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Ioannis Xenarios & Lydie Bougueleret
Swiss-Prot Group
University of Geneva
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What do we do?

At the Swiss-Prot Group we develop, annotate and maintain the UniProtKB/Swiss-Prot protein sequence database, the most widely used protein information resource in the world. We also develop and maintain other databases including PROSITE, a database of protein families and domains, ENZYME, a database of enzyme nomenclature, HAMAP , a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules, Rhea, a curated database of chemical reactions and SwissLipids, an expert-curated resource that integrates lipidomics data with biological knowledge. We also offer to the virologists community the ViralZone portal. The group also co-heads the development and maintenance of the ExPASy proteomics website. We are one of the largest groups in the Swiss Institute of Bioinformatics.

Highlights 2016

Our group continues to produce and maintain the Swiss-Prot section of the UniProt knowledgebase, adding expert-curated knowledge from over 7000 new publications describing over 3300 new proteins and functions. Expert curation is essential to the development of Swiss-Prot, and remains the surest means of providing life science researchers with rapid access to comprehensive knowledge on protein function. In 2016 we performed a detailed and wide ranging investigation of published and curated literature in Swiss-Prot. This investigation revealed that the expert curation of UniProtKB/Swiss-Prot provides high coverage of available knowledge and that this activity is both scalable and sustainable.
While the majority of our efforts are directed at UniProtKB/Swiss-Prot, our group continues to develop a range of complementary and specialized knowledge resources for life scientists. These include the Rhea knowledgebase of expert curated biochemical reactions which has applications in enzyme annotation (Rhea will be used in UniProt from 2017 onwards) and the description of genome scale metabolic networks (Rhea is a reference resource for MetaNetX at Vital-IT). We introduced a new reaction classification  which complements and extends the widely-used enzyme classification of the IUBMB. Rhea currently describes over 9500 unique reactions curated from a similar number of publications.Our ViralZone team worked with collaborators from the University of KwaZulu-Natal to develop an improved resource for the life scientists working on HIV-1, the BioAfrica HIV-1 Proteome Resource. We collaborated with a number of SIB groups and other world renowned institutes on the development of standardized benchmarks for the phylogenetic inference, a cornerstone for both  evolutionary studies and functional annotation efforts.
Our group continues our SIB outreach and educational activities. The web-team plays an active and extensive role in the development of the SIB bioinformatics resource portal ExPASy.

Main publications 2016

  • Altenhoff AM, Boeckmann B et al. Standardized benchmarking in the Quest for orthologs. Nature Methods 2016; 13, 425-430.
  • Breuza L et al. The UniProtKB guide to the human proteome. Database (Oxford) 2016; pii:bav120.
  • Druce m et al. Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. Database (Oxford) 2016; pii:baw045.
  • Morgat A et al. Updates in Rhea - an expert curated resource of biochemical reactions. Nucleic Acids Res (Database issue) 2016; pii:gkw990.
  • Poux S et al. On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study. bioRxiv 2016; 094011

Our research topics: