Data Mining in Biomedicine Using Ontologies (Bioinformatics by Mihail Popescu, Dong Xu

By Mihail Popescu, Dong Xu

An ontology is a suite of vocabulary phrases with explicitly acknowledged meanings and family with different phrases. This source introduces researchers to the advancements in bio-ontologies. It offers the theoretical foundations and examples of ontologies, in addition to purposes of ontologies in biomedicine, from molecular degrees to scientific degrees.

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Hersh, “A Survey of Current Work in Biomedical Text Mining,” Brief Bioinform, Vol. 6, No. 1, 2005, pp. 57–71. , and D. Schomburg, “Concept-Based Annotation of Enzyme Classes,” Bioinformatics, Vol. 21, No. 9, 2005, pp. 2059–2066. Yang, J. , “An Integrated Database-Pipeline System for Studying Single Nucleotide Polymorphisms and Diseases,” BMC Bioinformatics, Vol. 9, Supplement 12, 2008, pp. S19. , “BioMeKe: An Ontology-Based Biomedical Knowledge Extraction System Devoted to Transcriptome Analysis,” Stud Health Technol Inform, Vol.

Much of this disagreement arises from the diversity of the ontologies and their applications 18 Introduction to Ontologies outlined in this chapter. Tension also arises from the computer-science use of the word and how it differs from the philosophical use. Whether they are directly describing entities in reality or the information about entities, ontologies are resources that contain computationally accessible, structured knowledge. Such knowledge can be accessed and applied in many research scenarios, such as the data-mining applications described in this book.

Other psychological research supports asymmetric assessment [6, 22] and justifies the selection of a referent, even when there is not an explicit referent. Different methods have been used to implicitly determine the referent in addition to selecting the object with more salient features [53]. In some cases, there may be a natural reference object or indicator [45]. In others, the degree of an object’s prototypicality [22] or informativeness [6] may be used to determine which object serves as the referent.

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