple pages for the subjects or scope of the project, and could be either open to the pu ...
that functioned as a user-contributed
database
In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases spa ...
of
protein structure
Protein structure is the molecular geometry, three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single ami ...
annotations, listing all the protein structures available in the
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, c ...
(PDB). It ran on the
MediaWiki
MediaWiki is a Free and open-source software, free and open-source wiki software. It is used on Wikipedia and almost all other Wikimedia movement, Wikimedia Website, websites, including Wiktionary, Wikimedia Commons and Wikidata; these sit ...
wiki application
Wiki software (also known as a wiki engine or a wiki application), is collaborative software that runs a wiki, which allows the users to create and collaboratively edit pages or entries via a web browser. A wiki system is usually a web application ...
from 2007 to 2013. The website went offline in 2014 and there has not been any way to subsequently access the information that was contributed. PDBWiki contained details of more than 50,000 protein structures and over 50 'user-contributed' annotations, making it a significant resource for the structural biology community.
Motivation
The
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, c ...
(PDB) is the central
archive
An archive is an accumulation of historical records or materials – in any medium – or the physical facility in which they are located.
Archives contain primary source documents that have accumulated over the course of an individual ...
of experimentally solved biomolecular structures. However, the PDB only allows data retrieval and does not provide functionality for collaboration or user feedback. In contrast, PDBWiki allows for sharing expert knowledge about structures deposited in the PDB. It provides tools for discussing and annotating proteins in a collaborative way. The goal is to create a central and freely-accessible repository of user-contributed information that will be useful for anyone working with PDB structures. As such PDBWiki can be considered a part of a wider effort in community-based biological databases curation.
[
{{Citation
, last = Stehr
, first = H.
, author2=Duarte, J.M. , author3=Lappe, M. , author4=Bhak, J. , author5=Bolser, D.M.
, title = PDBWiki
, place = Berlin, Germany
, date = 2009-04-22
, url = http://precedings.nature.com/documents/3123/version/1
, doi = 10.1038/npre.2009.3123.1
, journal = Nature Precedings
, doi-access = free
]
About
PDBWiki was developed as part of the
BioWiki initiative, and was entered into the third International Openfree Bioinformation Contents Competition organised by BiO.CC, a biological information website operated by
KOBIC
The Korean Bioinformation Center (KOBIC) is the Korean national research centre in bioinformatics, based in Daejeon, South Korea. The centre is comparable to the National Center for Biotechnology Information (NCBI) in the United States and the Eu ...
.
The Website went offline in January 2014, replaced with a notice redirecting to
Proteopedia
Proteopedia is a wiki, 3D encyclopedia of proteins and other molecules.
The site contains a page for every entry in the Protein Data Bank (>130,000 pages), as well as pages that are more descriptive of protein structures in general such as acetylch ...
, a similar wiki-based structural biology database project.
See also
*
Proteopedia
Proteopedia is a wiki, 3D encyclopedia of proteins and other molecules.
The site contains a page for every entry in the Protein Data Bank (>130,000 pages), as well as pages that are more descriptive of protein structures in general such as acetylch ...
* The
Molecular and Cellular Biology 'WikiProject'.
References
External links
* Th
PDBWikihomepage
About PDBWiki* Th
Worldwide Protein Data Bank
Biological databases
MediaWiki websites