Tuesday, August 23, 2005

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NIH News Public Collections of DNA and RNA Sequence Reach 100 Gigabases

"For nearly 20 years, the three leading public repositories for DNA and RNA sequence data have collaborated to provide access to the ever increasing amount of genetic data produced by institutions around the world. The three repositories have now reached a significant milestone by collecting and disseminating 100 gigabases of sequence data. For a frame of reference, one hundred billion bases is about equal to the number of nerve cells in a human brain and a bit less than the number of stars in the Milky Way.

These 100,000,000,000 bases, or “letters” of the genetic code, represent both individual genes and partial and complete genomes of over 165,000 organisms.

"Much has changed since the days when sequences were manually keyed in from the literature or sent on floppy disc and distributed to users on 9-track magnetic tapes, but the purpose of the databases — to make every nucleotide sequence in the public domain freely available to the scientific community as rapidly as possible — remains as strong now as it was in the beginning."

redux [03.03.04]
Wired News Hands Off! That Fact Is Mine

"Ostensibly, the Database and Collections of Information Misappropriation Act (HR3261) makes it a crime for anyone to copy and redistribute a substantial portion of data collected by commercial database companies and list publishers. But critics say the bill would give the companies ownership of facts -- stock quotes, historical health data, sports scores and voter lists. The bill would restrict the kinds of free exchange and shared resources that are essential to an informed citizenry, opponents say."

"An encyclopedia site not only could own the historical facts contained in its online entries, but could do so long after the copyright on authorship of the written entries had expired. Unlike copyright, which expires 70 years after the death of a work's author, the Misappropriation Act doesn't designate an expiration date."

redux [02.05.04]
San Mateo County Times Online Incyte swaps genomics for drugs

"John Keller, Incyte's chief business officer, said the vast amount of genetic information available today has made it difficult to sell subscriptions to the company's genomic data product lines."

"Many firms hoped to profit from the mapping of the human genome, which was expected to usher in a new form of personalized medicine able to target potential diseases in individuals before they struck. The field was billed as one of the breakthroughs of the new century. But the human genome field was over-hyped for the near-term, although it may yet prove promising for the future."

redux [01.28.04]
GenomeWeb Among Databases, Open Access Is Growing Rare

"Many academic scientists see nothing wrong with making their commercial brethren pay for access. After all, they reason, industry has lots of money. Why not make them pay?"

"When you choose the "soak industry" option, you are implicitly expressing the following beliefs: (1) Your database is so useful for drug development that companies will pay handsomely for it. And (2) you're willing to delay the drug developers until the company comes up with the scratch. To hell with the patients who might benefit from the drug in question! Do you really believe this?"

redux [07.07.02]
The Scientist EU Database Directive Draws Fire
[requires 'free' registration]

"The blessings of an increasingly advanced digital world are many: faster data processing, massive data storage. But with these newfound capabilities come new questions about ownership. Who owns the mountains of data contained in databases--whether stock prices, real estate values, or countless genome sequences? What intellectual property rights do database creators have? And how much protection is too much? In recent years, a European Union (EU) database directive has brought a sense of urgency to such issues--and some scientists fear that the law has gone too far."

redux [04.12.02]
GenomeWeb On the European Bioinformatics Battlefield, the New 'Database Right' Wields Considerable Strength

"In the United States, innovators have traditionally relied on copyright and confidential-information rights to protect their databases. In Europe, however, database owners have a novel weapon in their IP armamentarium: the database right.

But there's a catch: Database innovators must have sufficient nexus with Europe--actually, the European Economic Area, or EEA--in order for their databases to qualify for protection. Perhaps it's time for US database makers to consider how they might create sufficient ties with Europe to benefit from this powerful new IP right."

redux [02.27.02]
Salon Genome liberation

"For the scientists working on the Human Genome Project, the data defining who we are is too important to be left to Celera -- or any other company. David Haussler, a team leader at the University of California at Santa Cruz who helped Kent and others put the genome online, expresses the credo of a data liberator succinctly: "Information about the human genome is better in public hands than secretly locked up somewhere."

"But it's not just the research data itself that is at the center of the tug of war between corporations and scientists. When working with data as complex and vast as the human genome, the software tools necessary to manipulate that data are as important as the genetic code itself."

Wired News An 'Atlas' to Count the Genes

"Analysts tend to value drug companies more favorably than those that sell information, and their response to Confirmant's announcement has been lukewarm.

Other biotech company officials with experience in selling database information said that large, general databases such as the protein atlas might have a challenge in finding a market.

"What we have found out is that people ... want technologies that apply to their specific research," said Lior Ma'ayan, executive vice president of corporate development at Compugen, a biotech company based in Tel Aviv."

redux [03.10.01]
eCompany Future Boy: We've Mapped the Human Genome. Now What?

"With information on the genome now rapidly becoming available, the business models for companies that sell information about the genome, such as Celera and Incyte, may soon be outmoded. Biotech companies will then have to earn their stripes the old-fashioned way: by developing blockbuster drugs. Of course, proteomics companies could arise to sell information about proteins to other drug companies, but Strosberg thinks this is a flawed approach. Given his history, he should know. "Incyte's business model," he recalls, "was originally to be an information provider. That period is over. People will not pay as much for information as they used to because so much of it is now publicly available. Information is becoming a commodity." Instead of selling information about proteins, he is focusing Hybrigenics on using its proteomics information to develop drugs, either alone or in partnership with larger pharmaceutical companies."

redux [03.20.02]
The Scientist The Rise of Biological Databases
[requires 'free' registration]

"The genomics revolution and the Internet have changed science in ways impossible to imagine 20 years ago. Among other advances, these forces have allowed the latest research to be routinely gathered, organized, and disseminated, typically at little or cost, through online biological information databases.

Arduous to use and filled with mostly unanalyzed data early on, these computer databases are now packed with valuable, up-to-date information made easily accessible with improved search engines. They have become so ubiquitous and integral to science today that almost every molecular biologist consults one when initiating research projects. "It would be impossible to do molecular biology properly these days without access to them."

redux [05.09.01]
GenomeWeb Survey Finds Only Half of Genome Database Users Aware of Free Resources

"It may seem surprising, considering the amount of publicity the Human Genome Project has garnered over the past year, but a recent Wellcome Trust survey indicates that only half of biomedical researchers using genome databases are familiar with the services provided by Ensembl and other freely available options.

Although the number of hits on the Ensembl website has doubled since the publication of the Human Genome Project's findings in Nature in February, a questionnaire sent to 777 individuals funded by the Wellcome Trust found that only 82 used Ensembl regularly, 189 used it occasionally, and only 50 percent of those who used DNA databases regularly used Ensembl at all.

Even more surprising was the finding that of those who didn't use Ensembl, 50 percent had never heard of it.""