The European Bioinformatics Institute (EMBL-EBI) in 2021

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2021 Dec 1

PMID 34850134

Citations 31

Authors

Gaia Cantelli

Alex Bateman

Cath Brooksbank

Anton I Petrov

Rahuman S Malik-Sheriff

Michele Ide-Smith

Henning Hermjakob

Paul Flicek

Rolf Apweiler

Ewan Birney

Johanna McEntyre

Affiliations

Soon will be listed here.

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.

Citing Articles

Predicting Fitness-Related Traits Using Gene Expression and Machine Learning.

Henry G, Stinchcombe J Genome Biol Evol. 2025; 17(2).

PMID: 39983007 PMC: 11844753. DOI: 10.1093/gbe/evae275.

The ISCB competency framework v. 3: a revised and extended standard for bioinformatics education and training.

Brooksbank C, Brazas M, Mulder N, Schwartz R, Ras V, Morgan S Bioinform Adv. 2024; 4(1):vbae166.

PMID: 39678208 PMC: 11646570. DOI: 10.1093/bioadv/vbae166.

Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.

Rendina M, Turnbaugh P, Bradley P bioRxiv. 2024; .

PMID: 39574613 PMC: 11580864. DOI: 10.1101/2024.11.06.622278.

The mendelian randomized study revealed the association of prostatitis with prostate cancer risk.

Chen J, Ye F, Shang K, Li N, Li C, He H Sci Rep. 2024; 14(1):24643.

PMID: 39428439 PMC: 11491451. DOI: 10.1038/s41598-024-76355-4.

An ontology-based knowledge graph for representing interactions involving RNA molecules.

Cavalleri E, Cabri A, Soto-Gomez M, Bonfitto S, Perlasca P, Gliozzo J Sci Data. 2024; 11(1):906.

PMID: 39174566 PMC: 11341713. DOI: 10.1038/s41597-024-03673-7.

References

Moreno P, Fexova S, George N, Manning J, Miao Z, Mohammed S . Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Res. 2021; 50(D1):D129-D140. PMC: 8728300. DOI: 10.1093/nar/gkab1030. View

Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee G . Accurate prediction of protein structures and interactions using a three-track neural network. Science. 2021; 373(6557):871-876. PMC: 7612213. DOI: 10.1126/science.abj8754. View

Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A . The reactome pathway knowledgebase 2022. Nucleic Acids Res. 2021; 50(D1):D687-D692. PMC: 8689983. DOI: 10.1093/nar/gkab1028. View

Cezard T, Cunningham F, Hunt S, Koylass B, Kumar N, Saunders G . The European Variation Archive: a FAIR resource of genomic variation for all species. Nucleic Acids Res. 2021; 50(D1):D1216-D1220. PMC: 8728205. DOI: 10.1093/nar/gkab960. View

Sarkans U, Chiu W, Collinson L, Darrow M, Ellenberg J, Grunwald D . REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Nat Methods. 2021; 18(12):1418-1422. PMC: 8606015. DOI: 10.1038/s41592-021-01166-8. View

Meldal B, Perfetto L, Combe C, Lubiana T, Cavalcante J, Bye-A-Jee H . Complex Portal 2022: new curation frontiers. Nucleic Acids Res. 2021; 50(D1):D578-D586. PMC: 8689886. DOI: 10.1093/nar/gkab991. View

Freeberg M, Fromont L, DAltri T, Romero A, Ciges J, Jene A . The European Genome-phenome Archive in 2021. Nucleic Acids Res. 2021; 50(D1):D980-D987. PMC: 8728218. DOI: 10.1093/nar/gkab1059. View

Lambert S, Gil L, Jupp S, Ritchie S, Xu Y, Buniello A . The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation. Nat Genet. 2021; 53(4):420-425. PMC: 11165303. DOI: 10.1038/s41588-021-00783-5. View

Yates A, Allen J, Amode R, Azov A, Barba M, Becerra A . Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Res. 2021; 50(D1):D996-D1003. PMC: 8728113. DOI: 10.1093/nar/gkab1007. View

10.

McGrath A, Champ K, Shang C, van Dam E, Brooksbank C, Morgan S . From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training. PLoS Comput Biol. 2019; 15(6):e1006923. PMC: 6597034. DOI: 10.1371/journal.pcbi.1006923. View

11.

Tunyasuvunakool K, Adler J, Wu Z, Green T, Zielinski M, Zidek A . Highly accurate protein structure prediction for the human proteome. Nature. 2021; 596(7873):590-596. PMC: 8387240. DOI: 10.1038/s41586-021-03828-1. View

12.

Malik-Sheriff R, Glont M, Nguyen T, Tiwari K, Roberts M, Xavier A . BioModels-15 years of sharing computational models in life science. Nucleic Acids Res. 2019; 48(D1):D407-D415. PMC: 7145643. DOI: 10.1093/nar/gkz1055. View

13.

De Silva N, Bhai J, Chakiachvili M, Contreras-Moreira B, Cummins C, Frankish A . The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data. Nucleic Acids Res. 2021; 50(D1):D765-D770. PMC: 8524594. DOI: 10.1093/nar/gkab889. View

14.

Kalvari I, Nawrocki E, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M . Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. 2020; 49(D1):D192-D200. PMC: 7779021. DOI: 10.1093/nar/gkaa1047. View

15.

Wand H, Lambert S, Tamburro C, Iacocca M, OSullivan J, Sillari C . Improving reporting standards for polygenic scores in risk prediction studies. Nature. 2021; 591(7849):211-219. PMC: 8609771. DOI: 10.1038/s41586-021-03243-6. View

16.

Wilkinson M, Dumontier M, Aalbersberg I, Appleton G, Axton M, Baak A . The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016; 3:160018. PMC: 4792175. DOI: 10.1038/sdata.2016.18. View

17.

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O . Highly accurate protein structure prediction with AlphaFold. Nature. 2021; 596(7873):583-589. PMC: 8371605. DOI: 10.1038/s41586-021-03819-2. View

18.

Del Toro N, Shrivastava A, Ragueneau E, Meldal B, Combe C, Barrera E . The IntAct database: efficient access to fine-grained molecular interaction data. Nucleic Acids Res. 2021; 50(D1):D648-D653. PMC: 8728211. DOI: 10.1093/nar/gkab1006. View

19.

Garcia L, Batut B, Burke M, Kuzak M, Psomopoulos F, Arcila R . Ten simple rules for making training materials FAIR. PLoS Comput Biol. 2020; 16(5):e1007854. PMC: 7241697. DOI: 10.1371/journal.pcbi.1007854. View

20.

Courtot M, Cherubin L, Faulconbridge A, Vaughan D, Green M, Richardson D . BioSamples database: an updated sample metadata hub. Nucleic Acids Res. 2018; 47(D1):D1172-D1178. PMC: 6323949. DOI: 10.1093/nar/gky1061. View