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Year:: 2017
Contributor:: Superdock, Michael (creator); Uzun, Alper (creator); Sarkar, Indra Neil (creator); Padbury, James (creator)
Genre:: posters
Subject:: Machine learning; Genetics; Premature infants

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Description

Abstract:: Manual curation of primary literature is a common, time-intensive approach for identifying genes associated with a disease of interest. This project aims to minimize the workload of manual curation for genetic studies by semi-automating the curation process. A computational pipeline was created using text-mining techniques to extract genetic data and other distinguishing features from articles. Five predictive models were trained on these features to classify articles as "considered" or "not considered" for later review by curators. The models were evaluated against manual classifications of curated papers from the Database for Preeclampsia (dbPEC) and the Database for Preterm Birth (dbPTB). A Random Forest classifier performed best for both datasets, with an AUC of 0.825 for dbPEC articles and an AUC of 0.918 for dbPTB articles. This classifier had results consistent with a 32.5% workload reduction for the curation of dbPEC articles and a 79.6% workload reduction for the curation of dbPTB articles, while still capturing over 95% of validated genes.
Notes:: Scholarly concentration: Biomedical Informatics; All rights reserved

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Citation

Superdock, Michael, Uzun, Alper, Sarkar, Indra Neil, et al., "Automated Text Mining to Improve the Curation of Genes Associated with Complex Disease" (2017). Warren Alpert Medical School Academic Symposium. Brown Digital Repository. Brown University Library. https://repository.library.brown.edu/studio/item/bdr:698122/

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Warren Alpert Medical School Academic Symposium

The Warren Alpert Medical School Academic Symposium is an annual event at Warren Alpert Medical School of Brown University that provides Year II medical students a venue to present their summer research in a poster format. Participation in the Symposium …
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Automated Text Mining to Improve the Curation of Genes Associated with Complex Disease