Following agreement with the Heads of Nodes committee, ELIXIR 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.
Starting in 2019 with ELIXIR’s next Scientific Programme (2019-2023), Use Cases will be referred to as “Communities”. This will avoid ambiguity with the more established meaning of ‘use case’ used in the engineering field. The word ‘community’ also better characterises how ELIXIR coordinates its experts and services for scientists within a particular domain.
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 had discussed ELIXIR’s activities in the field of proteomics at a strategic meeting in March. Evidence-based recommendations formed 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. As with the Proteomics Use Case, the outcomes of this meeting have been described in a paper published 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 worked closely through a dedicated Galaxy Working Group.
- ELIXIR’s four current Use Cases
- Vizcaíno JA, Walzer M, Jiménez RC et al. A community proposal to integrate proteomics activities in ELIXIR. F1000 Research 2017, 6:875 (doi: 10.12688/f1000research.11751.1)
- van Rijswijk M, Beirnaert C, Caron C et al. The future of metabolomics in ELIXIR. F1000Research 2017, 6(ELIXIR):1649 (doi: 10.12688/f1000research.12342.1)
- ELIXIR’s Galaxy Working Group: https://www.elixir-europe.org/about/groups/galaxy-wg