Services: Data 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.

A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. 

Transcription factor - target gene interaction and binding site database for multiple species

The European Nucleotide Archive (ENA) contains all the nucleotide sequences in the public domain and consolidates data from EMBL-Bank, the European Trace Archive and the Sequence Read Archive.

Database of membrane localization of transmembrane protein structures estimated by AlphaFold2

Based on ICGC PanCancer infrastructure for organising and processing NGS data using workflow plugins including:  

• Workflow Plug-Ins - provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).
• Cloud/HPC - IT Infrastructure for de.NBI users based on ICGC and TCGA PanCancer technology
• OTP - "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing.
• Roddy - a framework for large scale NGS processing pipelines on Petabyte scale for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

Database of experimentally determined topological data of transmembrane proteins

This catalogue lists available Translational Medicine datasets, coming from academic and industry research projects as well as from clinical cohorts and genome consortia. 

The Norwegian services for sensitive data, is a platform enabling collection, storage and analysis of sensitive research data in a secure environment.

Database of key transmembrane target proteins

Type (Strain) Genome Server allows you to identify or classify prokaryotic strains and provides genome-based phylogenies with branch support, (sub-)species delineation via digital DDH, differences in genomic G+C content and much more.

The glycomic MS database and repository.

Universal Catalog Database for biological findings

UniLectin is a platform integrating information regarding non-enzymatic carbohydrate-binding proteins usually referred to as lectins with the prospect of building and refining a structural and functional classification of these proteins. It includes the reference Lectin3D a database of 3D structures curated from the PDB. Interactive resource for the exploration of lectins

UniProt produces and maintains automatic and manually curated annotation of all publicly available protein sequences and serves these to users through various interfaces. 

Curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, with experimentally validated functional motifs and cross-links to interacting regulatory proteins.

Collection of validation results for the entire Protein Data Bank.