What are the biggest challenges facing Swiss-Prot today?
Aside from the obvious scientific challenges (ensuring that our resources continue to keep pace with emerging trends in biological research), one of the main challenges we face is one that will be familiar to many developers of knowledge resources, data repositories, and bioinformatics infrastructures: to ensure stable long term funding for our resources.
Resources such as UniProtKB/Swiss-Prot are used by thousands of researchers worldwide every day, but are supported by only a few countries - Switzerland (SERI), the US (NIH), and a number of European countries and partners (EMBL) being the main funders in this case.
This is neither equitable nor sustainable, and a better, fairer system is needed, one where an international coalition of funders supports core data resources according to objective criteria (such as their usage, research budget or Gross Domestic Product).
One of the goals of initiatives such as ELIXIR and the International Coalition to Sustain Core Data Resources – to which SIB is actively committed – is to create such a system. While this work is moving in the right direction, it will probably require years before any type of agreement is reached between the international funding agencies involved.
In the meantime, we are currently waiting on the results of our latest NIH application...
The SIB Swiss Institute of Bioinformatics was created in 1998 to ensure the financial sustainability of Swiss-Prot. What do you expect SIB’s role will be in the coming years in the field of bioinformatics resources?
SIB was a very early pioneer in the development of bioinformatics infrastructures and resources – like the Swiss-Prot database – and in developing mechanisms to fund them.
Initiatives like ELIXIR are attempting to reproduce this success at an international level, and we expect that SIB will continue to be an active advocate for Swiss bioinformatics inside ELIXIR, helping to foster recognition and to create a more sustainable funding landscape for the future.
On a scientific level the SIB provides a fantastic environment for collaboration between developers of world-class bioinformatics resources – such as neXtProt, STRING and STITCH, SWISS-MODEL, SwissDrugDesign, and others – and we will continue to explore synergies and common ground with these resources.
As one example, we will begin to annotate enzymatic reaction data in UniProtKB from 2018 using the Rhea resource of biochemical reactions, which provides an explicit representation of chemical structures. This will further enhance the semantic search capacities of neXtProt, protein-metabolite networks in resources like STRING/STITCH, drug metabolism data for SwissDrugDesign, enzyme annotation for glycobiology and glycomics resources, and so on.
Could you tell us about a concrete example where the biocuration expertise from Swiss-Prot was used in a project and led to major scientific advances?
We showcased one example at a recent ELIXIR meeting in Brussels, where UniProtKB/Swiss-Prot was used in the discovery of a new form of cellulase.
Cellulase is an enzyme crucial for the production of biofuels from cellulose - an abundant source of renewable biomass – and is considered an industrial blockbuster with a potential market value of billions of Swiss francs worldwide. By using UniProtKB/Swiss-Prot for only a few minutes, a consortium of European researchers were able to identify a new thermostable cellulase suitable for industrial applications by screening metagenomic data from hot springs.
This example highlights not only the value of UniProtKB/Swiss-Prot, but also some of the difficulties we can encounter when trying to quantify the impact of such resources from simple usage figures. There is clearly a pressing need to develop more accurate and complete indicators of economic and scientific benefit, and to meet this need SIB has commissioned a study on economic impact and resource indicators. We eagerly await the results in 2018.