A recent Nucleic Acids Research (NAR) paper features Metaboligths: the first general-purpose, open access repository for metabolomics studies, storing the studies raw experimental data and associated metadata. You can find the paper here. Metabolights is powered by the the open source ISA metadata framework, and thus is part of the ISA commons, and it is deployed at the European Bioinformatics Institute (EBI).
Some of the characteristics of the database are: it is cross-species and cross-techniques, it covers metabolite structures and their reference spectra, their biological roles, locations, concentrations, and raw data from metabolic experiments.
The paper describes the database content and technical architecture, the functionalities for searching and browsing the data, how to download data and get programmatic access to the database, and the data submission process, among other things.
A new paper, featuring the ISA team as authors is now available to read on MetaboLights (EMBL-EBI metabolomics repository).
MetaboLights, part of the ISA commons is the new European repository for metabolomic data held at the EBI. Their infrastructure is built upon the ISA software stack, utilising ISAcreator for data entry, ISA-Tab as the format then the BII data manager and database for persistence and storage respectively.
Click here to access the MetaboLights repository.
Our commentary, named “Toward interoperable bioscience data” has just been released in Nature Genetics. In it, we focus on working towards an ISA commons, where one day we’ll all be able to share our experimental metadata in one common, easy to use format, supporting minimal information checklists and ontologies (via the ISA-Tab format and respective tools).
The editor speaks about the paper, paraphrased here:
“Reformatting data is a full-time job for many researchers, even before the minimum reporting guidelines, terminologies and formats of each field are taken into consideration. In this issue, we present a Commentary and a Perspective suggesting solutions to these problems that have been developed by a process of community consultation and open review to which the journal was a party. In the Commentary, Susanna-Assunta Sansone and colleagues identify one central problem, namely that “most repositories are designed for specific assay types, necessitating the fragmentation of complex datasets,” and they offer a unified view of the metadata formatting that will be needed to ensure that biomedical research datasets become interoperable. This solution is the overarching ISA framework, where the acronym stands for ‘Investigation’ (the project context), ‘Study’ (a unit of research) and ‘Assay’ (analytical measurement) (p 121). This proposal shifts the sets of reporting standards agreed upon by each community into the infrastructure and formatting of the data files themselves. Sansone and colleagues also list a set of participant communities that can pioneer the approach and teach by example.”
Many thanks to all who contributed to the paper and to the growing success of ISA (commons and tools).
The Harvard Stem Cell Discovery Engine (SCDE) is now published in NAR. The SCDE is one of many systems now utilising the ISA tools and ISA-Tab format. Check out the publication.