title: Generation of open biomedical datasets through ontology-driven transformation and integration processes.
abstract: BACKGROUND
  Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natural technological space for data integration and exploitation by generating content readable by machines. Linked Open Data is a Semantic Web initiative that promotes the publication and sharing of data in machine readable semantic formats.
  
  
  METHODS
  We present an approach for the transformation and integration of heterogeneous biomedical data with the objective of generating open biomedical datasets in Semantic Web formats. The transformation of the data is based on the mappings between the entities of the data schema and the ontological infrastructure that provides the meaning to the content. Our approach permits different types of mappings and includes the possibility of defining complex transformation patterns. Once the mappings are defined, they can be automatically applied to datasets to generate logically consistent content and the mappings can be reused in further transformation processes.
  
  
  RESULTS
  The results of our research are (1) a common transformation and integration process for heterogeneous biomedical data; (2) the application of Linked Open Data principles to generate interoperable, open, biomedical datasets; (3) a software tool, called SWIT, that implements the approach. In this paper we also describe how we have applied SWIT in different biomedical scenarios and some lessons learned.
  
  
  CONCLUSIONS
  We have presented an approach that is able to generate open biomedical repositories in Semantic Web formats. SWIT is able to apply the Linked Open Data principles in the generation of the datasets, so allowing for linking their content to external repositories and creating linked open datasets. SWIT datasets may contain data from multiple sources and schemas, thus becoming integrated datasets.
authors.affiliation: Departamento de Informática y Sistemas, Universidad de Murcia, IMIB-Arrixaca, Murcia, 30071, Spain.
authors.forename: María Del
authors.initials: MD
authors.lastname: Carmen Legaz-García
authors.affiliation: Institute of Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, 8036, Austria.
authors.forename: José Antonio
authors.initials: JA
authors.lastname: Miñarro-Giménez
authors.affiliation: Departamento de Informática y Sistemas, Universidad de Murcia, IMIB-Arrixaca, Murcia, 30071, Spain.
authors.forename: Marcos
authors.initials: M
authors.lastname: Menárguez-Tortosa
authors.affiliation: Departamento de Informática y Sistemas, Universidad de Murcia, IMIB-Arrixaca, Murcia, 30071, Spain. jfernand@um.es.
authors.forename: Jesualdo Tomás
authors.initials: JT
authors.lastname: Fernández-Breis
mesh_terms: D064229:Biological Ontologies; D035843:Biomedical Research; D016208:Databases, Factual; D057286:Electronic Health Records; D006801:Humans; D020407:Internet; D012660:Semantics
keywords: Biomedical open data; Data transformation; Ontologies; Semantic web