Information Technology Reference
In-Depth Information
Swiss-Prot: juggling between evolution and
stability
Amos BAIROCH, Brigitte BOECKMANN, Serenella FERRO ROJAS, and Elisabeth
GASTEIGER
Swiss Institute of Bioinformatics, Centre Médical Universitaire, 1 Rue Michel Servet, 1211
Geneva 4, Switzerland
Abstract.
We describe some of the aspects of Swiss-Prot that make it unique,
explain what are the developments we believe to be necessary for the database to
continue to play its role as a focal point of protein knowledge, and provide advice
pertinent to the development of high quality knowledge resources on one aspect or
the other of the life sciences.
Introduction
The goal of this article is not to depict the history of Swiss-Prot [1], this has already been
done elsewhere [2], but rather to explore some of the consequences of decisions taken about
20 years ago, to discuss how the database has constantly evolved and to describe the
challenges that it currently faces. To say that the last twenty years have been exciting would
be a major understatement. Most young scientists that are now starting a career in the Life
Science fields are not aware of how much the combined technological revolutions that led
to high throughput sequencing and the WWW have quantitatively and qualitatively
changed the universe of knowledge on proteins. Yet, while we now have to cater in the
Swiss-Prot and TrEMBL sections of the UniProt knowledgebase [3] for more than 1
million protein sequences, there is a continuously widening chasm between truly
characterised proteins and those which have been solely predicted by genome-sequencing
projects. For us, in Swiss-Prot, the ultimate in terms of a well-characterised protein is one
for which not only the exact sequence, post-translational modifications, sub-cellular
location, tissue specificity, interaction partners and 3D structure are known, but more
crucially for which a functional role can be assigned.
What we hope to convey in this article are the particular aspects of Swiss-Prot that
make it unique, and hopefully derive some advice that would be pertinent to someone
embarking on the development of a high quality knowledge resource on one aspect or the
other of the life sciences. But before we do so, we want to enumerate six observations that
we believe are important to communicate to any would-be developers of such databases:
x Your task will be much more complex and far bigger that you ever thought it could be;
x If your database is successful and useful to the user community, then you will have to
dedicate all your efforts to develop it for a much longer period of time than you would
have thought possible;
x You will always wonder why life scientists abhor complying with nomenclature
guidelines or standardization efforts that would simplify your and their life;
x You will have to continually fight to obtain a minimal amount of funding;
