The SWISS-PROT Funding Crisis

Iddo Friedberg

About public databases and public money

What I'd like to talk about in this essay may seem like a byline to biocomputing - indeed to all science- but it is not. It is the question of money. Let me assure you that I am not asking you to reach for your pocketbooks (though I won't stop you either), and this will not be another gung-ho plead of an impoverished researcher for public money. I would just like to tell you a story regarding a certain enterprise which has to do with biocomputing, the funding crisis it went through, (hopefully the past tense is appropriate here), and the power of the Internet: both in the machinations of this enterprise, and in helping to alleviate the crisis.

The SWISS-PROT Database

One of the most important databanks and collection of utility programs related to biocomputing, and indeed to other fields of biological/medical interest, is the ExPASy World Wide Web (WWW) molecular biology server of the Geneva University Hospital and the University of Geneva, Switzerland. This server contains a database which is a household (labhold?) name among biochemists, molecular biologists, medical researchers, and, yes, biocomputists. The SWISS-PROT database contains sequences of just about every protein which has been discovered and sequenced. This is a LOT of information. Currently SWISS-PROT holds circa 52000 sequences, and it is growing. This project was founded 10 years ago and is currently being maintained and updated by a dedicated small team of 20 people. Well, twenty people might appear to be a lot for what seems like a simple data repository, but this service is more than that. Information about proteins may be expressed in different ways for different researchers. Indeed, a "dictionary" of sequence sites and patterns has been built alongside SWISS-PROT, known as Prosite. Certain recurring sequences of amino acids in different proteins are known to provide identical funcions: the bonding of a sugar molecule, or a code for reaching a certain part of the cell. A researcher who wishes to investigate a protein in that respect will go to the "dictionary", and see if a particular "word" ( a functional, recurring amino-acid sequence, better known as 'motif') appears in the protein she/he is looking at. One way of seperating proteins in the lab for isolation and analysis of a specific protein is a technique called 2D-PAGE. Information extracted from various 2D-PAGEs performed over the years may help the scientist doing 2D-PAGE in interpreting her/his own. Yes, you've guessed it, there is a SWISS-2D-PAGE database. If you would like to see what proteins look like, the SWISS-3D IMAGE database is for you, containing images of the structures of many proteins.

Here are a couple of pictures from SWISS-3D Image (click the small images to receive full-size pictures):

HIV reverse-transcriptase, an important viral protein involved in AIDS, and a target for many drug design efforts, such as AZT, DDI, and Nevirapine. Here is a close-up on the drug-binding areas.

Hemoglobin is a much researched protein, and the first to have its three-dimensional structured determined. Its function is to transport oxygen in the bloodstream. The reason blood is red is the oxygenated iron atom at the core of every hemoglobin molecule, marked here as a silver sphere.

In addition ExPASy has links to some 50 tools operable via the WWW or automated email servers. These tools are invaluable in assisting researchers in the analysis of various aspects of protein structure and sequence. The entire service is provided free of charge, in concordance with the philosophy that dissemination of scientific knowledge should be as unhindered as possible.

The SWISS-PROT Funding Crisis

At this point I suggest you read about the SWISS-PROT funding crisis, as described on their site by Amos Bairoch. In brief, the story is as follows: a decision was reached in Switzerland that due to the international nature of SWISS-Prot, it should not be funded by money reserved for Swiss national projects, but from funds intented for projects at an international level. A proposal was submitted and reviewed favorably by scientific experts of the EU, but was not accepted at a higher level. However, there was some sort of misunderstanding: the reviewers were under the impression that the money was needed for future development, while it was actually needed for current activities, as the usual Swiss funding was about to be cut. We, of the VSNS-BCD course have drafted our own letter of support. This letter presents several arguments as to why such a service should continue. From the letter:

"The SWISS-Prot database is updated by the work of scientists working in non-profit organizations (universities, research institutes, etc.) who also form the lion's share of the customers of this service. This, in addition to the fact that collaboration among researchers should be as uninhibited as possible, gives a strong argument to not charging fees from customers. Public money is used in supporting the PDB & NCBI, two services which are in constant use by biologists and available freely world-wide. There is no reason why public money should not support ExPASy, whose long-term use to the public, in terms of reaping the benefits from applied & basic research, far outstrip the maintainance costs."

The VSNS-BCD course is a course in biocomputing given over the Internet. More about the course can be found here. Also, please take a look at the course's home page.

The SWISS-PROT Funding Crisis - Resolved ?

Apparently, the publication of the crisis on the ExPASy WWW server drew an overwhelming response, and an interim solution, hopefully as a precursor to a more permanent one, has been reached. Furthermore, the crisis was reported in leading scientific publications such as Nature and Science.

I hope this short essay helped in understanding a bit of the "real life" problems a field of research might go through, and the importance of international collaboration among scientists: not only for research purposes, but also in lending a hand in the maintainance of global resources. Last, but not least, there is the power the Internet in facilitating such collaboration with ease and rapidity. I suggest you also read Peter Hjelmström's essay about ethical issues in biocomputing which discusses, among other things, ethical aspects of genetic databases.

I'd like to thank Georg Fuellen, Gustavo Glusman and David Croke for their help. The images are taken from the SWISS-3D database; their reproduction is subject to the following terms.

Iddo Friedberg
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