ELIXIR Interoperability Platform (2024-26)

The Interoperability Platform aims to help people and machines discover, access, integrate and analyse biological data. The Platform has created an ecosystem of products and information and is now maturing into a sustainable framework to address challenges involving identifiers, discoverability, ontologies, metadata, and vocabularies, as well as APIs and workflows.

The FAIR-enabling activities of the Interoperability Platform have strengthened the recognition of Research Data Management (RDM) as a discipline in its own right, which has led to the creation of the ELIXIR RDM Community. This Community will be instrumental in this new phase of the Platform, in order to share, co-create, and reuse resources, tools and services to achieve greater real-world impact.

The Interoperability Platform's vision now covers three themes (designated “The 3 Ps”): mature Products that enable FAIRification and responsible RDM, specific Processes that use (or need) Products, and broader Practices that enable a user to succeed.

  • Products: the goal is to provide a comprehensive and context-aware collection of FAIR-enabling and RDM-supportive products, within the broader context of the European Open Science Cloud (EOSC) framework.
  • Processes: we aim to develop a common framework for the application of the Products to support FAIRification of data and services across ELIXIR Nodes, Communities, and projects, while also aligning with EOSC and global partners.
  • Practices: we will enable users to convert knowledge gathered into actionable content, including guidance materials based on the interoperability stories. These should empower users to navigate and successfully utilise the resources within the portfolio. 

Lead partners: University of Oxford (UK), EMBL-EBI, Maastricht University (The Netherlands)

This WP aims to:

  • Facilitate communication and collaboration among Platform members by chairing monthly coordination calls.
  • Coordinate the scientific agenda for the annual Platform face-to-face meeting.
  • Oversee the implementation of the Platform Work Plan to ensure objectives are met within the designated time frame.
  • Provide reporting and progress updates to ELIXIR governance bodies and stakeholders, where necessary, to foster transparency and accountability.
  • Regularly review Platform strategy to identify areas for improvement and propose necessary adjustments for enhanced efficiency and effectiveness.
  • Establish communication channels with other ELIXIR Platforms to ensure alignment and knowledge sharing.
  • Participate in joint-platform activities to leverage collective expertise and resources.
  • Actively engage with external partners and organisations to seek collaboration and resource-sharing opportunities to enhance Platform capabilities and impact.
  • Where appropriate, pursue additional avenues of funding and support, including industry engagement, to boost sustainability.
  • Contribute to the broader impact of the Platform, by aligning with the ELIXIR Programme and other Research Infrastructures and initiatives, such as EOSC.
  • Communicate Platform activities by engaging with ELIXIR Communities and research communities in general.
  • Represent the Platform in external contexts and strategic partnerships.
  • Coordinate and contribute to drafting and finalisation of Platform Work Plan for remainder of 2024-2028 Programme.

Lead partners: University of Luxembourg (Luxembourg)

This WP aims to:

  • Align and coordinate the development of the RDMkit and FAIR Cookbook;
  • Map out the landscape of FAIR-enabling products, including services and standards, within ELIXIR.

Activity 1: Coordination of the RDMkit and FAIR Cookbook in the wider context of the RDM ecosystem

The aim of this activity is to formalise the coordination between the RDMkit and FAIR Cookbook to:

  1. help their developers with growth, synchronisation and sustainability of the resources;
  2. better serve the ELIXIR and wider user community with complementary and comprehensive coverage; and
  3. engage efficiently with the RDM and other ELIXIR Communities, as well as external collaborators.

Specifically, in this Activity we will bring together their respective editorial boards to:

  • Define an aligned strategic vision across the two resources;
  • Further develop the technical and operational alignments currently in place;
  • Identify gaps/new content from a range of avenues, including outcomes from WP2 Activity 2, WP3 and 4, as well as ELIXIR Communities and Focus Groups;
  • Coordinate the addition of new content in alignment with the resources' remits and the shared strategic vision;
  • Continue to ensure cross-links between the two resources, and to others such as FAIRsharing, DSW, and bio.tools;
  • Organise focus groups, joint hackathons, and contentathons to add guidelines and recipes on topics of strategic relevance to ELIXIR RDM and other Communities.

Activity 2: Establish portfolio of endorsed FAIR-enabling services and standards

The aim of this activity is to formalise and endorse a portfolio of services and standards that support and enable FAIRness. We will leverage activities from WP3 and WP4, as well as review the impact of the RIRs, to identify revisions and improvements required for this process.

