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MeSHDD: Literature-based drug-drug similarity for drug repositioning
Objective: Drug repositioning is a promising methodology for reducing the cost and duration of the drug discovery pipeline. We sought to develop a computational repositioning method leveraging annotations in the literature, such as Medical Subject Heading (MeSH) terms. Methods: We developed software...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391732/ https://www.ncbi.nlm.nih.gov/pubmed/27678460 http://dx.doi.org/10.1093/jamia/ocw142 |
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author | Brown, Adam S Patel, Chirag J |
author_facet | Brown, Adam S Patel, Chirag J |
author_sort | Brown, Adam S |
collection | PubMed |
description | Objective: Drug repositioning is a promising methodology for reducing the cost and duration of the drug discovery pipeline. We sought to develop a computational repositioning method leveraging annotations in the literature, such as Medical Subject Heading (MeSH) terms. Methods: We developed software to determine significantly co-occurring drug-MeSH term pairs and a method to estimate pair-wise literature-derived distances between drugs. Results We found that literature-based drug-drug similarities predicted the number of shared indications across drug-drug pairs. Clustering drugs based on their similarity revealed both known and novel drug indications. We demonstrate the utility of our approach by generating repositioning hypotheses for the commonly used diabetes drug metformin. Conclusion: Our study demonstrates that literature-derived similarity is useful for identifying potential repositioning opportunities. We provided open-source code and deployed a free-to-use, interactive application to explore our database of similarity-based drug clusters (available at http://apps.chiragjpgroup.org/MeSHDD/). |
format | Online Article Text |
id | pubmed-5391732 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-53917322017-04-21 MeSHDD: Literature-based drug-drug similarity for drug repositioning Brown, Adam S Patel, Chirag J J Am Med Inform Assoc Brief Communication Objective: Drug repositioning is a promising methodology for reducing the cost and duration of the drug discovery pipeline. We sought to develop a computational repositioning method leveraging annotations in the literature, such as Medical Subject Heading (MeSH) terms. Methods: We developed software to determine significantly co-occurring drug-MeSH term pairs and a method to estimate pair-wise literature-derived distances between drugs. Results We found that literature-based drug-drug similarities predicted the number of shared indications across drug-drug pairs. Clustering drugs based on their similarity revealed both known and novel drug indications. We demonstrate the utility of our approach by generating repositioning hypotheses for the commonly used diabetes drug metformin. Conclusion: Our study demonstrates that literature-derived similarity is useful for identifying potential repositioning opportunities. We provided open-source code and deployed a free-to-use, interactive application to explore our database of similarity-based drug clusters (available at http://apps.chiragjpgroup.org/MeSHDD/). Oxford University Press 2017-05 2016-09-27 /pmc/articles/PMC5391732/ /pubmed/27678460 http://dx.doi.org/10.1093/jamia/ocw142 Text en © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Brief Communication Brown, Adam S Patel, Chirag J MeSHDD: Literature-based drug-drug similarity for drug repositioning |
title | MeSHDD: Literature-based drug-drug similarity for drug repositioning |
title_full | MeSHDD: Literature-based drug-drug similarity for drug repositioning |
title_fullStr | MeSHDD: Literature-based drug-drug similarity for drug repositioning |
title_full_unstemmed | MeSHDD: Literature-based drug-drug similarity for drug repositioning |
title_short | MeSHDD: Literature-based drug-drug similarity for drug repositioning |
title_sort | meshdd: literature-based drug-drug similarity for drug repositioning |
topic | Brief Communication |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391732/ https://www.ncbi.nlm.nih.gov/pubmed/27678460 http://dx.doi.org/10.1093/jamia/ocw142 |
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