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).
Platform highlights
- 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.
- Data resource services: this list is updated as Nodes finalise or review their Service Delivery Plans (see How countries join).
What the Platform does
To achieve its goals the Platform works in four Tasks.
Task 1. Community and Data Management network engagement
Leader: Silvio Tosatto (ELIXIR-IT)
Goal: To engage the Communities, increase the uptake of Services and align the Data Platform with other related activities such as FAIRPlus, ELIXIR CONVERGE, ELIXIR Interoperability Platform and the work of the Registries Focus Group.
Activities:
- Anchoring the Data Management Expert network (CONVERGE WP1) to the Data Platform for long-term development beyond CONVERGE.
- Developing plans around Community data resources through landscape analyses.
- Developing data science workflows that ensure raw and processed data from experiments are made available via Core Data Resources (CDR), ELIXIR Deposition Databases (EDD) and ELIXIR Community data resources.
- Engaging ELIXIR Communities around Data Platform services through outreach and training activities to ensure data management plans reflect the use of CDRs, EDDs and community data resources to maximise reuse.
Task 2. Data Integration
Leaders: Patrick Ruch (ELIXIR-CH) and Ivan Mičetić (ELIXIR-IT)
Goal: To explore extending the connected ecosystem to any ELIXIR data resource, incorporating and aggregating more orphan data and human data, and providing connectivity with other elements of the ELIXIR infrastructure.
Activities:
- Integrating the “long tail” of data into FAIR databases.
- Fostering the adoption of light-weight FAIR criteria for community-specific data resources, e.g. Bioschemas.
- Building and establishing aggregation databases, the aggregation database landscape and best practices.
Task 3. Scalable Curation
Leader: Patrick Ruch (ELIXIR-CH)
Goal: To maximise the ability of expert human curators to enrich the ELIXIR knowledgebases through providing trans-resource and scalable curation solutions.
Activities:
- Semantic annotating of Europe PMC documents, linked to underlying data resources.
- Investigating scalable article triage systems.
- Providing technology to support deep linking between Europe PMC and databases.
- Exploring opportunities and roles for community curation.
Task 4. Administration and support for Core Data Resource (CDR), Deposition Database (EDD) portfolio and Community Data Resources
Leader: Sirarat Sarntivijai (ELIXIR-Hub)
Goal: To support the establishment, and continue the monitoring of global partnerships in the Global Biodata Coalition and business cases for the long term sustainability of Core Data Resources, ELIXIR Deposition Databases, and ELIXIR Community Resources.
Activities:
- Sharing 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.
- Influencing 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.
Commissioned Services
The Data Platform is involved in a number of short-term, technical projects called Commissioned Services. These are currently:
- Community and Data Management network engagement
- Data Integration
- Scalable Curation
- Administration and support for Core Data Resource (CDR) and Deposition Database (EDD) portfolio
For completed projects see the Commissioned Services page.
Leadership
Ulrike Wittig
(ELIXIR Germany)
Platform Lead
(ELIXIR Switzerland)
Platform Lead
(ELIXIR Italy)
Platform Lead
(Platform Coordinator, ELIXIR Hub)
Gavin Farrell
(ELIXIR Hub)
Platform Officer
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)
- Rachel Drysdale, Charles E Cook, Robert Petryszak, et al. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences, Bioinformatics, btz959 (doi: https://doi.org/10.1093/bioinformatics/btz959)
- Drysdale R, McEntyre J, Durinx C et al. The Annual Indicator Monitoring and Periodic Review Processes: ELIXIR Core Data Resources and Deposition Databases [version 1; not peer reviewed]. F1000Research 2020, 9(ELIXIR):114 (document) (https://doi.org/10.7490/f1000research.1117816.1)
- 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.
