From ArrayExpress to BioStudies.

Nucleic Acids Research
Ugis SarkansAlvis Brazma

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 la...Continue Reading

References

Jan 10, 2003·Nucleic Acids Research·Alvis BrazmaSusanna-Assunta Sansone
Nov 8, 2006·BMC Bioinformatics·Tim F RaynerAlvis Brazma
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Nov 2, 2014·Nucleic Acids Research·Nikolay KolesnikovAlvis Brazma
Dec 17, 2014·Bioinformatics·Diana M HendrickxJos C S Kleinjans
Dec 25, 2015·Molecular Systems Biology·Jo McEntyreAlvis Brazma
Aug 2, 2017·Nature Methods·Marlon StoeckiusPeter Smibert
Oct 27, 2017·Nucleic Acids Research·Ugis SarkansJohanna McEntyre
Nov 1, 2017·Nature Methods·Robin LiechtiThomas Lemberger
Nov 22, 2017·Nucleic Acids Research·Maria LevchenkoJohanna McEntyre
Sep 27, 2018·F1000Research·Mikael LindenTommi Nyrönen
Oct 26, 2018·Nucleic Acids Research·Awais AtharAlvis Brazma
Nov 1, 2018·Nature Methods·Jan EllenbergEwan Birney
Nov 6, 2018·Nucleic Acids Research·Yasset Perez-RiverolJuan Antonio Vizcaíno
Jan 18, 2020·Bioinformatics·Rachel DrysdaleJohanna McEntyre

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Citations

Oct 8, 2021·Nature Communications·Chengxin DaiYasset Perez-Riverol
Oct 12, 2021·Nucleic Acids Research·Yin-Ying WangPeilin Jia

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Methods Mentioned

BETA
methylation profiling
RNA-seq
genotyping
electron microscopy
PLANS
CITE-Seq
light microscopy

Software Mentioned

ELIXIR
PRIDE
Annotare
TAB
Visium
SourceData
Expression Atlas
Aspera
ELIXIR AAI
MAGE

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