ArrayExpress update--simplifying data submissions

Abstract

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository for data supporting peer-reviewed publications. It contains data from over 7000 public sequencing and 42,000 array-based studies comprising over 1.5 million assays in total. The proportion of sequencing-based submissions has grown significantly over the last few years and has doubled in the last 18 months, whilst the rate of microarray submissions is growing slightly. All data in ArrayExpress are available in the MAGE-TAB format, which allows robust linking to data analysis and visualization tools and standardized analysis. The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold. In the near future, Annotare will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines. ArrayExpress is a stable and highly accessed resource. Our future tasks include automation of data flows and further integration with other EMBL-EBI resources for the representation of multi-omics data.

Figure 1.

An Annotare sample submission form. In the Annotare submission system appropriate sample attributes can be chosen (e.g. disease, individual identifier, sex) and then populated either with terms selected from the Experimental Factor Ontology (EFO) or using free text. EFO terms are suggested as the user starts to type in a field. Samples can be easily added or deleted. Following sample creation submitters are guided through the assignment of labelling information for nucleic acid extracts in microarray submissions or library information such as the library layout in high-throughput sequencing submissions. Finally, users are guided through the submission of their data files.