SWISS-PROT should have been 10 years old in July 1996, but it may disappear on June 30, 1996

Due to funding problems, SWISS-PROT as well as PROSITE, and the ENZYME nomenclature databases will disappear on June 30, 1996 if no solution is found before that date. The ExPASy WWW server and all services associated with it will also shut down. The distribution of the SWISS- 2DPAGE database will also be discontinued. Other external databases, WWW services and software packages that depend on SWISS-PROT, PROSITE and ENZYME as well as on the links provided between biomolecular databases will also be severely affected by this problem. Users of services and databases such as ENTREZ, BLOCKS, SRS, Owl, etc. should also be aware that most annotations at the protein level available through these services originate from SWISS-PROT or PROSITE.

While the databases listed above as well as the ExPASy server are used in almost every laboratory doing molecular biology in the world, the funding for these projects has always been very modest (to say the least) and is now, due to procedural problems, going to disappear.

If you are not interested in the details of these problems and you want to send us a email or letter (fax) of support explaining why you think that these resources should stay available to the biological user community, you can skip the following section and jump to the end of this message

Summary of the current situation and what should have happened

Currently SWISS-PROT is developed as a collaboration between two sites:

The Medical Biochemistry Department of the University of Geneva, where in addition to the principal investigator of the project (Amos Bairoch), five annotators and a programmer are working on SWISS-PROT and related projects. Three of the five annotators are paid by a Swiss National Fund (FNRS) grant that ends on June 30. One additional annotator position, which is paid for by a special EMBL grant which also ends at the same time. The last position is on a Glaxo academic grant which will end in December.
The EMBL outstation, the European Bioinformatics Institute (EBI) in Hinxton, where six persons are working on SWISS-PROT: a coordinator (Rolf Apweiler), four annotators and a programmer. The EBI has recently embarked on major work to complement SWISS-PROT with a computer annotated supplement called TrEMBL which together with SWISS-PROT produces the first really non-redundant annotated protein sequence database. The completion of this work will require expanded resources at the EBI.

About two years ago, a decision was reached in Switzerland that due to the international nature of the SWISS-PROT database, it ought not be funded by money reserved for national projects, but rather from funds intended for projects at the European or International level and to which Switzerland participates. Therefore we were asked to write a grant proposal at the European level. As such a proposal requires participants from at least two or more EU states (which Switzerland is not), an application was submitted in December 1995 which requests:

Five positions in Geneva for the annotators whose contracts will otherwise end in June 1996.
Four positions at EBI, to allow the development of TrEMBL and to cope with the increasing flow of data from genomic projects.
One position in Ireland, with Prof. Keith Tipton, to maintain and update the enzyme nomenclature (EC number) of the International Union of Biology and Molecular Biology (IUBMB). This nomenclature is the backbone of the ENZYME database.
One position at the Weizmann Institute in Israel and a partial position at the company Compugen to develop, in collaboration, the Bioccelerator sequence search hardware engine in ways that will help the maintenance of TrEMBL.
One position at INRIA in France, to develop software in collaboration with Compugen.

We have been advised that this proposal was evaluated favorably by the scientific experts of the EU (equivalent of an US Study Section), but was not accepted at a higher level. The main (and apparently only) reason seems to be that those judging the proposal were under the impression that it requested funds solely for new developments. They were unaware that the current activities could not be maintained without this funding. They also seem to have failed to take note of the fact that the money for the Swiss operation was not coming out of the EU budget, but directly from Swiss government funds, provided that the EU approved the project.

They therefore rejected this project while accepting other projects which themselves depend on the existence of SWISS-PROT (for example, a project in which Geneva is also involved, to establish a G-protein linked receptor database which will extend SWISS-PROT to provide information specific to this field of research).

Having learned the extent of the problem, the EU seems genuinely concerned but does not seem to have the means of reversing such a decision. They are asking us to resubmit the proposal. But such a process will take almost a year and we only have two months left of salaries.... In Switzerland, money for SWISS-PROT is available, but can not be assigned to such a purpose before the EU accepts the grant. So we are in a catch 22 situation where everyone agrees that there is a problem, that it should be solved, but that they are unable to do anything for procedural reasons !

What can we and you do ?

In the absence of public funding two scenarios seem possible. SWISS-PROT and PROSITE could pass into private hands as proprietary databases, or some non-profit association could be established which would recoup the entire costs of the operation through subscriptions. Two pharmaceutical companies have already expressed interest in the former solution, and existing examples of the latter are CAS (Chemical abstracts) and CCDC (Cambridge Crystallographic Data Centre). However we see enormous benefits to the user community from the public availability of the data. The first of these solutions would be incompatible with the mission of our partners at the EBI, but if it comes between a complete disappearance and such a solution, there does not seem to be a choice.

At the time when there is growing concern about the privatisation of genomic data, we are facing a situation that could lead to the disappearance of what we think are the most widely used information resources on protein sequences because of our reliance on soft public money.

We would much prefer to continue to offer and extend services to all the biological user community free of charge. To do so we need your help to convince the various funding agencies that you need these services for your research.

We are therefore asking our user community to send emails of support stating why you think that these resources should continue to be available. You can send these messages to:

help.sprot@hon.ch

If you wish to write a letter of support, you can fax it to the following number:

+ 41-22-346 87 58

Or send it by post to:


      Amos Bairoch

      Dept. Medical Biochemistry

      1, rue Michel Servet

      1211 Geneva 4

      Switzerland

Many thanks to all of you.

Amos Bairoch

PS: Feel free to forward this message to colleagues.

Click here to read about recent (mainly positive) developments.