Important announcement concerning SWISS-PROT
bairoch at cmu.unige.ch
Thu Jul 16 23:01:05 EST 1998
In the summer of 1996, more than 2000 SWISS-PROT users responded to
our call for help by sending a message of support and/or signing
petitions concerning the funding problem that was threatening the
existence of SWISS-PROT, PROSITE and other databases as well as the
ExPASy WWW server. This acute funding problem was, in retrospect, due
to a misunderstanding between European Union and Swiss scientific
funding agencies and to the lack of an infrastructure for
bioinformatics activities in Switzerland (as it is also the case in
many other countries).
The collective response of the SWISS-PROT user community was of
tremendous help to put on the agenda, both in Switzerland and
elsewhere, the problem of long-term support for biomolecular
The state of Geneva reacted promptly by providing the necessary
financial resources for the second semester of 1996. For the years
1997 to 1999, interim funding for SWISS-PROT was provided by the Swiss
National Science Foundation (SNSF), the Federal Office for Education
and Science (FOES) as well as other institutional scientific partners.
During this three-year period discussions would take place so as to
find a longer-term and more stable funding solution. Such a solution
would also be synchronized with the next Swiss scientific budget
four-year cycle, covering the period 2000 to 2003.
As a results of these discussions, the SNSF and the FOES proposed the
creation of an institute for bioinformatics which would seek to obtain
directly from the Swiss federal government funding for part of its
activities and in particular for the database support and management
tasks. Following this proposition we established the legal and
organizational groundwork which lead to the creation in March 1998 of
the Swiss Institute of Bioinformatics (SIB), a non-profit foundation
SIB is tightly associated to the University of Geneva, the University
of Lausanne, the Geneva University Hospital, the Swiss Institute for
Cancer Research (ISREC) and the Ludwig Institute and will also operate
in association with industrial partners. The activities of the
Institute are organized around several research and service areas,
each of which is headed by a group leader. One of the five groups at
SIB is the SWISS-PROT group, headed by myself.
The creation of SIB should allow the Swiss scientific funding agencies
to provide a stable base of funding for SWISS-PROT from January 1,
In parallel with these positive developments, it became more and more
obvious that the tremendous increase in data flow has created a
requirement for resources which cannot be addressed in full by public
funding. This is causing databases to fall behind the research. We
believe that the only solution to the resource shortfall is to ask
commercial users to participate by paying a license fee. No fee will
be charged to academic users, nor will any restriction be imposed on
their use or reuse of the data. The databases available on ExPASy that
are currently concerned by these changes are: SWISS-PROT, PROSITE and
SWISS-2DPAGE. SWISS-MODEL Repository might be affected at a later
stage. ENZYME, SeqAnalRef and CD40Lbase are not concerned by these
changes nor are there any plans to change their status.
You will find attached to this message a document fully describing
what will be the impact of this change for SWISS-PROT. You can also
access the document as well as other relevant ones from:
If you do not have the time to read this document, the most important
take- home message is that these changes should not have any impact on
the way SWISS-PROT is accessed or redistributed. Academic users will
not be affected by these changes. Industrial end-users will also not
directly be affected as long as their employer pays the license fee.
The same holds true for bioinformatics companies. Academic software or
database developers as well as providers of database distribution
services will be only minimally affected by these changes. We hope to
be able to keep the spirit of SWISS-PROT alive and at the same time
ensure its long-term financial survival. We sincerely hope and believe
that in the next two years the only change that will matter will be
the increase in scope and timeliness of the database.
I also want to use this opportunity to extend my personal thanks as
well as those of the SWISS-PROT staff in Geneva and at EBI for your
Director of the SWISS-PROT group at the Swiss Institute of
Important announcement concerning SWISS-PROT
o SWISS-PROT was created by Amos Bairoch in 1986 at the
Department of Medical Biochemistry of the University of
Geneva and has been a collaborative effort of the
Department and the European Molecular Biology Laboratory
(EMBL) since 1987. SWISS-PROT is now an equal partnership
between the EMBL and the Swiss Institute of Bioinformatics
(SIB), to which Bairochs team is also affiliated, with
Bairoch retaining ultimate responsibility for the
scientific content and format of SWISS-PROT. The EMBL
activities are carried out by its Hinxton Outstation, the
European Bioinformatics Institute (EBI).
o SWISS-PROT is a curated, added-value database, not a
repository of primary information.
o SWISS-PROT's curation team adds detailed annotation and
organization to protein sequences, the overwhelming
majority of which come from translations from the public
nucleotide sequence databases. The value of SWISS-PROT to
the academic and commercial research community is widely
accepted. It is the gold standard for scientific databases
and must be rendered secure.
o The SWISS-PROT team draws heavily on the support of
experts throughout the world, and the contribution of
those experts is appreciated and will always be
o Increased data flow has created a requirement for
resources which cannot be addressed in full by public
funding. This has caused the database to fall behind the
research. While increased automation and the creation of
TrEMBL, a computer-annotated supplement to SWISS-PROT,
have gone some way to solving the problem, there is still
a substantial resource shortfall.
o We believe that the only solution to the resource
shortfall is to ask commercial users to pay a license fee.
o No license fee will be charged to academic users, nor will
any restrictions be imposed on their use or reuse of the
o The funds raised will be used at SIB and the EBI to bring
SWISS-PROT up to date, to keep it up to date, and to
further enhance its quality.
o Future releases of SWISS-PROT will be copyright (releases
up to and including number 36 will not be).
Access to SWISS-PROT
o Nothing will change in the methods by which academic or
commercial users can access SWISS-PROT, but commercial
users will be informed that their company is liable to pay
a license fee irrespective of the method by which they
access the database.
o Third party organizations providing services which make
use of SWISS-PROT need not change those services at all,
but will be asked to provide lists of commercial users of
their services. Companies using these "secondary services"
will be approached for license fees.
Incorporation of SWISS-PROT data into other databases and
o Where an information resource makes use of some SWISS-PROT
information, adds value and is not a possible substitute
for SWISS-PROT, a license fee will not normally be
required, but such instances will be discussed on a case-
For some commercial uses no license fee will be required
o Use of SWISS-PROT for educational and training purposes
(where this is the sole reason for the use of the
o Inclusion of the SWISS-PROT database in similarity
searches that report SWISS-PROT hits but do not download
o Reference to, or printing of SWISS-PROT entries (within
reason) in publications.
Service providers must:
o Distribute only up-to-date data.
o Distribute the data in one of a few recognized formats.
o Not "degrade" the database, for example by removing
o Under no circumstances remove the copyright notice.
o Make all reasonable effort to provide logs of commercial
We are willing to discuss exceptions
o In the gray area between academic and commercial usage.
o If needs arise for new distribution structures and formats
which do not degrade the database.
Why the funding model of SWISS-PROT is not applicable to
nucleotide sequence databases
o EMBL/EBI and SIB consider that the funding model that has
to be adopted to secure the viability of SWISS-PROT is not
applicable to nucleotide sequence databases, even though
these are also curated. Nucleotide sequences, from which
SWISS-PROT entries are derived, must remain in the public
domain in recognition of the fact that they are the
primary data, and have been submitted to public-domain
collections by individual scientists. This same
consideration holds for primary databases of
For a much more detailed description, please go to
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