Over the next five years, WormBase—a Caltech-led, multi-institutional effort to make genetic information about nematodes, or roundworms, freely available to the world—will receive $14.8 million in additional funding from the National Institutes of Health. As many as 1 million nematode species are thought to live on Earth, and many are pests or parasites that ravage crops and spread diseases. They also happen to share many genes that are found in humans. Therefore, the squirmy creatures are intensively researched by labs around the world.
The WormBase project began in 2000 with the original goal of creating an online clearinghouse for data related to the most widely studied nematode, the model organism Caenorhabditis elegans. The project's website (www.wormbase.org) now hosts genomic data for more than 50 nematodes as well as vast amounts of other experimental data. In fact, about 1,200 scientific papers are added to the searchable database every year. And with more than 1,000 laboratories currently registered as users, WormBase has become an invaluable tool for the biomedical and agricultural research communities.
"WormBase has made it much easier for bench researchers to access a lot of information that they need much more rapidly. That accelerates research," says Paul Sternberg, the Thomas Hunt Morgan Professor of Biology at Caltech and leader of the WormBase project. "It has enabled studies that just would not have been possible without all of this information being available in a single place."
The bioinformatics resource serves a number of different communities. One of those is the group of scientists working with less-studied nematode species. "A lot of the research comes from individual researchers studying a specific problem. They generate a lot of facts and observations along the way; that information, if you aggregate it, ends up being quite valuable and extensive," Sternberg explains. "So, WormBase collects those bits of information and stores them in one place. It ends up being more than the sum of the parts."
WormBase also serves basic biomedical researchers who have used the database to investigate everything from cancer genes and axon growth to aging and kidney disease. Finally, WormBase is helpful for those scientists who study disease-causing nematodes and those species that infect and wreak havoc on crops and livestock.
Going forward, the WormBase project hopes to help researchers understand in greater detail the mechanisms through which nematode genes work together in pathways by making certain types of data more accessible and richer. "We have the parts list," Sternberg says. "Now the question is, how do all of the parts really work together to make the intricate mechanisms?"
WormBase is also working with the organizers of similar databases for other model organisms—such as the fruit fly and the mouse—that share many genes with nematodes. They are trying to align the databases, in terms of the formats they use and their interfaces, so that researchers can easily search all of them. So, for example, researchers studying a human gene who want information about that gene's counterparts in the worm or fruit fly would be able to switch between the databases quickly and easily. "We are also sharing the development of text-mining software that allows us to extract information from papers more efficiently," Sternberg says.
WormBase is an international consortium led by Caltech. Current collaborators include the Ontario Institute for Cancer Research in Toronto, Canada, and the European Bioinformatics Institute in Cambridge, England.