munich

The Swiss-Prot protein sequence databank, one of the world's most widely used reference sources on proteins, is introducing a system of licensing for private companies to ensure stable financing and help fund an expansion of its activities. Academic researchers will still be able to use the databank without charge.

Swiss-Prot is a joint enterprise between the newly created Swiss Institute of Bioinformatics and the European Bioinformatics Institute, the Cambridge-based outstation of the European Molecular Biology Laboratory (EMBL).

It is particularly valued by scientists because of the information added to simple translations of publicly available nucleotide sequences through the detailed annotation applied by the database's staff.

Until now, Swiss-Prot has been fully supported by public funding, and has provided a free service to both industry and academic researchers. But it hit a major funding crisis in 1996 when two major grants from the Swiss government were not renewed (see Nature 381, 266; 1996). It only managed to avert closure through a campaign for interim support, and is currently running on support from Swiss funding agencies.

Amos Bairoch, who founded Swiss-Prot in 1986, says it resisted buy-out offers from several commercial companies because he and his colleagues were concerned that commercial interests might be reluctant to continue maintaining open access to academic researchers.

Instead they are planning to develop a more stable funding strategy under which Swiss-Prot would receive half of its funding from public sources and half through licence fees from private companies.

Bairoch helped to set up the Swiss Institute of Bioinformatics from five Geneva-based bioinformatics research groups, including those already involved in Swiss-Prot. It is independent of the university system.

As such, it is entitled to receive direct funding from the government without depending on university grant money. The government has already indicated that it considers Swiss-Prot a funding priority.

Bairoch says he also encouraged the creation last November of an independent Geneva-based company, GeneBio, which, in addition to its core business of developing high-quality specialized protein databases, will handle the administration of Swiss-Prot's licensing scheme.

Fees will range from US$2,500 for small start-up companies to US$90,000 for large companies. Pharmaceutical companies are used to paying this level of fee for databases, says Bairoch.

Fotis Kafatos, director-general of EMBL, emphasizes that the decision to impose licence fees will have no repercussions for nucleotide databases at the European Bioinformatics Institute, which are repositories of raw data. He points out that Swiss-Prot licensees will be paying for the “very labour-intensive expert curation”.

The new funding system will allow Swiss-Prot to expand. At present the database includes 73,000 proteins, but an additional stockpile of 150,000 ‘virtual proteins’ — those whose sequence is deduced from nucleotide information, but have not been functionally analysed — are waiting in the wings to be worked on.

Swiss-Prot staff stress that academics will continue to be exempt from charges. ‘Grey’ academic research areas involving small university-based start-up companies or industrial collaborators will be negotiated on a case-by-case basis, says Bairoch, adding that Swiss-Prot does not wish to interfere with academic enterprise.