Extracting Patient Data from Tables in Clinical Literature - Case Study on Extraction of BMI, Weight and Number of Patients

Nikola Milosevic, Cassie Gregson, Robert Hernandez, Goran Nenadic

2016

Abstract

Current biomedical text mining efforts are mostly focused on extracting information from the body of research articles. However, tables contain important information such as key characteristics of clinical trials. Here, we examine the feasibility of information extraction from tables. We focus on extracting data about clinical trial participants. We propose a rule-based method that decomposes tables into cell level structures and then extracts information from these structures. Our method performed with a F-measure of 83.3% for extraction of number of patients, 83.7% for extraction of patient’s body mass index and 57.75% for patient’s weight. These results are promising and show that information extraction from tables in biomedical literature is feasible.

Paper Citation

in Harvard Style

Milosevic N., Gregson C., Hernandez R. and Nenadic G. (2016). Extracting Patient Data from Tables in Clinical Literature - Case Study on Extraction of BMI, Weight and Number of Patients . In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, (BIOSTEC 2016) ISBN 978-989-758-170-0, pages 223-228. DOI: 10.5220/0005660102230228

in Bibtex Style

@conference{healthinf16,
author={Nikola Milosevic and Cassie Gregson and Robert Hernandez and Goran Nenadic},
title={Extracting Patient Data from Tables in Clinical Literature - Case Study on Extraction of BMI, Weight and Number of Patients},
booktitle={Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, (BIOSTEC 2016)},
year={2016},
pages={223-228},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005660102230228},
isbn={978-989-758-170-0},
}

in EndNote Style

TY - CONF
JO - Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, (BIOSTEC 2016)
TI - Extracting Patient Data from Tables in Clinical Literature - Case Study on Extraction of BMI, Weight and Number of Patients
SN - 978-989-758-170-0
AU - Milosevic N.
AU - Gregson C.
AU - Hernandez R.
AU - Nenadic G.
PY - 2016
SP - 223
EP - 228
DO - 10.5220/0005660102230228