The goal of the ELIXIR Data Platform is to drive the use, re-use and value of life science data. It aims to do this by providing users with robust, long-term sustainable data resources within a coordinated, scalable and connected data ecosystem.
Bioinformaticians and life science researchers in both academic and industrial settings need confidence in the sound governance, life cycle management, and long-term sustainability of those data resources.
They also need open access to technically and scientifically excellent data resources for effective data discovery, deposition, and re-use. The ELIXIR Data platform promotes Open Access as a core principle for publicly funded research. ELIXIR resources ideally reflect this commitment and have terms of use or a licence that enables the reuse and remixing of data (see Open Definition for a list of open licenses).
Services offered
- ELIXIR Core Data Resources: European data resources that are of fundamental importance to research in the life sciences and are committed to the long-term preservation of data.
- ELIXIR Deposition Databases: repositories recommended for the deposition of life sciences experimental data.
- Database services listing: this list is updated as Nodes finalise or review their Service Delivery Plans (see How countries join).
What the Data Platform does
To achieve its goals the Platform works in four Tasks.
Task 1. Core Data Resources and Deposition Databases
Leader: Rachel Drysdale (ELIXIR Hub)
Goal: To administer and support the Core Data Resource and Deposition Database portfolio.
Activities:
- Core Data Resource and Deposition Database selection.
- For an introduction to the Core Data Resources list, please view this summary.
- Core Data Resource Indicator collection and service monitoring.
Task 2. Literature-Data Integration
Leader: Jo McEntyre (EMBL-EBI)
Goal: To build a comprehensive, connected data ecosystem across ELIXIR, with deep integration to the scientific literature via the ELIXIR Core Data Resource, Europe PMC.
Activities:
- Support reproducibility of research by linking papers to underlying data in ELIXIR data resources.
- Ensure reference datasets in ELIXIR data resources, both deposited and curated, comprehensively link to Europe PMC.
- Provide technology to support deep linking between Europe PMC and databases.
- Provide support for ORCID integration into data resources.
Task 3. Scalable Curation
Leaders: Jo McEntyre (EMBL-EBI), Patrick Ruch (ELIXIR-CH) and Silvio Tosatto (ELIXIR-IT)
Goal: To maximise the ability of expert human curators to enrich the ELIXIR knowledgebases through providing trans-resource, scalable curation solutions.
Activities:
- Semantic annotation of Europe PMC documents, linked to underlying data resources.
- Investigating scalable article triage systems.
- Provide technology to support deep linking between Europe PMC and databases.
- Exploring opportunities and role for community curation.
Task 4. Long Term Sustainability
Leader: Christine Durinx (ELIXIR-CH)
Goal: To ensure the long term financial sustainability of the ELIXIR Core Data Resources by contributing to the establishment of a global, internationally shared, sustainable funding model for Core Data Resources.
Activities:
- Share the experience gained with the European life science data infrastructure from the ELIXIR Core Data Resource selection process, as considerations of global priorities and resource allocation proceed.
- Influence the development of Data Management Plans to ensure best practice and adoption of ELIXIR Core Data Resources and ELIXIR Deposition Databases.
- Participating in the international Global Biodata Coalition, working to ensure collective support for those data resources essential to the work of life science researchers, educators, and innovators worldwide.
An example of the Platform's work: community annotation of Europe PMC documents
The Data Platform has helped build a system that enables community annotations to appear in the abstracts in Europe PMC. These annotations can be clicked on for further information.
Before
Before: An abstract at Europe PMC without annotations. Before the annotation system was developed you could not highlight key terms or click on them to access other data resources related to that term across the web.
After
After: You can now highlight key terms, and click the terms for further information. Gene Function annotations, corresponding to GeneRIFs from Entrez Gene, have been mapped back to the articles by the Swiss Institute of Bioinformatics' text mining group, providing links to UniProt (an ELIXIR Core Data Resource). In the abstract above, the link is to the UniProt record for PTEN, where you can find a wealth of information about the protein, its function, the gene that encodes the protein, and the pathology caused by genetic variants.
The Platform is also involved in the following Commissioned Services:
- Apple as a Model for Genomic Information Exchange
- Establishment of an ELIXIR Contextual Data Clearinghouse
- Extending open proteomics data analysis pipelines in the cloud: Additional tools and focus on scalability, supporting the dramatic growth of public proteomics data
- FAIRness of the current ELIXIR Core resources: Application (and test) of newly available FAIR metrics, and identification of steps to increase interoperability
- Integration and standardization of intrinsically disordered protein data
- Increasing Interoperability between ELIXIR Protein Structure and Sequence Resources and Expanding these Resources with 3D-Models of CATH Domains, built by SWISS-MODEL
- Integrating reference taxonomic databases for metabarcoding and metagenomics identification
For all ELIXIR Commissioned Services, including completed ones, see the Commissioned Services page.
Leadership
(EMBL-EBI)
Platform Lead
(SIB, ELIXIR Switzerland)
Platform Lead
(ELIXIR Hub)
Platform Coordinator
Find out more
- Join the Data Platform group and its mailing list.
- Learn about the Core Data Resources work:
- Durinx C, McEntyre J, Appel R et al. Identifying ELIXIR Core Data Resources. F1000Research 2017, 5(ELIXIR):2422 (doi: 10.12688/f1000research.9656.2)
- Learn more about the global data resource initiative:
- Data management: A global coalition to sustain core data. Nature 543, 179 (09 March 2017) doi: 10.1038/543179a
- Towards Coordinated International Support Of Core Data Resources For The Life Sciences Biorxiv preprint (27 April 2017) doi: https://doi.org/10.1101/110825
- Stockinger H, Barlow M, Cook C et al. Plan for collation of metrics and quality data at the ELIXIR Hub. (Zenodo 2018) doi: https://doi.org/10.5281/zenodo.1194122
- See the current Database Services listing.
