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
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
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
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
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
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:
If you wish to write a letter of support, you can fax it to the
+ 41-22-346 87 58
Or send it by post to:
Dept. Medical Biochemistry
1, rue Michel Servet
1211 Geneva 4
Many thanks to all of you.
PS: Feel free to forward this message to colleagues.
Click here to read about recent (mainly positive) developments.