Important announcement concerning SWISS-PROT
A) Summary
Background
- 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 Bairoch's 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).
- SWISS-PROT is a curated, added-value database, not a repository of primary information.
- 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.
- 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 acknowledged.
- 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
- We believe that the only solution to the resource shortfall is to ask commercial users to pay a license fee.
- No license fee will be charged to academic users, nor will any restrictions be imposed on their use or reuse of the data.
- 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.
- Future releases of SWISS-PROT will be copyright (releases up to and including number 36 will not be).
Access to SWISS-PROT
- 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.
- 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
- 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
- Use of SWISS-PROT for educational and training purposes (where this is the sole reason for the use of the service).
- Inclusion of the SWISS-PROT database in similarity searches that report SWISS-PROT hits but do not download entries.
- Reference to, or printing of SWISS-PROT entries (within reason) in publications.
Service providers must:
- Distribute only up-to-date data.
- Distribute the data in one of a few recognized formats.
- Not "degrade" the database, for example by removing information.
- Under no circumstances remove the copyright notice.
- Make all reasonable effort to provide logs of commercial usage.
We are willing to discuss exceptions
- In the gray area between academic and commercial usage.
- 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
- 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.
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