Searching across hundreds of databases
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.
Pubmed ID: 20624717 RIS Download
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Organization that serves the scientific and educational needs of bioinformatic practitioners and the general public. They develop and maintain computational resources to facilitate world-wide communications and collaborations between people of all educational and professional levels. They provide and promote open access to the materials and methods required for, and derived from, research, development and education.
View all literature mentionsA server-based software wiki package written in PHP. It is a powerful, scalable software deigned for high-traffic websites. MediaWiki uses PHP to process and display data stored in a database such as MySQL. When a user submits an edit to a page, MediaWiki writes it to the database without deleting the previous versions, allowing easy reversions. MediaWiki is able to manage image and multimedia files, as well, which are stored in the filesystem.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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