Subject: prosite and swiss-prot will disappear ????

From: [email-masked]
Date: 10 May 96 13:54:10 +0200

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Subject: Closure of SWISS-PROT
Date: 10 May 1996 11:51:19 +0100
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   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:

                             [email-masked]

   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:

               http://expasy.hcuge.ch/sprot/help-sprot.html

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