The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Abstract

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article.

Genomic data integration systematically biases interactome mapping

“…RNA expression data from healthy human and mouse tissues was obtained from the Bgee database [ 37 ], and coexpression was calculated from normalized (FPKM) expression values using the Pearson correlation coefficient. Phylogenetic profiles were constructed by mapping human or mouse proteins to 272 other species using InParanoid [ 38 ], and calculating the Pearson correlation coefficient between binarized presence/absence values [ 39 ].…”

Computational Studies of Snake Venom Toxins

“…General databases, such as UniProt [ 17 , 18 ], NCBI Genbank/GenPept [ 19 ], and the Protein Data Bank (PDB) [ 20 , 21 ], play essential roles in simplifying access to information regarding protein sequences and three-dimensional structures [ 22 ]. However, the information about peptides and proteins from snake toxins is not standardized in these resources, especially the naming of toxins and pharmacological activities, and mining for snake venom peptides is difficult.…”

Best Practice Data Life Cycle Approaches for the Life Sciences

“…In the field of molecular biology, a number of bioinformatics-relevant organisations host public data repositories. National and international-level organisations of this kind include the European Bioinformatics Institute (EMBL-EBI) [31], the National Centre for Biotechnology Information (NCBI) [32], the DNA Data Bank of Japan (DDBJ) [33], the Swiss Institute of Bioinformatics (SIB) [34], and the four data center members of the worldwide Protein Data Bank [35], which mirror their shared data with regular, frequent updates. This shared central infrastructure is hugely valuable to research and development.…”