TY - JOUR
T1 - Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data
AU - Kaliyaperumal, Rajaram
AU - Wilkinson, Mark D.
AU - Moreno, Pablo Alarcón
AU - Benis, Nirupama
AU - Cornet, Ronald
AU - Dos Santos Vieira, Bruna
AU - Dumontier, Michel
AU - Bernabé, C. sar Henrique
AU - Jacobsen, Annika
AU - le Cornec, Clémence M. A.
AU - Godoy, Mario Prieto
AU - Queralt-Rosinach, N. ria
AU - Schultze Kool, Leo J.
AU - Swertz, Morris A.
AU - van Damme, Philip
AU - van der Velde, K. Joeri
AU - Lalout, Nawel
AU - Zhang, Shuxin
AU - Roos, Marco
N1 - Funding Information: All authors with the exception of MD are supported by the funding from the European Union’s Horizon 2020 research and innovation programme under the EJP RD COFUND-EJP N° 825575. Funding for MD is provided by the European Union’s Horizon 2020 research and innovation programme under grant agreement N° 824087. Funding Information: We would like to express our gratitude to the Duchenne Parent Project in the Netherlands for allowing the code for portions of their FAIR transformation solution to be open source and included in the CDE in a Box. This solution was specifically commissioned and developed for their patient-led registry - The Duchenne Data Platform - which had undergone a FAIRification process in 2021. Their generosity stems from their continuous belief in FAIR as a new paradigm for optimising data visiting and analysis and as a result, pledged to support others in their own FAIR data endeavours. We thank Foundation 29, the software developers of the Duchenne Data Platform, for their technical expertise and positive collaboration during the development of the Duchenne FAIR project. We furthermore wish to thank Leo Schultze Kool for helping us start the CDE modelling process for the FAIRification of the VASCA registry, his support for FAIR implementation of registries, and valuable feedback on the interpretation of CDEs from a clinical perspective, and Peter-Bram ?t Hoen for his continuous active support of our efforts. Finally, the authors acknowledge the support of Ana Rath and Franz Schaefer in the development of a conceptual framework for the EJP RD Virtual Platform. Publisher Copyright: © 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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.
KW - Common data elements
KW - Data transformation
KW - Disease registries
KW - FAIR data
KW - Interoperability
KW - Linked data
KW - Ontologies
KW - Rare disease
KW - Semantic web
UR - http://www.scopus.com/inward/record.url?scp=85126649363&partnerID=8YFLogxK
U2 - https://doi.org/10.1186/s13326-022-00264-6
DO - https://doi.org/10.1186/s13326-022-00264-6
M3 - Article
C2 - 35292119
SN - 2041-1480
VL - 13
SP - 9
JO - Journal of Biomedical Semantics
JF - Journal of Biomedical Semantics
IS - 1
M1 - 9
ER -