From ArrayExpress to BioStudies

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2020 Nov 19

PMID 33211879

Citations 45

Authors

Ugis Sarkans

Anja Fullgrabe

Ahmed Ali

Awais Athar

Ehsan Behrangi

Nestor Diaz

Silvie Fexova

Nancy George

Haider Iqbal

Sandeep Kurri

Jhoan Munoz

Juan Rada

Irene Papatheodorou

Alvis Brazma

Affiliations

Soon will be listed here.

Abstract

ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data at EMBL-EBI, established in 2002, initially as an archive for publication-related microarray data and was later extended to accept sequencing-based data. Over the last decade an increasing share of biological experiments involve multiple technologies assaying different biological modalities, such as epigenetics, and RNA and protein expression, and thus the BioStudies database (https://www.ebi.ac.uk/biostudies) was established to deal with such multimodal data. Its central concept is a study, which typically is associated with a publication. BioStudies stores metadata describing the study, provides links to the relevant databases, such as European Nucleotide Archive (ENA), as well as hosts the types of data for which specialized databases do not exist. With BioStudies now fully functional, we are able to further harmonize the archival data infrastructure at EMBL-EBI, and ArrayExpress is being migrated to BioStudies. In future, all functional genomics data will be archived at BioStudies. The process will be seamless for the users, who will continue to submit data using the online tool Annotare and will be able to query and download data largely in the same manner as before. Nevertheless, some technical aspects, particularly programmatic access, will change. This update guides the users through these changes.

Citing Articles

The role and application of bioinformatics techniques and tools in drug discovery.

Zhang S, Liu K, Liu Y, Hu X, Gu X Front Pharmacol. 2025; 16:1547131.

PMID: 40017606 PMC: 11865229. DOI: 10.3389/fphar.2025.1547131.

Nitidine chloride inhibits the progression of hepatocellular carcinoma by suppressing IGF2BP3 and modulates metabolic pathways in an mA-dependent manner.

Xiong D, Chen Z, Li J, Deng Y, He R, Huang Z Mol Med. 2025; 31(1):47.

PMID: 39910429 PMC: 11796242. DOI: 10.1186/s10020-025-01095-8.

Identification of lethality-related m7G methylation modification patterns and the regulatory features of immune microenvironment in sepsis.

Wang D, Huo R, Ye L Heliyon. 2025; 11(1):e40870.

PMID: 39758389 PMC: 11699318. DOI: 10.1016/j.heliyon.2024.e40870.

Potential association between COVID-19 and neurological disorders: analysis of common genes and therapeutics.

Chen W, Jiang S, Li C, Li S, Wang J, Xu R Front Neurol. 2024; 15:1417183.

PMID: 39469068 PMC: 11513677. DOI: 10.3389/fneur.2024.1417183.

On discovery of novel hub genes for ER+ and TN breast cancer types through RNA seq data analyses and classification models.

Saddiqa A, Zakir M, Sheikh M, Muneer Z, Hassan A, Ali I Sci Rep. 2024; 14(1):20840.

PMID: 39242688 PMC: 11379961. DOI: 10.1038/s41598-024-69721-9.

References

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

Sarkans U, Gostev M, Athar A, Behrangi E, Melnichuk O, Ali A . The BioStudies database-one stop shop for all data supporting a life sciences study. Nucleic Acids Res. 2017; 46(D1):D1266-D1270. PMC: 5753238. DOI: 10.1093/nar/gkx965. View

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay P, Swerdlow H . Simultaneous epitope and transcriptome measurement in single cells. Nat Methods. 2017; 14(9):865-868. PMC: 5669064. DOI: 10.1038/nmeth.4380. 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

Amid C, Alako B, Kadhirvelu V, Burdett T, Burgin J, Fan J . The European Nucleotide Archive in 2019. Nucleic Acids Res. 2019; 48(D1):D70-D76. PMC: 7145635. DOI: 10.1093/nar/gkz1063. View

Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N . ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003; 31(1):68-71. PMC: 165538. DOI: 10.1093/nar/gkg091. View

Linden M, Prochazka M, Lappalainen I, Bucik D, Vyskocil P, Kuba M . Common ELIXIR Service for Researcher Authentication and Authorisation. F1000Res. 2018; 7. PMC: 6124379. DOI: 10.12688/f1000research.15161.1. View

Cook C, Stroe O, Cochrane G, Birney E, Apweiler R . The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. Nucleic Acids Res. 2019; 48(D1):D17-D23. PMC: 6943058. DOI: 10.1093/nar/gkz1033. View

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C . Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001; 29(4):365-71. DOI: 10.1038/ng1201-365. View

10.

Rayner T, Rocca-Serra P, Spellman P, Causton H, Farne A, Holloway E . A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006; 7:489. PMC: 1687205. DOI: 10.1186/1471-2105-7-489. View

11.

Drysdale R, Cook C, Petryszak R, Baillie-Gerritsen V, Barlow M, Gasteiger E . The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinformatics. 2020; 36(8):2636-2642. PMC: 7446027. DOI: 10.1093/bioinformatics/btz959. View

12.

Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M . ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res. 2010; 39(Database issue):D1002-4. PMC: 3013660. DOI: 10.1093/nar/gkq1040. View

13.

Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang Y, Williams E . ArrayExpress update--simplifying data submissions. Nucleic Acids Res. 2014; 43(Database issue):D1113-6. PMC: 4383899. DOI: 10.1093/nar/gku1057. View

14.

Liechti R, George N, Gotz L, El-Gebali S, Chasapi A, Crespo I . SourceData: a semantic platform for curating and searching figures. Nat Methods. 2017; 14(11):1021-1022. DOI: 10.1038/nmeth.4471. View

15.

Wang Z, Gerstein M, Snyder M . RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2008; 10(1):57-63. PMC: 2949280. DOI: 10.1038/nrg2484. View

16.

Hendrickx D, Aerts H, Caiment F, Clark D, Ebbels T, Evelo C . diXa: a data infrastructure for chemical safety assessment. Bioinformatics. 2014; 31(9):1505-7. PMC: 4410652. DOI: 10.1093/bioinformatics/btu827. View

17.

Levchenko M, Gou Y, Graef F, Hamelers A, Huang Z, Ide-Smith M . Europe PMC in 2017. Nucleic Acids Res. 2017; 46(D1):D1254-D1260. PMC: 5753258. DOI: 10.1093/nar/gkx1005. View

18.

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

19.

Papatheodorou I, Moreno P, Manning J, Munoz-Pomer Fuentes A, George N, Fexova S . Expression Atlas update: from tissues to single cells. Nucleic Acids Res. 2019; 48(D1):D77-D83. PMC: 7145605. DOI: 10.1093/nar/gkz947. View

20.

McEntyre J, Sarkans U, Brazma A . The BioStudies database. Mol Syst Biol. 2015; 11(12):847. PMC: 4704487. DOI: 10.15252/msb.20156658. View