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medpie: an information extraction package for medical message board posts.
1University of Pennsylvania School of Medicine, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, PA 19104, USA.
Bioinformatics (Oxford, England)
|January 21, 2012
Summary
A new software package, medpie, aids in analyzing medical message boards. It extracts patient data on drugs, herbs, and adverse effects, improving data mining for health research.
Area of Science:
- Computational linguistics
- Bioinformatics
- Medical informatics
Background:
- Medical message boards are rich sources of patient-reported drug and herb experiences.
- Extracting structured data from these informal sources presents significant challenges.
Purpose of the Study:
- To develop a software package for processing medical message board data.
- To enable extraction of patient mentions and statistics for drugs, herbs, and adverse effects.
Main Methods:
- The medpie package includes modules for web-crawling, HTML cleaning, de-identification, and information extraction.
- Utilizes Python 2.6 or 2.7.
- Includes a controlled vocabulary for drugs, herbs, and adverse effect terms.
Main Results:
- Successfully developed medpie software for medical message board corpus preparation.
- Enables extraction of patient mentions and statistics related to drug and herb usage.
- Facilitates identification of adverse effects associated with medications and herbal remedies.
Conclusions:
- medpie provides a robust solution for preparing and analyzing medical message board data.
- The software facilitates the extraction of valuable patient-reported outcomes and safety information.
- A controlled vocabulary enhances the accuracy and consistency of information extraction.
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