Databases and tools

EMBL-EBI offers a comprehensive range of freely available, up-to-date molecular databases. You can work locally by downloading our data and software, or use our web services to access our resources programmatically. You can read more about our services in the journal Nucleic Acids Research.

Our services are made possible by scientists all over the world sharing their data. This increases the impact of individual research projects, and allows science to progress more rapidly. To submit your data to the public archives, visit our Data Submission Wizard.


genes, genomes & variation

Gene expression

RNA, protein & metabolite expression


sequences, families & motifs


Molecular & cellular structures


reactions, interactions & pathways

Chemical biology

chemogenomics & metabolomics


taxonomies & controlled vocabularies


Scientific publications & patents

Cross domain

cross-domain tools & resources

Principles of service provision

  • Open - Our data and tools are freely available, without restriction. The only exception is potentially identifiable human genetic information, for which access depends on research consent agreements.
  • Compatible - EMBL-EBI is a world leader in the development of global bioinformatics standards, which are key to data sharing.
  • Comprehensive - Thanks to our many data-sharing agreements, EMBL-EBI resources are comprehensive and up to date. We work with publishers to ensure that biological data must be placed in a public repository and cross-referenced in the relevant publication.
  • Portable - All of our data and many of our software systems can be downloaded and installed locally.
  • High quality - Our databases are enhanced through annotation: highly qualified biologists add value to databases by incorporating features of genes or proteins from other sources, and automated annotation is subjected to rigorous quality control.

Programmatic access

EMBL-EBI web services allow you to query our large biological databases programmatically, so that you can develop data analysis pipelines or integrate public data with your own applications. The web services technologies we use are built on open standards to ensure client and server software from various sources will work well together.

Embassy Cloud

The Embassy Cloud provides EMBL-EBI collaborators with direct access to their datasets hosted here, and to the institute’s powerful computing resources. This shared, high-performance workspace allows project partners in many locations to analyse their data alongside public offerings, using their own approaches. Access to the Embassy Cloud is available to collaborators working on projects with EMBL-EBI.