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.

MetaboLights is a database for metabolomics experiments and derived information. 

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

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.

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.

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. 

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.

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. 

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.

Orphanet is the reference resource for information and data on rare diseases and orphan drugs. Orphanet derives from its knowledge base an ontology of rare diseases, information on rare diseases and data on rare diseases.

OrthoDB is a comprehensive catalog of evolutionary and functional annotations of orthologs, covering over 22 million genes from over 5000 species of animals, fungi, plants, archaea, bacteria, and viruses. 

A service for the publishing, archiving and re-using data.

ParameciumDB is a community model organism database for the ciliate Paramecium. The web site gives access to genomes of many Paramecium species and their annotations. ParameciumDB also  integrates  genome-wide datasets (DNA-seq, RNA-seq, ChIP-seq) provided by the community. This portal is used to query, retrieve, visualize and compare the most up-to-date public data.

Pfam is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). 

A catalogue of experimentally-verified pathogenicity infecting animal, plant, fungal and insect hosts. 

Database focusing on crop plants hosting functional annotation data.

A comprehensive ontology for the plant domain, that is useful for data integration and querying heterogeneous data.

Providing a data and information resource for individual plant species

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.

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.