SIB experts and resources are taking part in the global effort to develop dedicated data services, analysis tools, training offer - and to improve knowledge sharing to fight the COVID-19 pandemic. Those resources are also accessible from Expasy, Swiss Bioinformatics Resource Portal.
Dedicated data services
- Cellosaurus - Frequently updated information page on the cell lines useful for the study of SARS-CoV-2, provided by: CALIPHO Group
- Corona OMA Browser - Website with all the functionality of the OMA Browser, but for 119 Nidovirales species, incl. the human SARS viruses, but also other coronaviruses and other single-stranded RNA viruses, provided by: Laboratory of Computational Evolutionary Biology
- COVID-19 Integrated Knowledgebase - SPARQL endpoint providing access to integrated data from various sources relevant for research on SARS-CoV-2, provided by: Swiss-Prot Group
- COVID literature dataset - Automatically annotated literature corpus related to COVID-19, provided by: BioMeXT Group
- COVID social media dataset - Twitter chatter dataset with automated classification, provided by: BioMeXT Group
- COVID repository of clinically-relevant literature - The main purpose of this resource is to simplify the access to COVID-19 literature for medical professional in the Spanish speaking world, provided by: BioMeXT Group
- CovidTriage - a search engine developed as part of SIBiLS to rank the COVID-19 literature (Medline, PMC, Cord-19) according to the 9 axis of the COVoc ontology, provided by: Text Mining Group
- COVoc - Controled vocabulary to support literature triage for COVID-19, provided by: Text Mining Group
- GlyConnect - Glycosylation information of COVID-19 spike protein produced from recombinant proteins (here and here | watch the course), provided by: Proteome Informatics Group
- HAMAP - Family profiles and annotation rules for the detection and annotation of betacoronaviruses, provided by: Swiss-Prot Group
- neXtProt - Information about human proteins that bind SARS-CoV-2 (here and here), provided by: CALIPHO Group
- PROSITE - Profiles and patterns for detection and annotation of SARS-CoV-2 proteins and homologs (JA Sigrist C et al. Antiviral Research 2020), provided by: Swiss-Prot Group
- SIBiLS/COVoc - Search and text mining services to support literature triage of coronavirus related contents, provided by: Text Mining Group
- SWISS-MODEL - Three-dimensional homology models and links to experimental structures in PDB for SARS-CoV-2 proteins (updated weekly - read more), provided by: Computational Structural Biology Group
- UniProtKB/Swiss-Prot - Knowledge of SARS-CoV-2 protein sequences and how they function in a special early release, provided by: Swiss-Prot Group
- ViralZone - Biological insights, including a detailed comparison with the SARS virus’ genome as well as cross-links to complementary resources (watch the course), provided by: Swiss-Prot Group
Dedicated analysis tools
- BEAST2: Use of EpiEstim to quantify epidemiological dynamics in real time based on viral genomes and confirmed case data, provided by: Computational Evolution Group
- Covid-19 Scenarios - Public health planning tool for COVID-19 outbreaks in communities across the world, provided by: Microbial Evolution Group
- covSPECTRUM - Interactive platform aiming to help scientists investigate and identify variants of SARS-CoV-2, provided by: Microbial Evolution Group
- ISMARA - Summary results of gene expression response to SARS-CoV-2 infection, provided by: Genome Systems Biology Group
- Nextstrain - Real-time tracking of the coronavirus genome evolution and regular reports, provided by: Microbial Evolution Group
- OGER web API - API for automated text annotation, including COVID-specific vocabulary, provided by: BioMeXT Group
- STRING - New COVID-19 oriented version enabling users to explore the host-side of the disease, while keeping a focus on putative COVID-19-interacting human proteins, provided by: Bioinformatics / Systems Biology Group
- SPSP Swiss Pathogen Surveillance Platform - Collaborative and secure platform centralizing all SARS-CoV-2 sequences in Switzerland and submitting them to ENA and GISAID (read more), provided by: Clinical Bioinformatics Group
- V-pipe - Detection of within-host genetic variation of SARS-CoV-2 from viral NGS data, provided by: Computational Biology Group
Data collection initiative
- Covid19Survey - Collecting national population data about COVID-19 related symptoms, provided by: Biomedical Informatics Group
And more...
- ABCD database - Sequences of antibodies binding to SARS-CoV-2 and host proteins, provided by: the Geneva Antibody Facility (UNIGE) with the support of the Swiss-Prot Group
- SwissDrugDesign - Large collection of web-based tools to support all aspects of computer-aided drug design (CADD) and which can be used to tackle COVID-19, provided by: Molecular Modeling Group
Find complementary information on ELIXIR's dedicated webpage