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The challenge of managing the evolution of genomics data over time: a conceptual model-based approach

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The challenge of managing the evolution of genomics data over time: a conceptual model-based approach

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dc.contributor.author García-Simón, Alberto es_ES
dc.contributor.author Costa-Sánchez, Mireia es_ES
dc.contributor.author León-Palacio, Ana es_ES
dc.contributor.author Pastor López, Oscar es_ES
dc.date.accessioned 2023-07-21T18:03:55Z
dc.date.available 2023-07-21T18:03:55Z
dc.date.issued 2022-11-09 es_ES
dc.identifier.issn 1471-2105 es_ES
dc.identifier.uri http://hdl.handle.net/10251/195316
dc.description.abstract [EN] Background Precision medicine is a promising approach that has revolutionized disease prevention and individualized treatment. The DELFOS oracle is a model-driven genomics platform that aids clinicians in identifying relevant variations that are associated with diseases. In its previous version, the DELFOS oracle did not consider the high degree of variability of genomics data over time. However, changes in genomics data have had a profound impact on clinicians¿ work and pose the need for changing past, present, and future clinical actions. Therefore, our objective in this work is to consider changes in genomics data over time in the DELFOS oracle. Methods Our objective has been achieved through three steps. First, we studied the characteristics of each database from which the DELFOS oracle extracts data. Second, we characterized which genomics concepts of the conceptual schema that supports the DELFOS oracle change over time. Third, we updated the DELFOS Oracle so that it can manage the temporal dimension. To validate our approach, we carried out a use case to illustrate how the new version of the DELFOS oracle handles the temporal dimension. Results Three events can change genomics data, namely, the addition of a new variation, the addition of a new link between a variation and a phenotype, and the update of a link between a variation and a phenotype. These events have been linked to the entities of the conceptual model that are affected by them. Finally, a new version of the DELFOS oracle that can deal with the temporal dimension has been implemented. Conclusion Huge amounts of genomics data that is associated with diseases change over time, impacting patients¿ diagnosis and treatment. Including this information in the DELFOS oracle added an extra layer of complexity, but using a model-driven based approach mitigated the cost of implementing the needed changes. The new version handles the temporal dimension appropriately and eases clinicians¿ work. es_ES
dc.description.sponsorship This work has been developed with the financial support of the Generalitat Valenciana and the Valencian Innovation Agency under the projects MICIN/AEI/ 10.13039/501100011033, PDC2021-121243-I00, CIPROM/2021/023, 2021/AP2021-05, ACIF/2021/117, and INNEST/2021/57 and co-financed with ERDF. It also has been supported by the Polytechnic University of Valencia through grant 20220366. es_ES
dc.language Inglés es_ES
dc.publisher Springer (Biomed Central Ltd.) es_ES
dc.relation.ispartof BMC Bioinformatics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Bioinformatics es_ES
dc.subject Temporal dimension es_ES
dc.subject Conceptual models es_ES
dc.subject SILE method es_ES
dc.subject DELFOS oracle es_ES
dc.subject.classification LENGUAJES Y SISTEMAS INFORMATICOS es_ES
dc.title The challenge of managing the evolution of genomics data over time: a conceptual model-based approach es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12859-022-04944-z es_ES
dc.relation.projectID info:eu-repo/grantAgreement/AGENCIA ESTATAL DE INVESTIGACION//PDC2021-121243-I00//PLATAFORMA DELFOS: SISTEMA DE INFORMACIÓN PARA LA GESTIÓN DE VARIACIONES GENOMICAS/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/UPV//20220366/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/GVA//CIPROM%2F2021%2F023/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/AVI//INNEST%2F2021%2F57/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/CIUCSD//ACIF%2F2021%2F117/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Escola Tècnica Superior d'Enginyeria Informàtica es_ES
dc.description.bibliographicCitation García-Simón, A.; Costa-Sánchez, M.; León-Palacio, A.; Pastor López, O. (2022). The challenge of managing the evolution of genomics data over time: a conceptual model-based approach. BMC Bioinformatics. 23:1-32. https://doi.org/10.1186/s12859-022-04944-z es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/s12859-022-04944-z es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 32 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 23 es_ES
dc.identifier.pmid 36352353 es_ES
dc.identifier.pmcid PMC9648044 es_ES
dc.relation.pasarela S\477202 es_ES
dc.contributor.funder Generalitat Valenciana es_ES
dc.contributor.funder AGENCIA ESTATAL DE INVESTIGACION es_ES
dc.contributor.funder European Regional Development Fund es_ES
dc.contributor.funder Agència Valenciana de la Innovació es_ES
dc.contributor.funder Universitat Politècnica de València es_ES
dc.contributor.funder Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital, Generalitat Valenciana es_ES
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