Important announcement concerning SWISS-PROT

Amos Bairoch 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
(see http://www.isb-sib.ch/).

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,
2000 onward.

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

Amos Bairoch
Director of the SWISS-PROT group at the Swiss Institute of


           Important announcement concerning SWISS-PROT

                            A) Summary


   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.

   Raising revenue

   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
   information resources

   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-
     by-case basis.

   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
     macromolecular structures.

For a much more detailed description, please go to

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