Geneticists are up in arms over the introduction of a subscription fee for access to the protein databases owned and maintained by Incyte Genomics, a private company based in Palo Alto, California.

The databases, which contain information about protein structure and function in important model organisms studied by biologists, had been free to academics. But Incyte last month introduced an annual access charge of $2,000 per laboratory — a move that has already prompted an effort to secure more funding for public databases.

Many biologists claim that they would be prepared to pay a small fee to support the maintenance of high-quality databases — even though most of the data were generated by the researchers themselves in publicly funded labs. But some are crying foul over the size of Incyte's fee. “The fee is simply too high for small laboratories,” says Gustav Ammerer, a yeast geneticist at the University of Vienna.

Incyte's database collection, known as the Proteome BioKnowledge Library, covers model organisms such as yeast (Saccharomyces cerevisiae and Schizosaccharomyces pombe) and the nematode Caenorhabditis elegans, and also features some mammalian and microbial databases.

The library was founded in 1995 by James Garrels, whose company, Massachusetts-based Proteome, offered academics free access to the data but charged industrial users. Garrels sold the company to Incyte at the end of 2000, when he assured geneticists that the databases would remain free on the web to academics. Incyte was unavailable for comment on the reasons for the change.

Peer Bork (left) and Michael Cherry would like to see more money for public protein databases.

The move has already caused researchers some difficulties. Peer Bork, a bioinformaticist at the European Molecular Biology Laboratory in Heidelberg, had to withdraw some information from a recent paper (C. von Mering et al. Nature 417, 399–403; 2002) just before it was published, when Incyte changed the terms under which the data in it could be shared. The paper compared different analyses of protein interactions in yeast.

But with the introduction of the access fee, restrictions have become even tighter. “Now I don't know how to respond to enquiries about the data we used,” Bork says, adding that he is unsure whether he can share his data with other researchers.

Bork and other researchers say that Incyte is just filling a void caused by a lack of funding for public-sector databases. Annotation — the process of assigning functional and other information to the genes and proteins in databases — is a skill that needs to be paid for, Bork says. “If a company is prepared to fill in the niche, then the argument is only with the pricing policy,” he says.

Peter Okkema, a biologist at the University of Illinois at Chicago, agrees that the controversy over commercial databases “is a matter of price rather than principle”. When he learned in May that a subscription fee for Incyte's databases was imminent, he sent a letter signed by 160 scientists to Incyte's board of directors requesting reconsideration, but received no reply, he says. The silence, he adds, reveals a further problem with Incyte — its alleged lack of communication with the scientific community.

Chris Hogue, who runs BIND, a protein-interaction database based at the Samuel Lunenfeld Research Institute in Toronto, says that active input from researchers often isn't enough to keep a database going. Researchers “usually prefer someone else” to do the work needed to keep the database in shape. “My plea to researchers is to take database curation into your own hands,” he says. “Everyone has to pitch in if they are to be freely available.”

In the United States, scientists running model-organism databases in the public sector are lobbying for more support from the National Institutes of Health. Michael Cherry of Stanford University, who helps to run the Saccharomyces Genome Database there, says that more funds for its expansion would help to compensate those who cannot afford to access Incyte's yeast database.