Services: data resources

The Protein Model Database stores manually built 3D models of proteins.

PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation.

PomBase also provides a community hub for researchers, providing genome statistics, a community curation interface, news, events, documentation and mailing lists.

A prediction system for GPI-anchored proteins.

PRIDE (The Proteomics Identifications Database) is a standards-compliant, public repository for proteomics data. It contains protein and peptide identifications and their associated supporting evidence.

PROSITE consists of entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. PROSITE is a key element of the UniProt annotation pipeline “UniRule”. 

The Protein Data Bank in Europe (PDBe) is the European part of the wwPDB for the collection, organisation and dissemination of data on biological macromolecular structures.

An open-source, curated and peer reviewed pathway database. Its goal is to provide tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling and systems biology.

A database annotating organellar RNA editing processes in their biological context.

A database of RNA editing events in humans from RNA-Seq and DNA-Seq data.

A database of annotated tandem repeat protein structures, combining computer-based methods and manual curation.

REXdb: a reference database of transposable element protein domains

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs).

Rhea is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. 

Web interface accessing a curated database with information about biochemical reactions and kinetic properties in an experimental or environmental context.

A comprehensive data resource for salmonids species based on different omics data

A database with high-quality curated and freely accessible SARS-CoV-2 genomics- and contextual resources.

The Swiss Institute of Bioinformatics Literature Services (SIBiLS) provide personalized Information Retrieval in the biological literature. Indeed, SIBiLS allow fully customizable search in semantically enriched contents, based on keywords and/or mapped biomedical entities from a growing set of standardized and legacy vocabularies.  (https://pubmed.ncbi.nlm.nih.gov/32379317/)

SIDER is a web-based resource that contains information on marketed medicines and their recorded adverse drug reactions. This information is extracted from public documents and package inserts. SIDER makes available side effect frequency, drug and side effect classifications as well as links to further information, for example drug–target relations. It currently covers associations between 5,868 side effects and 1,430 drugs. Part of the Human Omics Analysis Toolbox. 

The SIGnaling Network Open Resource annotates signaling information from the literature as binary causative relationships.

SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

Prediction of single point protein mutations likely to be involved in disease.

A database of RNA-binding splicing regulatory proteins reporting functional domains, protein and chemical interactors and expression data.

A validated reference peptide database for targeted proteomics. (Formerly QSDB)

STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. 

SugarBind covers knowledge of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals.

SulfAtlas is a knowledge-based database which (i) helps to better annotate sulfatases in (meta)genomic data and notably to improve the prediction of substrate specificities; (ii) guides the experimental biologists to select target sulfatases which remain to be characterized in term of function and structure. The data contained in SulfAtlas is curated by experts, based on our phylogeny-based classification system and on literature.

Database of protein expression time series for specific experiments on streptomyces, caulobacter, neiseria.

SWISS-MODEL Repository is a continuously updated database of annotated protein structure homology models generated by the fully automated SWISS-MODEL modelling pipeline. 

SwissBioPics is a freely available library of interactive biological images for visualizing subcellular location data. It includes cell types from all kingdoms of life - from muscle, neuronal and epithelial cells of animals to rods, cocci, clubs, spirals, and other more exotic forms of bacteria and archaea.

A knowledge resource for lipids and their biology.