Services: Data Resources

The List of Prokaryotic names with Standing in Nomenclature (LPSN) provides comprehensive information on the nomenclature of prokaryotes and much more.

The Mass Centric Peptide Database contains the tryptic in silico digest of all known proteins in UniProt KB, stored in an efficient manner to be quickly searched.

dSysMap (Mapping of Human disease-related mutations at the systemic level) displays Human disease-related mutations on the structural interactome. Mapping of mutations on protein structures and on interaction interfaces allows you to visualize the region of the interactome that they affect and helps in rationalizing their mechanism of action.

Freely accessible microbial genomics and metagenomics reference databases that include MarRef, MarDB, and MarCat. The MMP also includes a search engine that you can use to query all three databases at once.

MatrixDB is a database focused on molecular interactions of extracellular matrix proteins and glycosaminoglycans. The advanced query interface allows users to browse MatrixDB data, to build and to visualize specific interaction networks based on transcriptomic or quantitative proteomic data, diseases, biological processes or molecular functions. MatrixDB hosts the GAG builder tool to build on line 3D models of GAG sequences binding to proteins. 

The world's largest collection of cultivation media. The mission of MediaDive is to transform poorly structured media recipes into a standardized database.

A comprehensive collection of data from manually curated protein-protein interaction databases adhering to the IMEx consortium.

MESBL GC-MS metabolite peak database is a standardized library of more than 900 metabolite peaks from MS-reconstructed gas chromatograms integrating the in-house standard compound and peak library of the FORTH/ICE-HT Metabolic Engineering and Systems Biology Laboratory, appropriately filtered GOLM database peak information and Human Metabolome database information.

Open-source infrastructure service for research and engineering of metabolism in model organisms and human

MetaboLights is a database for metabolomics experiments and derived information. 

A public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories. 

Formerly called EBI Metagenomics, MGnify is an automated pipeline for the analysis and archiving of metagenomic data.

The MHC Motif Atlas helps visualize, analyse, and compare the different binding specificities of thousands of class I and class II MHC molecules, and includes binding motifs, peptide length distributions, motifs of phosphorylated ligands, multiple specificities, or links to X-ray crystallography structures.

MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts.

The Molecular INTeraction Database of protein-protein interactions curated from peer-reviewed papers. An ELIXIR Core Data Resources and founder member of the IMEx Consortium.

A manually curated database of animal small non-coding RNAs

MITOchondrial genome database of metaZOAns, a resource for comparative analyses of metazoan mitochondrial genomes at the sequence and genomic levels.

A database of protein disorder and mobility annotations, designed centralize resources for annotations of intrinsic protein disorder and its function. Part of the InterPro consortium, an ELIXIR Core Data Resource.

The archive for structural models which are not based on experimental data and complements the PDB archive for experimental structures and PDB- Dev for integrative structures. Any type of macromolecular structure which would otherwise be suitable for the PDB but whose coordinates are not based on experimental data can be deposited in ModelArchive. This includes single chains or complexes consisting of proteins, RNA, DNA, or carbohydrates including small molecules bound to them.

The NERC Environmental Omics Facility (NEOF) will enable environmental researchers in the UK to access the full range of omics supporting technology.

An innovative knowledge platform dedicated to human proteins. It contains a wealth of data on all the human proteins that are produced by the 20'000 protein- coding genes found in the human genome. 

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response. This resource supports COVID-19 / SARS-CoV-2 research.

Norine has been and remains the unique resource dedicated to nonribosomal peptides (NRPs). It contains a database complemented with analysis tools (structure comparison, inference of monomer structure from chemical structure, mass spectrum analysis, NRP annotation for submission to the database). NRPs are secondary metabolites produced by bacteria and fungi and display a diverse spectrum of biological activity.

The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping raw sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive world maps and ecological plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.

Curated database of oligogenic diseases and genetic variants causing these diseases. The successor of DIDA, a similar database for digenic diseases

OMA identifies orthologs among 2000 genomes from all domains of life. Other distinctive characteristics are the high quality of its inferences, the feature-rich web interface, and frequent update schedule of two releases per year. 

A database of causal protein-protein interactions, transcriptional and post-transcriptional regulation, enzyme-PTM interactions, protein complexes, annotations (function, disease roles, expression, localization, structure) and intercellular communication. Integrates data from more than 100 resources.

OpenEBench (https://openebench.bsc.es) is the ELIXIR benchmarking and technical monitoring platform for bioinformatics tools, web servers and workflows. 

Orphadata provides the scientific community with comprehensive, quality data sets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats.