ELIXIR to establish new Use Cases for proteomics, metabolomics, and Galaxy

ELIXIR Europe has announced that it will continue its four current Use Cases (Marine Metagenomics, Plant Sciences, Rare Diseases, and Human Data), and establish three new ones covering Proteomics, Metabolomics, and Galaxy.

ELIXIR is the European research infrastructure for life sciences data. It brings together European resources such as databases, software tools, training materials, cloud storage, and supercomputers. DTL hosts the Dutch node of ELIXIR (Read more.) To ensure that the services developed by ELIXIR platforms are fit for purpose, ELIXIR collaborates with the scientific community in specific domains, the so-called Use Cases.


In ELIXIR’s next Scientific Programme (2019-2023), Use Cases will be referred to as ‘Communities’. Communities will function similarly to Use Cases, where activities will be funded through a variety of sources including Hub-funded Commissioned Services, project-based funding from the European Commission, and commitments from ELIXIR Nodes. ELIXIR Heads of Nodes will decide at their next meeting in December whether to establish further communities in new areas, and if so, which ones to establish.


The Proteomics Use Case aims to align ELIXIR activities with the needs of scientists researching the expression and interactions of proteins. Merging sustainable proteomics resources into existing ELIXIR Platforms and Use Cases would help integrate proteomics data with multi-omics data, improve data processing and analysis pipelines and create guidelines for proteomics data management and annotation. Representatives from 11 Nodes have discussed ELIXIR’s activities in the field of proteomics at a strategic meeting in March. Evidence-based recommendations from this meeting were published in ELIXIR’s F1000 Research channel.


The Metabolomics Use Case will facilitate an ELIXIR infrastructure for metabolite identification, which helps scientists to better understand the biochemistry of organisms. The tools used for metabolite identification produce large data sets that are more efficiently analysed, reported and stored using resources connected by ELIXIR. Representatives from ten Nodes met in April to discuss metabolomics within the scope of ELIXIR. This meeting was organised by ELIXIR-NL, ELIXIR Germany, the PhenoMeNal project, and the Netherlands Metabolomics Centre. As with the Proteomics Use Case, the outcomes of this meeting have been described in a paper in ELIXIR’s F1000 Research channel.


Galaxy is a workflow management system that removes the need for users to compile and install tools — at the same time facilitating the sharing of data and results so that science is reproducible. As a Use Case, Galaxy will continue to support communities such as the Proteomics and Metabolomics Use Cases, develop a strategy with the Nodes to increase availability of data visualisation tools, integrate the Galaxy resources with ELIXIR AAI and further develop training materials and events. The Galaxy community in ELIXIR has already collaborated through a dedicated Galaxy Working Group.

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