Abstract
Abstract
Background
The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Diseases (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles.
Results
Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR.
Conclusions
Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them.
Funder
horizon 2020 research and innovation programme
Publisher
Springer Science and Business Media LLC
Subject
Computer Networks and Communications,Health Informatics,Computer Science Applications,Information Systems
Reference52 articles.
1. Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, et al. Comment: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. England. 2016;3:160018.
2. Set of Common Data Elements | EU RD Platform [Internet]. [cited 2021 Jul 8]. Available from: https://eu-rd-platform.jrc.ec.europa.eu/set-of-common-data-elements_en
3. Lopes P, Roos M. Bring your own data parties and beyond: make your data linkable to speed up rare disease research. Rare Dis Orphan Drugs [Internet]. 2014;1:21–4 Available from: http://rarejournal.org/index.php/rarejournal/article/download/69/93.
4. Roos M, Gray A, Waagmeester A, Thompson M, Kaliyaperumal R, Horst EVD, et al. Bring Your Own Data Workshops: A Mechanism to Aid Data Owners to Comply with Linked Data Best Practices. Proc 7th Int Work Semant Web Appl Tools Life Sci (SWAT4LS 2014). 2014;
5. DCMI: DCMI Metadata Terms [Internet]. [cited 2021 Dec 14]. Available from: https://www.dublincore.org/specifications/dublin-core/dcmi-terms/
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