Specifically, we will:

  • Survey and analyse the landscape of FAIR-enabling services and standards used across the ELIXIR RDM and other Communities and Nodes;
  • Identify core services and standards, as well as gaps in the ELIXIR portfolio, working closely with WP3 and informed by the 'interoperability stories';
  • Review and update the RIRs procedures, categorisation, and evaluation criteria for services, based on experiences to date (does RIR serve its purpose?);
  • Create ‘live’ representations of standards and their profiles in FAIRsharing, to track their status and maximise their use by data resources;
  • Formalise the ELIXIR portfolio and how it is disseminated to the user, enhancing relevant pages of the ELIXIR website.

Lead partners: SIB (Switzerland), Uppsala University (Sweden)

This WP aims to:

  • Define the components of a common framework for interoperability that will support FAIRification of data and services across ELIXIR Nodes, Communities and Projects and promote alignment with EOSC and ELIXIR’s global partners
  • Curate a comprehensive and well-organised library of interoperability case studies and use cases that will serve as input to initiatives across ELIXIR Platforms, and as examples including lessons learned to a wide range of stakeholders across ELIXIR

This work package will identify, assess, refine and test processes, resources and best practices in FAIR data management. It will consolidate them into a common FAIRification framework. Ultimately, this framework will be used as a reference to which FAIR implementations across ELIXIR Nodes, Communities and Projects can be realigned.

The common FAIRification framework will describe the requirements, recommendations, processes and resources that drive successful FAIR implementations to deliver the objectives of the ELIXIR Interoperability Platform. The work will be organised under two activities:

  1. defining the common FAIRification framework
  2. collecting a comprehensive library of 'Interoperability stories' that illustrate how the framework manifests in use cases across ELIXIR

Activity 1: Converge communities around the use of a common FAIRification framework

Data stewards across ELIXIR routinely define new, ad hoc approaches and workflows in an attempt to create FAIR data, despite the existing resources supporting interoperability. Activity 1 will establish a common framework that will enable ELIXIR data stewards to approach FAIRification of data and services with a systematic and scalable process.

The work will initially build and improve on the FAIR in action FAIRification framework and supporting initiatives such as the FAIR Dataset Maturity model, FAIRification goal development, and FAIR Cookbook in alignment with the EIP FAIR Services architecture Framework.

This work will formalise a practical framework for FAIRification tasks, based on feedback from work in WP2 (landscaping) and guided by the ‘interoperability stories’ in WP3, Activity 2. This framework will be validated practically and refined over the course of the work plan through the proposed series of BYOD workshops.

Plan of work:

  • Analyse a selection of FAIRification and interoperability frameworks that are well-documented and familiar to the WP contributors, to create an initial list of requirements and a first minimal draft framework.
  • Define a minimal reporting structure for the workshop events to collect experiences to guide the future revisions and validation of the framework.
  • Iteratively select/define use cases to focus on for each of the workshops, to maximise the utility of the framework and demonstrate its efficacy across EIP stakeholders—arranging the workshops in coordination with Activity 2.
  • Define a candidate release of the framework and call for EIP members to review and provide feedback for final revisions and validation.
  • Finalise the framework and alignment with Activity 2.

Activity 2: Collect a comprehensive library of 'Interoperability stories' from across ELIXIR

This activity will extend the number of stories that represent the stakeholders of the EIP, and adopt a common structure to support the development of the common FAIRification framework of Activity 1.

The work will begin by analysing the current collection of ‘interoperability stories’ to identify recurring concepts and use cases of relevance to the framework of Activity 1, and to define an initial list of gaps with regards to the types of tools and use cases covered.

The work will involve soliciting new and more detailed ‘interoperability stories’ by reaching out to ELIXIR Projects, Nodes and Communities and a selection of relevant EOSC initiatives and other external partners to request and support their contributions.

The structure and content will be refined as the framework evolves and the work will shift focus towards consolidating the stories into a library of case studies and use cases, and soliciting feedback to ensure that the library can be used as input to future initiatives and stakeholders across ELIXIR.

Plan of work:

  • Identify recurring concepts and use cases of relevance to the framework of Activity 1 in EIP’s current collection of ‘interoperability stories’, and define a list of gaps in the tools and use cases covered.
  • Define a minimal common reporting structure for the workshop events, to facilitate contributions of new and more detailed ‘interoperability stories’, and to assess their utility for EIP stakeholders.
  • Identify opportunities to improve the structure of the library, to support the workshops and to avoid overlaps with existing resources (such as in the RDMkit / FAIR Cookbook), arranging the workshops in coordination with Activity 1.
  • Define a candidate release of the library and proposed path to integrating the ‘interoperability stories’ in RDMkit, FAIR Cookbook and the wider RDM ecosystem, followed by a call for EIP members to review and provide feedback for revision and validation.
  • Design and open a call for contributions of 'interoperability stories’ from ELIXIR Projects, Nodes and Communities and a selection of relevant EOSC initiatives and other external partners.
  • Finalise the library and alignment with Activity 1 and extract a summary of the FAIR enabling technologies in use while highlighting emerging tools and use cases.

