Swiss-Prot (fwd)

Ian J. Tickle (
Wed, 22 May 1996 11:49:50 +0100 (BST)

May be of interest to our viewers....

Forwarded message:
> From Tue May 21 20:37:28 1996
> Precedence: first-class
> Date: Sat, 20 Apr 1996 15:42:21 -0400
> From: Joshua Sakon <>
> Message-Id: <>
> To:
> __________________________________________________________________________________
> 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]
> 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 !
> 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:
> Do not forget to include in such an email, your full name, title and
> organization to which you belong.
> 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
> PS1: Feel free to forward this message to colleagues.
> PS2: Apologies to all those of you who have (will) receive multiple
> copies of this message.
> PS3: This text is also available on WWW at:

-- Ian

Ian J. Tickle
Department of Crystallography | Phone: (+44) 171 631 6854
Birkbeck College (University of London) | Fax: (+44) 171 631 6803
Malet Street, LONDON WC1E 7HX, UK | e-mail: