Meet the FREYA partners: EMBL-EBI

Author: Christine Ferguson, Information Scientist (EMBL-EBI) and FREYA Project Lead for Literature Services

Many different organizations are involved in FREYA and in this blog post series we take a closer look at the partners and their work. This time you can read about the European Bioinformatics Institute (EMBL-EBI), ‘Europe’s home for big data in biology’.


What is the mission of your organisation?

‘Europe’s home for big data in biology’, the European Bioinformatics Institute (EMBL-EBI) can be found on the super-slick and shiny Wellcome Genome Campus in Hinxton, Cambridgeshire in the UK. EMBL-EBI is a part of the European Molecular Biology Laboratory (EMBL), an intergovernmental research organisation across six sites in Europe. A truly international staff of 650 members from 66 nations work to promote scientific progress by providing biological data services, investigator-driven research and training in bioinformatics, disseminating cutting-edge technologies to industry and by hosting an ELIXIR node, supporting coordination of data provision in Europe. 

Why are Persistent Identifiers important for your organisation?

At EMBL-EBI, we use bioinformatics - the science of analysing, managing, storing and sharing biological information - and infrastructure to help scientists everywhere find answers. We need persistent identifiers to reliably access scholarly data resources, which at the EBI are indexed in 39 different repositories including data repositories for all types of molecular biology data, from genomes to pathways to chemistry, as well as for biomedical publications and published datasets. Using persistent identifiers means that a researcher can specify for e.g. the exact ‘BioSample’, genome sequence from the ‘ENA’ (European Nucleotide Archive) or reference datasets from ‘Ensembl’  to investigate the potential effects of genetic variation. These types of biological resources are assigned identifiers known as accession numbers. The ability to identify all of these resources unambiguously reduces the time and cost required to find the required data and importantly, helps with scientific reproducibility. Biological research needs persistent identifiers for all manner of scholarly resources beyond data and literature, such as grants, organisations, instruments, facilities, … the list is long and these are all awaiting the advent of new global identifiers.


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What is your role in the FREYA project?

EMBL-EBI represents the life sciences on this multi-partner and cross-disciplinary project. We’ve been tasked with leading the work package focussed on identifying where new persistent identifier types are needed in the research ecosystem and then building select service prototypes that begin to implement new persistent identifiers.   We’re contributing through Europe PMC at the EBI, which with PubMedCentral USA, are the go-to repositories for indexing of biomedical research publications: we’re demonstrating how better connecting existing identifiers for publications (DOIs), data (accession numbers), researchers (ORCID IDs) increases the speed of discovery and allows us to allows to answer additional questions more easily, such as how to demonstrate the impact of funding. EMBL-EBI also contributes to best practices guidelines for infrastructures supporting identifiers through lessons learned at, a service at the EBI to provide reliable addresses for biomedical objects on the Web.  

EMBL-EBI leads by example when it comes to promoting the value and uptake of persistent identifiers. Since 2017, EMBL-EBI have been using ORCID records of academic staff members to track scientific publications produced by the organisation. Each staff member is strongly encouraged to have an ORCID ID and by using Europe PMC’s "ORCID wizard" to link our publications to our ORCID IDs. Furthermore, a growing number of EBI-based databases provide functionality whereby researchers can link data records that they’ve submitted or curated, to their ORCID IDs. Most recently, Reactome (a database of biological pathways) announced their integration of ORCID-linking functionality. 

What would your perfect Persistent ID world look like?

In an ideal world researchers would refer to persistent identifiers for any scholarly resources used or produced in their work, especially when committing that work to lab notes, poster presentations, journal articles, or submitting datasets to a database. This would allow for any resource to be reliably identified in perpetuity, ultimately serving to speed up scientific progress. 

More information

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