Public Release:  Large-scale community protein annotation -- WikiProteins

BioMed Central

Today sees the launch of a new collaborative website initially focusing on proteins and their role in biology and medicine. The WikiProfessional technology underlying the site has been developed based upon the collaborative Wikipedia approach. Described in BioMed Central's open access journal Genome Biology, WikiProteins provides a method for community annotation on a huge scale.

The article is written by Barend Mons of the Erasmus Medical Center in Rotterdam, and the Leiden University Medical Center, The Netherlands, and his co-authors from Brazil, The Netherlands, Switzerland, the UK and the USA. They include Amos Bairoch of UniProt, Michael Ashburner of GO and Jimmy Wales, the founder of Wikipedia.

The source material for WikiProteins comes from a mixture of existing authoritative databases (such as the Unified Medical Language System, UniProtKB/Swiss-Prot, IntAct and GO), supplemented by concepts mined from scientific papers published in public literature databases. The automated data mining identifies 'facts' in these available resources, such as protein functions or protein-disease relationships. This process created over one million biomedical concept clouds - called 'Knowlets' - around each individual concept. The developers of the site now hope that many researchers will follow their call to annotate, via WikiProteins, the Knowlets for which they are leading experts. The method enables researchers to add data even from sources that are not openly available, such as from journals only accessible via publishers' databases, immensely enhancing the potential for comprehensive coverage. Each page of text called up via the system is automatically indexed and concepts are connected to the WikiSpace, so that their definition comes up and the information can be edited directly from the page.

The resulting data in the Wiki is fully and freely accessible to the public, and entries can be annotated by any registered user. Mons said: "We here call on a million minds to annotate a million concepts and collect new facts from full-text literature with the immediate reward of collaborative knowledge discovery and recognition of Wiki-contributions to the scientific community."


Launched in 2001, Wikipedia is a freely available, collaboratively created online encyclopedia. WikiProteins maps to Wikipedia and has been created as part of the WikiProfessional initiative and there are plans to add new workspaces such as WikiPeople (an intellectual networking environment), and WikiChemicals for other communities.

A preview of the WikiProtein technology is available at:

Notes to Editors:


1. Calling on a million minds for community annotation in WikiProteins
Barend Mons, Michael Ashburner, Christine Chichester, Erik van Mulligen, Marc Weeber, Johan T den Dunnen, Mark Musen, Matthew Cockerill, Henning Hermjakob, Abel Packer, Roberto Pacheco, Suzanna Lewis, Alfred Berkeley, William Melton, Nickolas Barris, Katy Borner, Gerard Meijssen, Erik Moeller, Peter Jan Roes, Albert Mons, Gert-Jan van Ommen, Jimmy Wales,and Amos Bairoch
Genome Biology (in press)

During embargo, article available here:

After the embargo, article available at the journal website:

Please add the link to the published article in your report. Article citation and URL available on request at on the day of publication

2. The WikiProfessional application is available at

3. Genome Biology publishes articles from the full spectrum of biology. Subjects covered include any aspect of molecular, cellular, organismal or population biology studied from a genomic perspective, as well as genomics, proteomics, bioinformatics, genomic methods (including structure prediction), computational biology, sequence analysis (including large-scale and cross-genome analyses), comparative biology and evolution. Genome Biology has an impact factor of 7.12.

4. BioMed Central ( is an independent online publishing house committed to providing immediate access without charge to the peer-reviewed biological and medical research it publishes. This commitment is based on the view that open access to research is essential to the rapid and efficient communication of science.

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