Data: Sustaining Europe’s life science data infrastructure The ELIXIR Data Platform drives the use, re-use and value of life science data. The main objective is to build and maintain a portfolio of interconnected data resources with the Core Data Resources (CDRs) and Deposition Databases (EDDs) at its centre. Based on quality criteria, the Platform also provides materials to support the discussion about sustainability of data resources within the Global Biodata Coalition. The Platform also connects data with scientific literature and supports scalable curation workflows for both professional and community curators.
Major achievements in 2019 Task 1: Administration and support for Core Data Resource and Deposition Database portfolio 2019 saw three publications focussed on the Core Data Resources and Deposition Databases portfolio: • The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences1 • The Annual Indicator Monitoring and Periodic Review Processes: ELIXIR Core Data Resources and Deposition Databases2 • The ELIXIR Core Data Resource Profiles slideset3 The third round of selection of ELIXIR Cores Data Resources and Deposition Databases was launched in October 2019, and will conclude in June of 2020.
Task 3: Scalable curation Experimental Methods tagging - The Data Platform conducted a user research project on curation practices, as part of the ELIXIR-EXCELERATE project. The aim of the project was to understand and identify common curation workflow patterns and practices. The analysis4 of the data showed that curators often look for the experimental methods as one of the key parameters in article selection for curation. By consulting domain experts, curators of ELIXIR Data Resources, a dictionary with experimental method terms and corresponding IDs was created and used to text mine those terms from literature. As a result, articles in Europe PMC can be retrieved based on experimental method mentions. In 2019 a new mechanism was established to enable deep links between added-value databases and research publications in Europe PMC. The ELIXIR Data Platform collaborated with the neXtprot database at SIB (ELIXIR Switzerland) to demonstrate the deep linking mechanism. Deep links point to the precise sentence in a full text article. Data records with deep links are therefore less ambiguous than simple links to the source article.
Task 4: Long term sustainability The Data Platform contributes to the Global Biodata Coalition (GBC)5, which is working on behalf of biomedical and life sciences research funders to help coordinate and sustain funding for the global infrastructure of biodata resources. The GBC Board of Funders will meet in June 2020 and consider, among other issues, their scientific programme.
Task 2: Literature-Data Integration In 2019 the plan for the Literature-data integration task was laid out. The aim is to build a connected ELIXIR data ecosystem through outreach activities such as webinars and hackathons that will promote deep integration between ELIXIR data resources. The Literature-Data Integration team developed an outreach campaign, starting with a webinar to take place in 2020 on how research articles can be linked to the underlying data via Europe PMC. Expanding on this, a hackathon will be organised to explain how to use the Europe PMC service ecosystem to develop new workflows and applications.
1 Drysdale R, Cook CE, Petryszak R et al, The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. Bioinformatics 2020, 36, pages 2636–2642 (https://doi.org/10.1093/bioinformatics/btz959) 2 Drysdale R, McEntyre J, Durinx C et al. The Annual Indicator Monitoring and Periodic Review Processes: ELIXIR Core Data Resources and Deposition Databases. F1000Research 2020, 9(ELIXIR):114 (document) (https://doi.org/10.7490/f1000research.1117816.1) 3 Drysdale R and Martin C. ELIXIR core data resources profiles. F1000Research 2019, 8(ELIXIR):236 (slides), (https://doi.org/10.7490/ f1000research.1116460.1) 4 Venkatesan A, Karamanis N, Ide-Smith M et al. Understanding life sciences data curation practices via user research. F1000Research 2019, 8(ELIXIR):1622 (https://doi.org/10.12688/f1000research.19427.1) 5 http://www.globalbiodata.org/
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ELIXIR Annual Report 2019
