Networks in the Life Sciences – Genomics, Proteomics and Systems Biology
14th EMBL PhD Symposium

25th–27th October 2012

Speaker: Prof. Dr. Amos Bairoch

  • Swiss Institute of Bioinformatics
  • Professor of Proteomics and Bioinformatics, University of Geneva
  • Co-founder of GeneBio & GeneProt

Background

Amos Bairoch Founding member and principal investigator at the Swiss Institute of Bioinformatics Amos Bairoch’s Ph.D. culminated in the development of PC/Gene, PROSITE & SWISS-PROT. He is currently developing two further resources: neXtProt, a comprehensive & informative database of human proteins and ICECUP (International Collective Effort for the Characterization of hUman Proteins).

Talk: neXtProt: a human protein-centric knowledge platform

In September 2008, the UniProt/Swiss-Prot group achieved a major milestone: the first complete manual annotation of the full set of human proteins (derived from about 20,000 genes). This corpus of data rich in information pertinent to modern biomolecular medical research, clearly shows that there is a large gap in our knowledge of human proteins in terms of functional information as well as protein characterization (PTMs, protein/protein interactions, subcellular locations, etc). This gap resides not only in the available experimental information, but also in the way this information has been stored, which is far from being sufficient to help researchers making sense of what all these human proteins do in our bodies. Therefore, in the framework of CALIPHO, an interdisciplinary group created jointly by the University of Geneva and the SIB, we are developing neXtProt, a new human-centric protein knowledge resource, with the aim to help researchers answer pertinent questions. To achieve this goal we need to build up on a corpus of both curated knowledge – originating mainly from the UniProtKB/Swiss-Prot knowledgebase – and carefully selected and filtered high-throughput data pertinent to human proteins. This data gathering and grading effort is complemented by the development of tools that allow data to be analyzed.

neXtProt is a work in progress. Currently we are involved in supporting the efforts of HUPO Human Proteomics Project (HPP). In this context we are integrating into neXtProt data originating from proteomics experiments, including peptides and PTMs identification. This will allow our users to make the best use of the information that is available in a platform providing export options (PEFF, XML) as well as programmatic access (API).There is a very long road in front of us, and the challenge of integrating the mass of heterogeneous knowledge on human proteins is a distant goal. We hope you will enjoy working with neXtProt, and by providing feedback will help it evolve in response to your specific needs.