A stringent selection process

SIB's External Scientific Advisory Board (SAB) is in charge of providing recommendations on the selection of SIB’s core resources every four years. Assessing competitive criteria, including the scientific impact and return-on-investment, along with SIB’s global portfolio management and strategic orientation, SAB members select best-in-class resources and provide guidelines for their continuous development. Once validated by the Board of Directors, the SIB Management team then assists the groups managing the SIB core resources in implementing their action plan and exchanging best practices.

 

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Click on the resource name to find out more about the resource and to access the corresponding webpage.

 

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UniProtKB/Swiss-Prot

Protein knowledgebase

Alan Bridge group

  • Type: Knowledgebase with manual expert curation
  • Description: Hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants.
  • Highlight: UniProtKB/Swiss-Prot is the expert curated part of UniProt, the most widely used protein information resource in the world, with over six million page views per month. Selected as an ELIXIR Core Data Resource.
 

 

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STRING

Protein-protein interactions

Christian von Mering group, contact person: Damian Szklarczyk

  • Type: Knowledgebase
  • Description: Resource for known and predicted protein-protein interactions, including direct (physical) and indirect (functional) associations derived from various sources, such as genomic context, high-throughput experiments, (conserved) co-expression and the literature.
  • Highlight: Currently includes 9,643,763 proteins from 2,031 organisms and is the most used resource of its kind. Selected as an ELIXIR Core Data Resource.

 

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neXtProt

Human protein knowledgebase

Amos Bairoch & Lydie Lane group

  • Type: Knowledgebase with manual expert curation
  • Description: Information on human protein biology such as function, involvement in diseases, mRNA/protein expression, protein/protein interactions, post-translational modifications, protein variations and their phenotypic effects.
  • Highlight: Advanced search options combining data at genomic, transcriptomic, proteomic and phenotypic levels.
 

 

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SWISS-MODEL

Protein structure homology-modelling

Torsten Schwede group, contact persons: This email address is being protected from spambots. You need JavaScript enabled to view it.

  • Type: Software tool and repository
  • Description: Automated protein structure homology-modelling platform for generating 3D models of a protein using a comparative approach, and database of annotated models for key reference proteomes based on UniProtKB.
  • Highlight: Easy-to-use web-based platform processing over one million model requests per year and also providing model information for non-specialists.

 

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Glycomics@ExPASy

Glyco(proteo)mics resource portal

Frédérique Lisacek group

  • Type: Web tools and knowledgebases with manual expert curation
  • Description: Extensive set of resources on sugar structures (UniCarb-DB), their relationships with the proteins that carry them (GlyConnect) and the proteins that bind them, with a special focus on interactions between pathogen proteins and mammalian glycans (SugarBind).
  • Highlight: Unique portal for glyco(proteo)mics data analysis and interpretation.
 

 

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SwissDrugDesign

Drug design

Olivier Michielin & Vincent Zoete group

  • Type: Software tools
  • Description: Web-based computer-aided drug design tools, from molecular docking (SwissDock) to pharmacokinetics and druglikeness (SwissADME), through virtual screening (SwissSimilarity) and target prediction of small molecules (SwissTargetPrediction).
  • Highlight: Comprehensive and integrated web-based drug design environment.
 

 

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SwissLipids

A knowledge resource for lipids

Alan Bridge group

  • Type: Knowledgebase  
  • Description: Information about known lipids, including knowledge of lipid structures, metabolism, interactions, and subcellular and tissular localization, providing a framework for the integration of lipid and lipidomic data with biological knowledge and models.  
  • Highlight: Contains information on over 400,000 lipid structures from over 180 major lipid classes.
 

 

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Bgee

Gene expression evolution

Marc Robinson-Rechavi group, contact person: This email address is being protected from spambots. You need JavaScript enabled to view it.

  • Type: Knowledgebase with manual expert curation
  • Description: Information on gene expression evolution (incl. all types of transcriptomes), allowing retrieval and comparison of expression patterns between animals including human, model organisms and diverse species of evolutionary or agronomical relevance.
  • Highlight: Only resource to provide homologous gene expression between species.

 

 

Swiss Regulon

SwissRegulon Portal

Tools and data for regulatory genomics

Erik van Nimwegen group

  • Type: Software tools and knowledgebases
  • Description: Web portal for regulatory genomics, including genome-wide annotations of regulatory sites and motifs, the webserver ISMARA for automated inference of regulatory networks and CRUNCH for automated analysis of ChIP-seq data.
  • Highlight: User can upload raw micro-array, RNA-seq or ChIP-seq data to automatically infer the core regulatory networks acting in the system of interest.
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EPD

Eukaryotic Promoter Database

Philipp Bucher group, contact person: Giovanna Ambrosini

  • Type: Knowledgebase with manual expert curation and software tools
  • Description: Quality-controlled information on experimentally defined promoters of higher organisms, as well as web-based tools for promoter analysis.
 

 

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V-Pipe

Viral genomics pipeline

Niko Beerenwinkel group

  • Type: Software tool
  • Description: Pipeline integrating existing and in-house pieces of software, designed for the clinical application of next-generation sequencing to viral pathogens.
  • Highlight: Enabling reliable and comparable viral genomics and epidemiological studies and facilitating clinical diagnostics of viruses.

 

Swiss Orthology

 

 

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OrthoDB

The hierarchical catalogue of orthologs

Evgeny Zdobnov group, contact person: Evgenia Kriventseva

  • Type: Automated phylogenomic database and software tool
  • Description: Comprehensive online catalogue of orthologs, including functional and evolutionary gene annotations and enabling the inference of putative gene functions.
  • Highlight: Largest orthology resource, enabling users to generate publication-quality comparative genomics charts, and to upload, analyse and interactively explore their own pre-publication data.
 

 

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OMA

Orthology MAtrix browser

Christophe Dessimoz group, contact person: Adrian Altenhoff

  • Type: Automated phylogenomic database and software tool
  • Description: High-quality orthology predictions among complete genomes.
  • Highlight: Broad scope and size, feature-rich web interface, availability in a wide range of formats and interfaces, frequent update schedule.