Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data
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 fi...
| Autores: | , , , , , , , , , , , , , , , , , , |
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| Tipo de documento: | artigo |
| Data de publicação: | 2022 |
| País: | España |
| Recursos: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositório: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/289592 |
| Acesso em linha: | http://hdl.handle.net/10261/289592 |
| Access Level: | Acceso aberto |
| Palavra-chave: | FAIR data Rare disease Interoperability Linked data Data transformation Semantic web Ontologies Common data elements Disease registries |
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Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry dataKaliyaperumal, RajaramWilkinson, Mark D.Alarcón-Moreno, PabloBenis, NirupamaCornet, RonaldDos Santos Vieira, BrunaMichel Dumontier, MichelBernabé, César HenriqueJacobsen, AnnikaLe Cornec, Clémence M. A.Prieto Godoy, MarioQueralt-Rosinach, NúriaSchultze Kool, Leo J.Swertz, Morris A.van Damme, PhilipVan der Velde, K. JoeriLalout, NawelZhang, ShuxinRoos, MarcoFAIR dataRare diseaseInteroperabilityLinked dataData transformationSemantic webOntologiesCommon data elementsDisease registriesBackground 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.BioMed CentralAlarcón-Moreno, Pablo [0000-0001-5974-589X]Dos Santos Vieira, Bruna [0000-0002-7245-9588]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202320232022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501http://hdl.handle.net/10261/289592reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésDepartamento de BiotecnologíaSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2895922026-05-22T06:33:51Z |
| dc.title.none.fl_str_mv |
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data |
| title |
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data |
| spellingShingle |
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data Kaliyaperumal, Rajaram FAIR data Rare disease Interoperability Linked data Data transformation Semantic web Ontologies Common data elements Disease registries |
| title_short |
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data |
| title_full |
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data |
| title_fullStr |
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data |
| title_full_unstemmed |
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data |
| title_sort |
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data |
| dc.creator.none.fl_str_mv |
Kaliyaperumal, Rajaram Wilkinson, Mark D. Alarcón-Moreno, Pablo Benis, Nirupama Cornet, Ronald Dos Santos Vieira, Bruna Michel Dumontier, Michel Bernabé, César Henrique Jacobsen, Annika Le Cornec, Clémence M. A. Prieto Godoy, Mario Queralt-Rosinach, Núria Schultze Kool, Leo J. Swertz, Morris A. van Damme, Philip Van der Velde, K. Joeri Lalout, Nawel Zhang, Shuxin Roos, Marco |
| author |
Kaliyaperumal, Rajaram |
| author_facet |
Kaliyaperumal, Rajaram Wilkinson, Mark D. Alarcón-Moreno, Pablo Benis, Nirupama Cornet, Ronald Dos Santos Vieira, Bruna Michel Dumontier, Michel Bernabé, César Henrique Jacobsen, Annika Le Cornec, Clémence M. A. Prieto Godoy, Mario Queralt-Rosinach, Núria Schultze Kool, Leo J. Swertz, Morris A. van Damme, Philip Van der Velde, K. Joeri Lalout, Nawel Zhang, Shuxin Roos, Marco |
| author_role |
author |
| author2 |
Wilkinson, Mark D. Alarcón-Moreno, Pablo Benis, Nirupama Cornet, Ronald Dos Santos Vieira, Bruna Michel Dumontier, Michel Bernabé, César Henrique Jacobsen, Annika Le Cornec, Clémence M. A. Prieto Godoy, Mario Queralt-Rosinach, Núria Schultze Kool, Leo J. Swertz, Morris A. van Damme, Philip Van der Velde, K. Joeri Lalout, Nawel Zhang, Shuxin Roos, Marco |
| author2_role |
author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Alarcón-Moreno, Pablo [0000-0001-5974-589X] Dos Santos Vieira, Bruna [0000-0002-7245-9588] Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] |
| dc.subject.none.fl_str_mv |
FAIR data Rare disease Interoperability Linked data Data transformation Semantic web Ontologies Common data elements Disease registries |
| topic |
FAIR data Rare disease Interoperability Linked data Data transformation Semantic web Ontologies Common data elements Disease registries |
| description |
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. |
| publishDate |
2022 |
| dc.date.none.fl_str_mv |
2022 2023 2023 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article http://purl.org/coar/resource_type/c_6501 |
| format |
article |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10261/289592 |
| url |
http://hdl.handle.net/10261/289592 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
Departamento de Biotecnología Sí |
| dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess |
| eu_rights_str_mv |
openAccess |
| dc.publisher.none.fl_str_mv |
BioMed Central |
| publisher.none.fl_str_mv |
BioMed Central |
| dc.source.none.fl_str_mv |
reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC instname:Consejo Superior de Investigaciones Científicas (CSIC) |
| instname_str |
Consejo Superior de Investigaciones Científicas (CSIC) |
| reponame_str |
DIGITAL.CSIC. Repositorio Institucional del CSIC |
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DIGITAL.CSIC. Repositorio Institucional del CSIC |
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1869404870423871488 |
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15.811543 |