WikiPathways gives the people the power to curate

The exponential growth of diverse types of biological data presents the research community with an unprecedented challenge to keep the flood of biological data as accessible, up-to-date, and integrated as possible.

But it also presents an unprecedented opportunity to cultivate new models of data curation and exchange by engaging the direct participation of the community. In a new article published this week in PLoS Biology, "WikiPathways: Pathway Editing for the People," Alexander R. Pico and his colleagues describe their efforts to embrace that opportunity and meet the challenge of collecting and curating vast amounts of biological information on cellular pathways.

Pathways are critical to understanding the functions of individual genes and proteins in the context of the systems and processes that contribute both to normal physiology and to disease. Each biological pathway must be constructed from a mass of biological information distributed across multiple publications and databases.

The researchers argue that their resource, WikiPathways, which combines a wiki-based pathway curation resource with an embedded graphical pathway editing tool, can meet the growing challenge presented by the influx of biological data, and provides an innovative example of content curation by the biology community. The new resource, which allows users to view, store, and edit biological pathway information, is completely free and open source.

Curating and archiving information on biological pathways present a special challenge because pathways comprise a myriad of interactions, reactions, and regulations, which are often identified piecemeal over extended periods and by a variety of researchers. Efforts to take on this challenge have typically relied on small groups of paid curators. Given the "Herculean task" of curating "all of biology," the researchers established WikiPathways to draw on the collective expertise of the scientific community to facilitate content collection and curation.

Just as Wikipedia and other innovative creative support tools have changed how we access, collect and manage information, WikiPathways presents a new, collaborative model for thinking about biological pathway information, they argue. The resource attempts to harness the power of the community to not only organize and maintain the vast amounts of biological data but also to maximize its value by providing the community with a wealth of annotated information.

"WikiPathways will be a powerful resource for the research community and a vital forum for pathway curation," the authors argue. "And we are hopeful that it will serve as an example for how the continuing flood of biological data can be managed and utilized by the community to irrigate future hypotheses and discoveries."

Citation:Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, et al. (2008) WikiPathways: Pathway editing for the people. PLoS Biol 6(7): e184.doi:10.1371/journal.pbio.0060184
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060184

Source: Public Library of Science

Related stories:

New approach may render disease-causing staph harmless
Researchers at the University of Illinois helped lead a collaborative effort to uncover a completely new treatment strategy for serious Staphylococcus aureus (“Staph”) infections. The research, published Feb. 14 in Science Express comes at a time when strains of antibiotic-resistant Staph (known as MRSA, for methicillin-resistant S. aureus) are spreading in epidemic proportions in hospital and community settings.
Popular arthritis drug may disrupt heart rhythm, UB research finds
Celebrex, a popular arthritis drug that blocks pain by inhibiting an enzyme known as COX-2, has been shown in laboratory studies to induce arrhythmia, or irregular beating of the heart, via a novel pathway unrelated to its COX-2 inhibition.
Collaborative cross attracting diverse genetics experiments
Mice that are part of the Collaborative Cross project at Oak Ridge National Laboratory are helping scientists around the world learn more about possible causes of drug abuse, diabetes, sleep disorders, stress and pain, kidney disease and a number of other conditions that affect millions of people.
Running on Microbes
What’s cleaner than coal, as renewable as solar energy and as ingenious as any of the cutting-edge alternative energy sources now being proposed for cars? The answer is microbe power, and if a USC team’s efforts to harness its electrical punch succeed, it may one day find uses in applications both big and small.
Genetic 'roadmap' charts links between drugs and human disease
A research team led by scientists at the Broad Institute of MIT and Harvard announced today the development of a new kind of genetic "roadmap" that can connect human diseases with potential drugs to treat them, as well as predict how new drugs work in human cells. Called the "Connectivity Map," the new tool and its uses are described in the September 29 issue of Science and in separate publications in the September 28 immediate early edition of Cancer Cell.
African parasite makes component of fat differently from all other organisms
Studying the parasite that causes African sleeping sickness, scientists at Johns Hopkins have discovered a previously unknown way of making fatty acids, a component of fat and the outer layer of all cells. The find unveils more about the biology of this hard-to-kill parasite and could lead to a target for designing new drugs to fight the illness that infects a half-million people and kills 50,000 a year worldwide.
In Bacterial Diversity, Amazon Is A 'Desert'; Desert Is An 'Amazon'
Ironically, in the diversity of soil bacteria, the otherwise species-rich Amazon is a more like a desert, while the arid desert is a teeming microbial Amazon, researchers have found. Their first-ever continental-scale genetic survey of soil bacteria revealed that the primary factor that seems to govern the diversity of soil bacteria is soil pH. Thus, the acidic soils of topical forests harbor fewer bacterial species than the neutral soils of deserts.
Life isn't 2-D, so why should our encyclopedias be?
Biologists and biochemists are now able to access 3D images of biomacromolecules underlying biological functions and disease. Rather than relying on text to provide the understanding of biomacromolecule structures, a collaborative website called Proteopedia now provides a new resource by linking written information and three-dimensional structural information.

News discussion:

General Science news