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SWISS-PROT funding crisis - Recent developments

Geneva, June 6, 1996.

About a month has elapsed since we publicized on this server and by email, the financial danger in which SWISS-PROT and associated databases find themselves.

The problem arose from the failure of a proposal to the European Union from the University of Geneva and the European Bioinformatics Institute to gain core funding essential to the continuation of the project.

Up to now, no long term satisfactory solution has been found, but the international response to this situation - which was reported in Science, Nature, as well as other publications (see at the end of this message) - allows us to believe that a solution will be reached.

We first want to express our gratitude to the more than 1500 persons and institutions in 39 different countries who have sent us emails, faxes or letters of support. All of these messages have been extremely useful. They demonstrated to those who were not yet aware of it, that these databases are not simple repositories of sequences, but resources which are essential to the work of many laboratories both in the academic and private sectors. The level of support which you have expressed has been highly appreciated by the entire SWISS-PROT staff and has shown us that our efforts in providing quality annotations on protein sequences and families is recognized by the user community (this is far from obvious as many users view databases only through sequence similarity search tools that strip away such annotations).

Personally, I was very moved emotionally by your letters. The only way I can conceive repaying back all of your support is by hoping that we can continue to improve and extend the scope of the SWISS-PROT, PROSITE, ExPASy and associated databases and services.

Your messages also prove that you want the databases to remain in the public domain. Otherwise some of you, especially in countries with economic difficulties, would be completely cut off from the flow of data. Even a solution based on a non-profit institution would severely disrupt the collaboration and the integration of the many databases that are linked to SWISS- PROT or that include part or all of our data. It would also cause severe problems to software companies that redistribute the databases.

The first concrete development in this crisis has been the announcement on Friday May 24 by M. Guy-Olivier Segond, the President of the Conseil d'Etat of Geneva, of financial support for the SWISS-PROT activities at the University of Geneva until December 31, 1996. It is hoped that this six month period will make it possible to find a long term solution to this problem by, for example, creating a Swiss national bioinformatics infrastructure.

Also, in the meantime, the European Union has consulted with the EBI and we anticipate that a solution will be found which will keep their part of the project alive at least until another bid can be made for secure funds.

It must be noted that, while we believe that the trigger for the SWISS- PROT funding crisis was due to a lack of understanding, at the European level, of the consequence of the decision not to fund the recent proposal to enhance the SWISS-PROT activities, the origin of the problem is more profound. Switzerland is one of the few European countries that completely lack an institutional framework for the support of bioinformatics. The only funding agency at the Swiss federal level is the FNRS (Swiss National Science Foundation) whose mandate is to provide grants for a limited period for specific research projects. There is no framework to fund activities that are to be sustained for longer periods and that contain significant elements of services to the Swiss or international communities. Such a lack of infrastructure has already caused the closure, a few months ago, of the Swiss EMBNet node at the BioZentrum in Basel. Switzerland is currently the only member state of EMBL to lack a national biocomputing resource.

We hope that this situation will be rectified, and that a comprehensive solution of these problems will be reached in the coming days. The only viable solution is one based on long term funding of the University of Geneva's core SWISS-PROT activities at the Swiss level (this represents less than $500'000 per year) with additional funds from voluntary contributions from industrial firms that are important 'customers' of our databases (about 25% of US accesses to ExPASy are from commercial sites). In addition to the activities based in Switzerland, the crucial activities of our partners at EBI would, we hope, continue to be funded by the EMBL budget and EU grants. In this respect it must be noted that the European Commission has been very helpful in the last weeks in trying to find a solution for the future enhancement of the SWISS-PROT activities.

The first industrial contribution has been received last week from Millennium Pharmaceuticals which has made a contribution of $ 20'000.

Meanwhile, we thank you again for your support. We will keep you informed of the evolution of the situation.

On the behalf of the SWISS-PROT staff,

Amos Bairoch

PS1: The tribulations of SWISS-PROT were reported in a number of publications, including:

Nature 381:266(1996).
Science 272:946(1996).
The Chronicle of Higher Education, May 23 issue.

PS2: French-speaking users of SWISS-PROT and ExPASy can look at the Web version of the article just published by the news magazine L'Hebdo at: