The European Bioinformatics Institute (EMBL-EBI) in 2021

Abstract

The European Bioinformatics Institute (EMBL-EBI) maintains a comprehensive range of freely available and up-to-date molecular data resources, which includes over 40 resources covering every major data type in the life sciences. This year's service update for EMBL-EBI includes new resources, PGS Catalog and AlphaFold DB, and updates on existing resources, including the COVID-19 Data Platform, trRosetta and RoseTTAfold models introduced in Pfam and InterPro, and the launch of Genome Integrations with Function and Sequence by UniProt and Ensembl. Furthermore, we highlight projects through which EMBL-EBI has contributed to the development of community-driven data standards and guidelines, including the Recommended Metadata for Biological Images (REMBI), and the BioModels Reproducibility Scorecard. Training is one of EMBL-EBI’s core missions and a key component of the provision of bioinformatics services to users: this year's update includes many of the improvements that have been developed to EMBL-EBI’s online training offering.

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

“…As usual, the Issue begins with updates from the major database providers at the European Bioinformatics Institute (EBI), the U.S. National Center for Biotechnology Information (NCBI), and the National Genomics Data Center (NGDC) in China ( 1–3 ). Thereafter, articles are placed in the usual categories: (i) nucleic acid sequence, structure and transcriptional regulation; (ii) protein sequence and structure; (iii) metabolic and signaling pathways, enzymes and networks; (iv) genomics of viruses, bacteria, protozoa and fungi; (v) genomics of human and model organisms plus comparative genomics; (vi) human genomic variation, diseases and drugs; (vii) plants and (viii) other topics, such as proteomics databases.…”

Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque

“…Systematic measurements of biological samples through omics technologies, together with efforts to distil the scientific literature into structured databases, are providing an ever-growing corpus of biomedical and biomolecular information 1 . Indeed, the data stored in the EMBL-EBI has increased sixfold in the last few years, from 40 petabytes in 2014 to over 250 in 2021 2 . Associated with this phenomenon, a variety of nomenclatures have been proposed, along with identifiers, levels of resolution (e.g., protein isoforms or gene splice variants) and experimental conditions, making data integration and harmonization across platforms a challenging step 3 .…”

Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque

“…Systematic measurements of biological samples through ‘omics’ technologies, together with efforts to distill the scientific literature into structured databases, are providing an ever-growing corpus of biomedical and biomolecular information 1 . Indeed, the data stored in the EMBL-EBI has increased sixfold in the last few years, from 40 petabytes in 2014 to over 250 in 2021 2 . Associated with this phenomenon, a variety of nomenclatures have been proposed, along with identifiers, levels of resolution (e.g., protein isoforms or gene splicing variants) and experimental conditions, making data integration and harmonization across platforms a challenging step 3 .…”