Life science research produces data in a variety of formats. The diversity of formats means that scientists cannot easily find and compare datasets from different sources, so their ability to make new discoveries is hampered.
The goal of the Interoperability Platform is to help people and machines to discover, access, integrate and analyse biological data. It encourages the life science community to adopt standardised file formats, metadata, vocabularies and identifiers.
The Platform works both within Europe and globally. For example, through organisations such as Research Data Alliance (RDA), which promotes data sharing and exchange around the world. See the RDA's ELIXIR Bridging Force Interest Group page for details of this collaboration.
- Request for proposals, Bioschemas Staff Exchange: rolling application process until June 2019.
- Recommended Interoperability Resource (RIR) Selection: deadline for applications 16 July 2018.
- Biohackathon: Paris, 12-16 November 2018
- FAIRsharing: a curated resource on data and metadata standards, inter-related to databases and policies.
- Identifiers.org: a resolving system to reference data in both a location-independent and resource-dependent manner.
- Ontology Lookup Service (OLS): a portal for biomedical ontologies, providing access to the latest ontology versions.
What the Platform does
- Identifies and promotes interoperability best practices for data providers and data integrators.
- Delivers the interoperability services that underpin ELIXIR Use Cases and Platforms.
To achieve these goals the Platform is split into seven projects, each with their sub-goals:
- To identify valuable interoperability services within ELIXIR and support their improvement. See the Recommended Interoperability Resource (RIR) page.
- To identify existing services outside ELIXIR and develop of strategic partnerships with them.
- To identify the interoperability services that need to be developed.
Leaders: Chris Evelo (ELIXIR Netherlands), Carole Goble (ELIXIR UK), Helen Parkinson (EMBL-EBI)
Goal: To encourage the use of schema.org markup within life sciences web resources to improve discoverability of information.
Leader: Rafael Jimenez (ELIXIR Hub), Carole Goble (ELIXIR UK), Alasdair Gray (ELIXIR UK)
- Developing specifications for content types relevant to the life science community e.g. Dataset, Protein, Sample, Standard (see the Bioschemas website for the current list of specifications).
- Creating tools that facilitate the validation and the discovery of web resources that use schema.org markup
- Meetings, hackathons, training in adoption - see the events section for upcoming events or the Bioschemas meetings page.
Goal: To harmonise existing practice in identifier assignment and resolution, to support resources in implementing community standards and to promote the creation of identifier services.
Leader: Carole Goble (ELIXIR UK)
- Working with the Rare Disease Use Case to assess and support their needs for identifier best practices, resolution, citation and mapping.
- Engaged with NIH BD2K and BioCADDIE/DCIP on identifier service harmonisation and data citation infrastructure.
- Implementation Study on Data Identification and Interoperability: a project to establish Identifiers.org as a stable ELIXIR system for uniform identifier resolution to major bioinformatics resources.
- Holding Bring Your Own Data workshops to support best practices and adoption of identifier services.
- For more information see the Identifiers group page.
Get involved: join the Identifiers group.
Goal: To design, test and implement a metadata strategy for ELIXIR using the Plant Sciences Use Case as a driver.
Leader: Helen Parkinson (EMBL-EBI), Alasdair Gray (ELIXIR UK), Carole Goble (ELIXIR UK), Susanna Sansone (ELIXIR UK)
- Working with the ELIXIR Use Cases to assess their complex requirements for metadata both for archival and added value resources.
- Developing a metadata strategy for ontology services, semantic services and best practice examples for the ELIXIR Plant Sciences Use Case.
- Providing training for ELIXIR-affiliated developers in the use of metadata (ontology) standards and existing ontology tools.
Goal: To deliver best practice for implementation and use of Linked Data in ELIXIR Use Cases and inform future development, deployment and sustainable production of linked data resources as ELIXIR resources. Not all ELIXIR Linked Data will be Linked Open Data (LOD); instead we will focus on technologies for Linked Data to help make data FAIR, resulting in what we call "Linked FAIR Data".
Leader: Chris Evelo (ELIXIR Netherlands), Marco Roos (ELIXIR Netherlands)
- Engaged with the Linked (Open) Data Community to define best practices.
Workflow and Tool interoperability
Goal: To create specifications that enable data scientists to describe analysis tools and workflows to make them interoperable across Use Cases.
Leader:Carole Goble (ELIXIR UK)
- Enabling the reuse, extension, scaling, and reproducibility of scientific workflows, an Implementation Study working with the Marine Metagenomics Use Case on using the Common Workflow Language (CWL).
- Promoting industry standards for API documentation.
- Engaged with the Common Workflow Language (CWL) community group and BioExcel Centre of Excellence for BioMolecular Simulation.
Interoperability Knowledge Hub
Goal: To create an online knowledge hub where infrastructure and tool developers can be informed about current ELIXIR Interoperability Platform activities, assess current best practice and determine which interoperability services and standards to implement under specific circumstances. This will build upon the initial description of activities as described on this page above.
Leaders: Sirarat Sarntivijai (ELIXIR Hub)
- In support of the project activities detailed above an ELIXIR Interoperability Knowledge Hub will be developed in collaboration with the ELIXIR Hub.
Find out more
- Contact Sirarat Sarntivijai (sirarat.sarntivijai[at]elixir-europe[dot]org).
- ELIXIR Interoperability Platform (EIP) roadmap
- Browse the list of Interoperability services provided by ELIXIR Nodes.
- Search for BYOD workshops in the Events section or ELIXIR's TeSS training portal.
- Learn more about the FAIR Principles:
- Dutch Techcentre for Life Sciences (DTL) - the ELIXIR Dutch node website.
- Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data 3:160018 doi: 10.1038/sdata.2016.18 (2016)