Data Platform

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

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.​

More information »

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.

More information »

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.

More information »

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.

More information »

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

Europe PMC abstract - 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

Europe PMC abstract - 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.

» View the article on Europe PMC

Commissioned Services

The Data Platform is involved in a number of short-term, technical projects called Commissioned Services. These are currently:

For completed projects see the Commissioned Services page.

Leadership

Ulrike Wittig

Ulrike Wittig
(ELIXIR Germany)
Platform Lead

Patrick Ruch
Patrick Ruch
(ELIXIR Switzerland)
Platform Lead
Silvio Tosatto
Silvio Tosatto
(ELIXIR Italy)
Platform Lead
Sirarat Sarntivijai
Sirarat Sarntivijai
(Platform Coordinator, ELIXIR Hub)

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