- The rapid accumulation of biological data today is a significant challenge for researchers. That challenge is prompting some scientists to focus on new ways to better manage that data and to make it readily available. The laboratory of Bruce Conklin in the Gladstone Institute of Cardiovascular Disease has created a new collaboration tool, WikiPathways to focus on the use of biological pathways.
"Biological pathways connect genes and proteins in systems that contribute to normal physiology and disease," said Dr. Conklin. "They also organize our thinking about these processes."
Each pathway has to be built from information in multiple publications and databases. New pathway details are being uncovered every day, but the information needs to be organized in a workable system. The pathways also need to be amenable to computation, integration or data exchange. Pathway experts work all around the world, and most have little time to learn about complex databases that need their expertise.
To address these many challenges, the Conklin team chose to develop a new community-based model for pathway curation. In the collaborative spirit, this project was jointly conceived and executed in a partnership with Chris Evelo's lab in Maastricht Netherlands. The project is described in the current issue of PLoS Biology.
WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for curating biological pathways. Building on the MediaWiki core that powers Wikipedia, they added a custom graphical pathway-editing tool and connections to major gene, protein and small molecule databases. This familiar web-based format makes it easy to participate. More importantly, it facilitates broad participation by the scientific community in peer review, editorial curation and maintenance of the pathway content.
"The wiki model as exemplified by Wikipedia, was an obvious place to start," said Alexander Pico, a postdoctoral fellow in the Conklin lab. "This strategy fits well with the current trend to information exchange through community-defined data formats, collaborative online environments, and the growing number of open access journals."
WikiPathways hands over the keys to the database, lowers the technical and hierarchical barriers with creative support tools, and let the data producer organize the data. By allowing anyone to contribute and edit content, they expect to increase the capacity for curation and better manage the increasing flood of data. Despite initial misgivings, Wikipedia has shown that these projects can succeed with the right balance of infrastructure, participation, and administrative principles.
Each pathway has a dedicated wiki page, which displays the current diagram, description, references, download options, version history, and component gene, protein and metabolite list. Any pathway can be edited from within its wiki page by activating an embedded pathway editor.
As the first wiki dedicated to biological pathways, WikiPathways is an experiment of sorts. "We recognize that several factors are critical for WikiPathways to be successful," said Dr. Pico. "Nevertheless, we believe that bringing a kind of democracy to the process will be helpful and that this example might encourage others to develop similar mechanisms for disseminating information."
About the Gladstone Institutes
The J. David Gladstone Institutes, an independent, non-profit biomedical research organization affiliated with the University of California, San Francisco (UCSF), is dedicated to the health and welfare of humankind through research into the causes and prevention of some of the world's most devastating diseases. Gladstone is comprised of the Gladstone Institute of Cardiovascular Disease, the Gladstone Institute of Virology and Immunology and the Gladstone Institute of Neurological Disease. More information can be found at www.gladstone.ucsf.edu.
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