The European Bioinformatics Institute in 2020: Building a Global Infrastructure of Interconnected Data Resources for the Life Sciences

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 Nov 9

PMID 31701143

Citations 18

Authors

Charles E Cook

Oana Stroe

Guy Cochrane

Ewan Birney

Rolf Apweiler

Affiliations

Soon will be listed here.

Abstract

Data resources at the European Bioinformatics Institute (EMBL-EBI, https://www.ebi.ac.uk/) archive, organize and provide added-value analysis of research data produced around the world. This year's update for EMBL-EBI focuses on data exchanges among resources, both within the institute and with a wider global infrastructure. Within EMBL-EBI, data resources exchange data through a rich network of data flows mediated by automated systems. This network ensures that users are served with as much information as possible from any search and any starting point within EMBL-EBI's websites. EMBL-EBI data resources also exchange data with hundreds of other data resources worldwide and collectively are a key component of a global infrastructure of interconnected life sciences data resources. We also describe the BioImage Archive, a deposition database for raw images derived from primary research that will supply data for future knowledgebases that will add value through curation of primary image data. We also report a new release of the PRIDE database with an improved technical infrastructure, a new API, a new webpage, and improved data exchange with UniProt and Expression Atlas. Training is a core mission of EMBL-EBI and in 2018 our training team served more users, both in-person and through web-based programmes, than ever before.

Citing Articles

PPCRKB: a risk factor knowledge base of postoperative pulmonary complications.

Duan J, Li P, Shao A, Hao X, Zhou R, Bi C Database (Oxford). 2024; 2024.

PMID: 39028753 PMC: 11259045. DOI: 10.1093/database/baae054.

The causal relationship between sleep and risk of psychiatric disorders: A two-sample mendelian randomization study.

Chen P, Qin J, Wang Y, Yuan J, Pan Y, Zhu B Front Genet. 2024; 15:1380544.

PMID: 38952712 PMC: 11215123. DOI: 10.3389/fgene.2024.1380544.

Perspectives on tracking data reuse across biodata resources.

Ross K, Bastian F, Buys M, Cook C, DEustachio P, Harrison M Bioinform Adv. 2024; 4(1):vbae057.

PMID: 38721398 PMC: 11076920. DOI: 10.1093/bioadv/vbae057.

A systematic review of non-coding RNA genes with differential expression profiles associated with autism spectrum disorders.

Stott J, Wright T, Holmes J, Wilson J, Griffiths-Jones S, Foster D PLoS One. 2023; 18(6):e0287131.

PMID: 37319303 PMC: 10270643. DOI: 10.1371/journal.pone.0287131.

Building cloud computing environments for genome analysis in Japan.

Ogasawara O Hum Genome Var. 2022; 9(1):46.

PMID: 36517473 PMC: 9751107. DOI: 10.1038/s41439-022-00223-8.

References

Tarkowska A, Carvalho-Silva D, Cook C, Turner E, Finn R, Yates A . Eleven quick tips to build a usable REST API for life sciences. PLoS Comput Biol. 2018; 14(12):e1006542. PMC: 6292566. DOI: 10.1371/journal.pcbi.1006542. View

Ochoa D, Jarnuczak A, Vieitez C, Gehre M, Soucheray M, Mateus A . The functional landscape of the human phosphoproteome. Nat Biotechnol. 2019; 38(3):365-373. PMC: 7100915. DOI: 10.1038/s41587-019-0344-3. View

Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V . ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2015; 44(D1):D1214-9. PMC: 4702775. DOI: 10.1093/nar/gkv1031. View

Athar A, Fullgrabe A, George N, Iqbal H, Huerta L, Ali A . ArrayExpress update - from bulk to single-cell expression data. Nucleic Acids Res. 2018; 47(D1):D711-D715. PMC: 6323929. DOI: 10.1093/nar/gky964. View

Mitchell A, Attwood T, Babbitt P, Blum M, Bork P, Bridge A . InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2018; 47(D1):D351-D360. PMC: 6323941. DOI: 10.1093/nar/gky1100. View

. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2018; 47(D1):D506-D515. PMC: 6323992. DOI: 10.1093/nar/gky1049. View

Williams E, Moore J, Li S, Rustici G, Tarkowska A, Chessel A . The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nat Methods. 2017; 14(8):775-781. PMC: 5536224. DOI: 10.1038/nmeth.4326. View

Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B . Bioinformatics curriculum guidelines: toward a definition of core competencies. PLoS Comput Biol. 2014; 10(3):e1003496. PMC: 3945096. DOI: 10.1371/journal.pcbi.1003496. View

Mulder N, Schwartz R, Brazas M, Brooksbank C, Gaeta B, Morgan S . The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS Comput Biol. 2018; 14(2):e1005772. PMC: 5794068. DOI: 10.1371/journal.pcbi.1005772. View

10.

Jarnuczak A, Najgebauer H, Barzine M, Kundu D, Ghavidel F, Perez-Riverol Y . An integrated landscape of protein expression in human cancer. Sci Data. 2021; 8(1):115. PMC: 8065022. DOI: 10.1038/s41597-021-00890-2. View

11.

Mir S, Alhroub Y, Anyango S, Armstrong D, Berrisford J, Clark A . PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. Nucleic Acids Res. 2017; 46(D1):D486-D492. PMC: 5753225. DOI: 10.1093/nar/gkx1070. View

12.

Ellenberg J, Swedlow J, Barlow M, Cook C, Sarkans U, Patwardhan A . A call for public archives for biological image data. Nat Methods. 2018; 15(11):849-854. PMC: 6884425. DOI: 10.1038/s41592-018-0195-8. View

13.

El-Gebali S, Mistry J, Bateman A, Eddy S, Luciani A, Potter S . The Pfam protein families database in 2019. Nucleic Acids Res. 2018; 47(D1):D427-D432. PMC: 6324024. DOI: 10.1093/nar/gky995. View

14.

Karsch-Mizrachi I, Takagi T, Cochrane G . The international nucleotide sequence database collaboration. Nucleic Acids Res. 2017; 46(D1):D48-D51. PMC: 5753279. DOI: 10.1093/nar/gkx1097. View

15.

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

16.

Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding J, Ur-Rehman S . The European Genome-phenome Archive of human data consented for biomedical research. Nat Genet. 2015; 47(7):692-5. PMC: 5426533. DOI: 10.1038/ng.3312. View

17.

Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu D . The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 2018; 47(D1):D442-D450. PMC: 6323896. DOI: 10.1093/nar/gky1106. View

18.

Iudin A, Korir P, Salavert-Torres J, Kleywegt G, Patwardhan A . EMPIAR: a public archive for raw electron microscopy image data. Nat Methods. 2016; 13(5):387-8. DOI: 10.1038/nmeth.3806. View

19.

Cook C, Lopez R, Stroe O, Cochrane G, Brooksbank C, Birney E . The European Bioinformatics Institute in 2018: tools, infrastructure and training. Nucleic Acids Res. 2018; 47(D1):D15-D22. PMC: 6323906. DOI: 10.1093/nar/gky1124. View

20.

Harrison P, Alako B, Amid C, Cerdeno-Tarraga A, Cleland I, Holt S . The European Nucleotide Archive in 2018. Nucleic Acids Res. 2018; 47(D1):D84-D88. PMC: 6323982. DOI: 10.1093/nar/gky1078. View