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On how to generalize specie-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome

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On how to generalize specie-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome

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dc.contributor.author García-Simón, Alberto es_ES
dc.contributor.author Casamayor Rodenas, Juan Carlos es_ES
dc.date.accessioned 2022-06-09T18:07:06Z
dc.date.available 2022-06-09T18:07:06Z
dc.date.issued 2021-09-30 es_ES
dc.identifier.issn 1471-2105 es_ES
dc.identifier.uri http://hdl.handle.net/10251/183165
dc.description.abstract [EN] Background Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and idiosyncrasy of genomic use cases mean that conceptual modeling techniques are used to generate conceptual schemes that focus on too specific scenarios (i.e., they are species-specific conceptual schemes). Our research group developed two different conceptual schemes. The first one is the Conceptual Schema of the Human Genome, which is intended to improve Precision Medicine and genetic diagnosis. The second one is the Conceptual Schema of the Citrus Genome, which is intended to identify the genetic cause of relevant phenotypes in the agri-food field. Methods Our two conceptual schemes have been ontologically compared to identify their similarities and differences. Based on this comparison, several changes have been performed in the Conceptual Schema of the Human Genome in order to obtain the first version of a species-independent Conceptual Schema of the Genome. Identifying the different genome information items used in each genomic case study has been essential in achieving our goal. The changes needed to provide an expanded, more generic version of the Conceptual Schema of the Human Genome are analyzed and discussed. Results This work presents a new CS called the Conceptual Schema of the Genome that is ready to be adapted to any specific working genome-based context (i.e., species-independent). Conclusion The generated Conceptual Schema of the Genome works as a global, generic element from which conceptual views can be created in order to work with any specific species. This first working version can be used in the human use case, in the citrus use case, and, potentially, in more use cases of other species. es_ES
dc.description.sponsorship This work was supported by the Spanish Ministry of Science and Innovation through Project DataME (ref: TIN2016-80811-P) and the Generalitat Valenciana through project GISPRO (PROMETEO/2018/176). 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 Conceptual modeling es_ES
dc.subject Genomics es_ES
dc.subject Bioinformatics es_ES
dc.subject.classification LENGUAJES Y SISTEMAS INFORMATICOS es_ES
dc.title On how to generalize specie-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12859-021-04237-x es_ES
dc.relation.projectID info:eu-repo/grantAgreement/AGENCIA ESTATAL DE INVESTIGACION//TIN2016-80811-P//UN METODO DE PRODUCCION DE SOFTWARE DIRIGIDO POR MODELOS PARA EL DESARROLLO DE APLICACIONES BIG DATA/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/GENERALITAT VALENCIANA//PROMETEO%2F2018%2F176//GISPRO-GENOMIC INFORMATION SYSTEMS PRODUCTION/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació es_ES
dc.description.bibliographicCitation García-Simón, A.; Casamayor Rodenas, JC. (2021). On how to generalize specie-specific conceptual schemes to generate a species-independent Conceptual Schema of the Genome. BMC Bioinformatics. 22(13):1-26. https://doi.org/10.1186/s12859-021-04237-x es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/s12859-021-04237-x es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 26 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 22 es_ES
dc.description.issue 13 es_ES
dc.identifier.pmid 34592923 es_ES
dc.identifier.pmcid PMC8482561 es_ES
dc.relation.pasarela S\446565 es_ES
dc.contributor.funder GENERALITAT VALENCIANA es_ES
dc.contributor.funder AGENCIA ESTATAL DE INVESTIGACION es_ES
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