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Querying semantic catalogues of biomedical databases

2023Journal article Open access
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dc.contributor.authorPereira, Arnaldo
dc.contributor.authorAlmeida, Joao Rafael
dc.contributor.authorLopes, Rui Pedro
dc.contributor.authorOliveira, José Luís
dc.date.accessioned2009-04-23T14:18:23Z
dc.date.available2009-04-23T14:18:23Z
dc.date.issued2023
dc.description.abstractBackground: Secondary use of health data is a valuable source of knowledge that boosts observational studies, leading to important discoveries in the medical and biomedical sciences. The fundamental guiding principle for performing a successful observational study is the research question and the approach in advance of executing a study. However, in multi-centre studies, finding suitable datasets to support the study is challenging, time-consuming, and sometimes impossible without a deep understanding of each dataset.Methods: We propose a strategy for retrieving biomedical datasets of interest that were semantically annotated, using an interface built by applying a methodology for transforming natural language questions into formal language queries. The advantages of creating biomedical semantic data are enhanced by using natural language interfaces to issue complex queries without manipulating a logical query language.Results: Our methodology was validated using Alzheimer's disease datasets published in a European platform for sharing and reusing biomedical data. We converted data to semantic information format using biomedical on-tologies in everyday use in the biomedical community and published it as a FAIR endpoint. We have considered natural language questions of three types: single-concept questions, questions with exclusion criteria, and multi-concept questions. Finally, we analysed the performance of the question-answering module we used and its limitations. The source code is publicly available at https:// bioinformatics-ua.github.io/BioKBQA/.Conclusion: We propose a strategy for using information extracted from biomedical data and transformed into a semantic format using open biomedical ontologies. Our method uses natural language to formulate questions to be answered by this semantic data without the direct use of formal query languages.en
dc.identifier.citationPereira, Arnaldo; Almeida, Joao Rafael; Lopes, Rui Pedro; Oliveira, Jose Luis. (2023). Querying semantic catalogues of biomedical databases. Journal of Biomedical Informatics. eISSN 1532-0480. 137, p. 1-12en
dc.identifier.doi10.1016/j.jbi.2022.104272
dc.identifier.eissn1532-0480
dc.identifier.issn1532-0464
dc.identifier.urihttp://hdl.handle.net/10198/1159
dc.language.isoengen
dc.peerreviewedyesen
dc.publisherElsevier
dc.subjectBiomedical dataen
dc.subjectKnowledge basesen
dc.subjectSemantic dataen
dc.subjectLinked dataen
dc.subjectInformation extraction
dc.subjectNatural language interfaces
dc.subjectQuestion answering
dc.titleQuerying semantic catalogues of biomedical databasesen
dc.typejournal article
dspace.entity.typePublication
oaire.citation.titleJournal of Biomedical Informatics
person.familyNameLopes
person.givenNameRui Pedro
person.identifier.ciencia-id8E14-54E4-4DB5
person.identifier.orcid0000-0002-9170-5078
rcaap.rightsopenAccessen
rcaap.typearticleen
relation.isAuthorOfPublicatione1e64423-0ec8-46ee-be96-33205c7c98a9
relation.isAuthorOfPublication.latestForDiscoverye1e64423-0ec8-46ee-be96-33205c7c98a9

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