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FAIR initiatives in the rare disease community #29

Open mroos opened 6 years ago

mroos commented 6 years ago

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FAIR initiatives in the rare disease community

Purpose of this document

The purpose of this document is to inform EU high level experts about emerging activity towards implementation of FAIR data principles, and the organisation thereof, in the European/international community of rare and undiagnosed disease stakeholders, particularly with respect to research infrastructure (RD-Connect, E-Rare, ELIXIR, BBMRI), patient organisations such as EURORDIS, and health care experts centres for rare diseases organised via ‘European Reference Networks’. The document is drafted in the context of the call for consultation: https://github.com/FAIR-Data-EG/consultation

Emerging FAIR activity in the rare disease domain

Synopsis

Significant activity is emerging within the rare disease community towards implementing FAIR data principles. The goal is to significantly increase the efficiency and potential of safely combining and exchanging various types of information across various types of data sources under various (complex) models of ownership. Activities include pilot projects and workshops supported by RD-Action, RD-Connect, ELIXIR, BBMRI, and national organisations. These are supported and monitored by a cross-project, global ‘rare disease linked data and ontology task force’. The next step is to organise and professionalise FAIR data services between rare disease stakeholders (e.g. rare disease expert centres organised in European Reference Networks) and solution providers (e.g. Orphanet, RD-Connect, ELIXIR, BBMRI, the Global Alliance for Genomics and Health). A group of operational leaders in the field (see contacts below) are currently exploring the concept of a GO-FAIR implementation network as a framework for this organisation. The group welcomes any further consultation with European Commission experts when desired.

Background and history

Rare diseases (RDs) are considered a challenge for Europe (Commission Communication on Europe’s challenges in the field of rare diseases, 2008), because they raise specific problems: poor recognition leading to diagnostic delay and inappropriate management and limited knowledge on natural history and pathophysiology leading to an insufficient development of new therapies. Around 50% of RD patients are considered un- or misdiagnosed, and only 5% of all RDs have a therapy available. To significantly improve these statistics for all patients with rare and undiagnosed conditions, an exponential increase in efficiency is required in all steps towards diagnosis and therapy. This includes the way data is handled at all stages. The low prevalence and the specificity of rare diseases make that a global, multi-stakeholder approach, intended to gather specific expertise and to build transversal, shared strategies is necessary. Data generation and sharing, and the ability to interrogate data across resources (under well defined conditions) are key and urgent elements of this strategy. With over 6000 diseases (source: Orphanet) and a high degree of diversity across institutes and countries, the data landscape for rare diseases is highly fragmented and heterogeneous. Data stewardship, the development of common semantic standards, and a federated approach are considered essential to achieve the desired increase in efficiency. For example, the Human Phenotype Ontology and the Orphanet Rare Diseases Ontology are already widely endorsed as milestones towards data interoperability, for which they acquired the status of ‘recognized resource’ by IRDiRC, the international consortium of rare disease research funding agencies. The application of the FAIR guiding principles as an IRDiRC recognized resource is in preparation. Progress towards the implementation of FAIR principles is further marked by pilot projects, workshops, and active discussion in fora organised by EURORDIS and RD-Action or online (e.g. [1,2]). A pilot study supported by RD-Connect, ELIXIR, and BBMRI tested interoperability services for enabling questions across biobanks and registries (an extensive report of the study recommendations is available through ELIXIR upon request). Numerous ‘Bring Your Own Data’ workshops were organised for hand-on experience with these techniques [3], in turn serving as inspiration for defining the FAIR guiding principles [4]. These activities were the basis for the organisation of a cross-project, multi-stakeholder ‘rare disease data linkage plan’ with additional support from RD-Connect, ELIXIR-EXCELERATE, ELIXIR, BBMRI, and patient organisation representatives. At the same time, ethical and legal constraints associated with access and reusability are addressed through collaborations between IRDiRC and the Global Alliance for Genomics and Health, and in organisations such as BBMRI. Automation of (re-)consent and privacy-preserving record linkage is under investigation. The currently running rare disease data linkage plan serves as a front-runner of a FAIR implementation service for the rare disease domain.

European Reference Networks for rare diseases

The recently started ‘European Reference Networks’ (ERNs) for rare diseases emphasize the importance of FAIR principles in the rare disease domain. The aim of ERNs is to make expertise of specific rare diseases, organised in expert centres across Europe (health care providers), available to rare disease patients across the European Union. Furthermore, they aim to stimulate translational use of different types of data in support of disease experts and new research. Requirements should be expected towards exchanging information about patient conditions between institutes in different European countries, including supporting (research) data. This will encompass the need to improve the quality of data at the expert centres in terms of the FAIR principles. In the rare disease domain, extending the adoption to FAIR principles to the valuable data held by patient organisations represents an additional important challenge. Therefore, ERNs have expressed a clear interest in FAIR principles as an aid to address part of their information needs.

Next steps

The rare disease data linkage plan is a starting point for further organising and professionalizing FAIR services in the rare disease domain. More fine-grained guidelines for the implementation of FAIR principles will need to be defined together with stakeholders, including lead representatives of ERNs, patient organisations such as EURORDIS, and solution providers such as Orphanet, ELIXIR and BBMRI. Therefore, a group of operational leaders in the rare disease domain (see contacts below) have recently started preparations towards the organisation of professional FAIR data services, using the GO-FAIR implementation network paradigm as a driver. The organisation is aimed to take effect in the fourth quarter of 2017. The seed organisers welcome any further questions towards the implementation of FAIR data principles in the rare disease domain and are available for further consultation by European Commission experts.

Contacts (Europe)

(In alphabetical order)

  • Virginie Bros-Facer, representative of the European organisation of rare disease patient organisation EURORDIS
  • Ronald Cornet, expert in ‘registration at the source’
  • David van Enckevort, technical leader rare disease data linkage plan
  • Victoria Hedley and Ana Rath, representatives of RD-Action, the organisation that supported the implementation of European Reference Networks and of the Orphanet nomenclature in health information systems.
  • Ana Rath and Marc Hanauer, representatives of Orphanet
  • Marco Roos*, co-lead of the ELIXIR rare disease community use case and co-lead of the rare disease data linkage plan, chair of the rare disease linked data and ontology task force.
  • Rachel Thompson, representative of RD-Connect
  • Mark Wilkinson, first author of the FAIR guiding principles

* For correspondence, please contact Marco Roos (m.roos@lumc.nl) and Petra van Overveld (P.G.M.van_Overveld@lumc.nl)

References

  1. Biocuration 2017 Conference Highlights, http://monarch-initiative.blogspot.nl/2017/04/biocuration-2017-conference-highlights.html
  2. Registries of Domain-Relevant Semantic Reference Models Help Bootstrap Interoperability in Domains with Fragmented Data Resources, Roos M., Wilkinson M. D. et al., Proceedings of the Semantic Web Applications and Tools for the Life Sciences, Amsterdam 2016, http://ceur-ws.org/Vol-1795/paper16.pdf
  3. The Organisation of Bring Your Own Data (BYOD) Workshops to Make Life Science Data Linkable at the Source, Jansen M, Carta C. et al., Proceedings of the Semantic Web Applications and Tools for the Life Sciences, Amsterdam 2016, http://ceur-ws.org/Vol-1795/paper18.pdf
  4. The FAIR Guiding Principles for scientific data management and stewardship, Wilkinson M. D. et al., Nature Scientific data, 2016, https://www.nature.com/articles/sdata201618