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. 2021 Jan 8;49(D1):D1502-D1506.
doi: 10.1093/nar/gkaa1062.

From ArrayExpress to BioStudies

Ugis Sarkans  1 , Anja Füllgrabe  1 , Ahmed Ali  1 , Awais Athar  1 , Ehsan Behrangi  1 , Nestor Diaz  1 , Silvie Fexova  1 , Nancy George  1 , Haider Iqbal  1 , Sandeep Kurri  1 , Jhoan Munoz  1 , Juan Rada  1 , Irene Papatheodorou  1 , Alvis Brazma  1
Affiliations

From ArrayExpress to BioStudies

Ugis Sarkans et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
Functional genomics data will be migrated to the ArrayExpress collection in BioStudies and new submissions will be loaded via Annotare into BioStudies (with sequencing data being brokered to ENA).
Figure 2.
Figure 2.
A refined template selection and fields to capture single-cell specific attributes have been added to Annotare.
Figure 3.
Figure 3.
Experiment submissions via Annotare from January 2019 to September 2020; (A) broken down by template type, which is composed of technology (inner ring) and biological starting material (outer ring); and (B) by experiment type, showing the increase of single-cell RNA-seq (note that ‘RNA-seq of total RNA’ was added new in May 2019).
See this image and copyright information in PMC

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