Database Commons

a catalog of worldwide biological databases

The BioStudies database is an EMBL-EBI resource, serving as a repository for descriptions of biological studies, providing links to associated data housed in both internal databases and external resources, and accommodating data that do not fit into specialised archives. BioStudies offers mechanisms for defining and implementing metadata guidelines tailored to specific data sources, projects, or emerging communities, and organises datasets into collections. The platform facilitates data acquisition across the entire scientific process lifecycle, supporting data sharing during collaborative projects, data deposition for manuscript submission, and creation of data packages post-publication. Furthermore, BioStudies has assisted various projects in transitioning from legacy data infrastructures by offering sustainable data archival and access services. This article discusses the data collections within BioStudies across these different data lifecycle stages and details the underlying technology developed for this generic data infrastructure. We report on the progress we have made since 2018 when the previous BioStudies article was published. This paper is targeted towards scientists seeking ways to publish heterogenous datasets associated to their manuscripts, data stewards looking to set up data sharing for a new project or data type, data scientists needing large volumes of life sciences data, as well as data management system developers. BioStudies is available at https://ebi.ac.uk/biostudies.

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.

BioStudies (www.ebi.ac.uk/biostudies) is a new public database that organizes data from biological studies. Typically, but not exclusively, a study is associated with a publication. BioStudies offers a simple way to describe the study structure, and provides flexible data deposition tools and data access interfaces. The actual data can be stored either in BioStudies or remotely, or both. BioStudies imports supplementary data from Europe PMC, and is a resource for authors and publishers for packaging data during the manuscript preparation process. It also can support data management needs of collaborative projects. The growth in multiomics experiments and other multi-faceted approaches to life sciences research mean that studies result in a diversity of data outputs in multiple locations. BioStudies presents a solution to ensuring that all these data and the associated publication(s) can be found coherently in the longer term.