Scientists: 'Gene wiki' could decode genome faster

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Message 781461 - Posted: 12 Jul 2008, 6:41:53 UTC

By Terri Somers
San Diego Union Tribune

July 10, 2008

Unraveling the mysteries of the human genome, the chain of chemicals that determine everything from a person's hair color to predisposition toward cancer, is a mammoth undertaking.

Just figuring out the sequence of the chemicals in the genome took scientists years. And it is expected to take many more years to figure out the significance of the sequences in individual genes.

A group of researchers from San Diego believes the advances will come much quicker if the effort is global and completely open.

And the vehicle the scientists are using is Wikipedia, the Internet encyclopedia founded in 2001 and constructed solely by volunteers with expertise in specific areas.

“I'm a big fan of community intelligence and the idea that together we can collaborate and edit documents and synthesize knowledge better than any one person could,” said Andrew Su, a senior researcher at the Genomics Institute of the Novartis Research Foundation in San Diego.

Wikipedia is a populist site where anyone can contribute. Its users are its editors, so an erroneous post made by one user is corrected or updated by a more informed user.

“With the entire community's input, we envision this 'gene wiki' evolving into a collection of collaboratively created, continually updated, community-reviewed articles for every gene in the human genome,” the scientists wrote in an article published on the Public Library of Science's online journal, PLoS Biology.

Seven of the article's eight authors, including Su, are from the Genomics Institute of the Novartis Research Foundation and San Diego State University. One is from Washington University in St. Louis.

The authors of the so-called gene wiki say they have created 7,500 Wikipedia entries on genes and are editing an additional 650 existing entries.

The developing compendium is a result of the widespread and intense interest in human genetics. It is also another in a long string of global information-sharing efforts in the field, beginning with the U.S. Human Genome Project.

Subsequent international efforts have studied the meaning of the differences in an individual's chain of genes, which is enabling scientists to link individual genes, or gene combinations to specific diseases.

As scientists continue to decipher the mysteries of genetics, the public has become more aware of the genetic basis for disease and is looking for information about genes' influence in public health, said Su.

“This project makes that information more accessible rather than having to read an article in a scientific journal such as Nature or Science,” which can be very technical, Su said.

Gene information is available to scientists through a number of Internet portals. But if a scientist sees a mistake, or thinks something is incomplete or misleading, it is difficult to get it corrected, Su said. Also, these sites are often structured as database tables and use a controlled, scientific vocabulary.

Wikipedia is different in that anyone can edit an entry and correct errors or fill in omissions, he said. And it reads like prose and has the capacity for photographs, diagrams and charts.

“I could see it being used on many different levels, by everyone from students at the high school or college level, through researchers and faculty in the field,” Su said.

As an example, he pointed to the Wikipedia page for Reelin, the protein involved in brain development that the gene RELN prompts the body to make. The page existed prior to this effort and shows how highly collaborative Wikipedia entries are, Su said.

A few dozen editors have tapped into the page and made hundreds of changes over several years. Lay readers can learn the relevance of the gene and its protein, and then see what it looks like. At the same time, scientists can get highly technical information that is meaningful to their research.

A local genetics expert reacted to the gene wiki idea with a bit of skepticism.

“It's a very creative notion. I'm just a little worried that unlike other gene databases, Wikipedia isn't policed by anyone except the public,” said Charles Cantor, chief scientific officer at Sequenom, a San Diego genetics diagnostics company.

“If it's going to be useful, it needs some kind of expert supervision because we are not talking about something like lumber yards,” he said. “Everyone who knows English knows the word 'lumber yard' and what it is.”

And scientists prefer to use well-established sites such as Swissprot, or the federally funded GenBank, Cantor said. In the United Kingdom, the European Bioinformatics Institute has publicly accessible databases, he said.

Those sites are clearly valuable resources for scientists, Su said, but don't allow for the “community intelligence” provided by Wikipedia's users. It has been shown in studies to be as accurate as the Encyclopedia Britannica, he said.

Twenty years ago, scientists would study one or two genes of interest and learn everything they could about it, Su said. But in recent years, tools have been developed that allow scientists to look at big sweeping pieces of genetic data and ask broad questions, such as what is the genetic difference between someone who has cancer and someone who does not, he said.

The answer might be a long list of genes that a scientist knows little about. The gene wiki pages could be a tool to speed the scientist's education and theories, he said.

Su and Cantor agreed on how this effort will be judged.

“I don't know whether the community as a whole will embrace this,” Su said. “Ultimately it will be judged by whether people choose to participate and spend their time.”

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Message 781512 - Posted: 12 Jul 2008, 10:58:27 UTC

community intelligence,i did not know it was called that,
i thought it was something with s
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Message boards : Science (non-SETI) : Scientists: 'Gene wiki' could decode genome faster

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