This WP aims to:

  • Evaluate and draw attention to issues of interoperability (positive or negative) that occur during data analysis or integration of different types of data, and also in relation to data and compute models.
  • Conduct a use case-driven inventory of individual steps and complete workflows, and the resources supporting these processes, to identify any missing components.
  • Evaluate resources with training materials for their content and links among these resources (think TeSS, Galaxy, WorkflowHub) and between them and bio.tools.
  • Assess both the content of training materials provided by resources such as TeSS, Galaxy and WorkflowHub, and the connections between those same resources and to others such as bio.tools.

Activity 1: Engage RDM and analysis experts to identify services, tools, workflows, and their usage, using data from deposition databases and example FAIR data

This activity will evaluate the interoperability approaches, workflows and tools used for data analysis, integration and reuse. By doing so, we aim to enhance the reusability of datasets and metadata that are being shared in selected (OMICS) deposition databases. To achieve this, we plan to establish connections between these deposited datasets and various other types of data using interoperable tools and workflows. This will also help identify existing methods we can better support and promote across ELIXIR and beyond. To accomplish this, we will:

  • Identify and select deposited datasets in ELIXIR deposition databases (specifically using OmicsDI, BioSamples, Biostudies in the process and then ArrayExpress, ENA, PRIDE, Metabolights and possibly EGA for the actual datasets) and evaluate their reusability.
  • Choose a number of example data reuse approaches to examine, and potentially improve their data requirements. Examples mentioned, but not yet chosen, were disease maps (used in many communities), ordinary differential equation based physiological kinetic models (as used in toxicology and systems biology communities), and whole genome metabolic maps (used in microbiome, food and nutrition, metabolomics). Collate use cases (stories) from Activity 2 WP3 that are relevant to different ELIXIR communities based on these approaches
  • Utilise the workflows collected from Activity 2 WP3 to link and integrate the chosen datasets.
  • Identify interoperability resources relevant during data reuse and for combining identical, related, or hierarchically related entities. Examples are ontology lookup and mapping (e.g. OLS, BioPortal, OxO, Zooma), database identifier resolution (e.g. identifiers.org and BridgeDb), chemical structure resolution and (sub)structure mapping (e.g. CDK, ontologies), executable transformations and models (e.g. Omnipy, conversions to and from SBML and to LaTeX), the whole set of sequence similarity tools (e.g. CleanUp). Evaluate relevant standards (e.g. SSSOM, SBML).
  • Evaluate the interoperability of the deposited datasets.
  • Evaluate a mechanism for post-deposition enrichment of annotation of data in the deposition databases, and an associated validation procedure.
  • Create a list of recommendations for dataset requirements, to ensure successful interoperability when reusing datasets. These recommendations may be generic and applicable to multiple workflows or specific to a particular interoperability task. Creation of FAIRsharing ELIXIR Community Champions to ensure enriched ELIXIR content and highlight recommendations of FAIR-enabling ELIXIR resources in WP2 and help with the profile of resources using FAIR data.

Activity 2: Outreach, dissemination and training

Based on the use cases of Activity 1, make an inventory of existing training material for workflows, molecular data analysis procedures and tutorials for analytical and interoperable tools relevant for data reuse and integration.

We will especially focus on interoperability resources that support finding relations and mappings needed during data reuse in the fields also covered in Activity 1 (i.e. text to ontologies, ontological terms mappings, database identifiers and their resolvability, chemical structure relationships, hierarchical relationships (e.g. SNPs to genes to processes or gene expression to proteins to tissue localization). Our work plan will be:

  • Decide on the best places to make these available (e.g. TeSS, Galaxy, FAIRsharing and/or WorkflowHub).
  • Improve training material metadata via ontology terms (e.g. from EDAM) and explore the interlinking between the different training resources (e.g. by using Bioschemas). Wherever possible, provide approaches for the reuse of these training materials and explore mechanisms for assessing their validity over time.
  • Work with the bio.tools and FAIRsharing platforms on better, ideally automated, links between training material and the involved tools, aiming at reducing annotation needs and increasing findability. Whenever possible, use the same technology approach for providing links among the actual training repositories.
  • Identify specific gaps in existing training material on data reuse, aligned to the findings of the other Activities in the Interoperability Platform. Work with the Training Platform and engage relevant ELIXIR Communities to fill them. Generate guidelines of good data reuse practices, so they can be included in existing and upcoming materials.

Platform/Community: