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 and the RDA/Force11's FAIRsharing Working Group for details of this collaboration.
- Initial portfolio of Recommended Interoperability Resources (RIRs) announced
- Interoperability Presentations: links to recent presentations.
- Bioschemas Staff Exchange: rolling application process until June 2019.
- Recommended Interoperability Resources (RIRs): as reviewed and selected by ELIXIR.
- Service Framework: the governance and implementation plan by platform leadership.
- Bioschemas: Schema.org extension tailored for life science concepts.
- Identifiers.org: a resolving system to reference data in both a location-independent and resource-dependent manner.
- Ontology Lookup Service (OLS): a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions.
- FAIRsharing.org: curated, informative and educational resource on data and metadata standards, inter-related to databases and data policies.
- Linked data: FAIRification via Bring-Your-Own-Data framework with ELIXIR Rare Disease Community Use Cases.
- CWL for Tool Interoperability: Common Workflow Language to aid interoperable software development.
- Interoperability Knowledgehub: governance and implementation of knowledge and service dissemination via web portal.
What the Platform does
- Identifies and promotes interoperability best practices for data providers and data integrators.
- Delivers the interoperability services that underpin ELIXIR Communities and Platforms.
To achieve these goals the Platform is split into seven projects:
- 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)
- Identify interoperability tools that facilitate FAIRification via the ELIXIR Recommended Interoperability Resource selection process.
- Defining and reviewing Interoperability Service Quality Indicators aligned with FAIR Principles and ELIXIR Core Data Resource indicators.
- Identifying what services are needed to serve common interoperability workflows.
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 Diseases Community 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 Community as a driver.
Leader: Helen Parkinson (EMBL-EBI), Alasdair Gray (ELIXIR UK), Carole Goble (ELIXIR UK), Susanna-Assunta Sansone and Philippe Rocca-Serra (ELIXIR UK)
- Working with the ELIXIR Communities 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 Community.
- Implementing a BRAPI 2 ISA conversion with ISA Tools to comply to the MIAPPI requirements.
- Providing training for ELIXIR-affiliated developers in the use of metadata (ontology) standards and existing ontology tools.
Workflow and Tool interoperability
Goal: To create specifications that enable data scientists to describe analysis tools and workflows to make them interoperable across Communities.
Leader:Carole Goble (ELIXIR UK)
- Enabling the reuse, extension, scaling, and reproducibility of scientific workflows, an Implementation Study working with the Marine Metagenomics Community 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.
ELIXIR funds a number of short term, technical projects (Implementation Studies) that to inform future service development, drive standards adoption and engage the Nodes.
- Data Identification and Interoperability (2016-Identifiers)
- Towards Data Stewardship (2018-DMP)
- FAIRness of the current ELIXIR Core Data Resources (2018-FAIRCDRs)
- FAIRification of Genomic Tracks (2018-Human-FAIRification)
- A Scalable approach to Personal FAIR Data (2018-Human-MyFAIR)
- Integration and standardization of intrinsically disordered proteins (2018-IDPs)
- Reuse, extension, scaling of scientific workflows (2018-cwl)
- Data Validation (2018-Validation)
- Increasing Interoperability of protein resources (2018-Proteininterop)
- Annotation and curation of human genomic variations (2018-Variation)
- Metabolite Identification (2018-Metabolomics)
- Bioschemas: Community Adoption and Training (2018-Bioschemas)
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)