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Relation Mining Experiments in the Pharmacogenomics Domain


Rinaldi, Fabio; Schneider, Gerold; Clematide, Simon (2012). Relation Mining Experiments in the Pharmacogenomics Domain. Journal of Biomedical Informatics, 45(5):851-861.

Abstract

The mutual interactions among genes, diseases, and drugs are at the heart of biomedical research, and are especially important for the pharmacological industry. The recent trend towards personalized medicine makes it increasingly relevant to be able to tailor drugs to specific genetic makeups. The pharmacogenetics and pharmacogenomics knowledge base (PharmGKB) aims at capturing relevant information about such interactions from several sources, including curation of the biomedical literature.

Advanced text mining tools which can support the process of manual curation are increasingly necessary in order to cope with the deluge of new published results. However, effective evaluation of those tools requires the availability of manually curated data as gold standard.

In this paper we discuss how the existing PharmGKB database can be used for such an evaluation task in a way similar to the usage of gold standard data derived from protein-protein interaction databases in one of the recent BioCreative shared tasks. Additionally, we present our own considerations and results on the feasibility and difficulty of such a task.

The mutual interactions among genes, diseases, and drugs are at the heart of biomedical research, and are especially important for the pharmacological industry. The recent trend towards personalized medicine makes it increasingly relevant to be able to tailor drugs to specific genetic makeups. The pharmacogenetics and pharmacogenomics knowledge base (PharmGKB) aims at capturing relevant information about such interactions from several sources, including curation of the biomedical literature.

Advanced text mining tools which can support the process of manual curation are increasingly necessary in order to cope with the deluge of new published results. However, effective evaluation of those tools requires the availability of manually curated data as gold standard.

In this paper we discuss how the existing PharmGKB database can be used for such an evaluation task in a way similar to the usage of gold standard data derived from protein-protein interaction databases in one of the recent BioCreative shared tasks. Additionally, we present our own considerations and results on the feasibility and difficulty of such a task.

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6 citations in Web of Science®
12 citations in Scopus®
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:06 Faculty of Arts > Institute of Computational Linguistics
Dewey Decimal Classification:000 Computer science, knowledge & systems
410 Linguistics
Date:2012
Deposited On:07 May 2012 09:06
Last Modified:05 Apr 2016 15:47
Publisher:Elsevier
ISSN:1532-0464
Additional Information:Special Issue on mining the pharmacogenomics literature
Publisher DOI:https://doi.org/10.1016/j.jbi.2012.04.014
Related URLs:http://www.journals.elsevier.com/journal-of-biomedical-informatics/special-issues/
http://www.sciencedirect.com/science/article/pii/S1532046412000676
Permanent URL: https://doi.org/10.5167/uzh-62070

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