TY - GEN
T1 - Constructing dynamic ontologies from biomedical publications
AU - Nagabhushan, Megha
AU - Nagulapati, Rohithkumar
AU - Chandrashekar, Mayanka
AU - Lee, Yugyung
N1 - Publisher Copyright:
© 2017 IEEE.
PY - 2017/12/15
Y1 - 2017/12/15
N2 - In recent years, there has been explosive growth in the amount of biomedical publications. In this paper, we propose a semantic framework that aims to automatically generate an ontology by extracting assertions and topics from multiple free-text scientific publications in PubMed. The pipeline approach for knowledge discovery and ontology generation in the proposed framework has been implemented on the Spark parallel engine based on the Stanford CoreNLP for Natural Language Processing, TF-IDF (Term Frequency Inverse Document Frequency) for feature extraction, OpenIE (Open Information Extraction) for relation extraction, K-Means clustering for topic discovery and OWL API for ontology generation. We have shown that the ontology generated may be very effective in biomedical applications (such as paper search and summarization) with scientific publications.
AB - In recent years, there has been explosive growth in the amount of biomedical publications. In this paper, we propose a semantic framework that aims to automatically generate an ontology by extracting assertions and topics from multiple free-text scientific publications in PubMed. The pipeline approach for knowledge discovery and ontology generation in the proposed framework has been implemented on the Spark parallel engine based on the Stanford CoreNLP for Natural Language Processing, TF-IDF (Term Frequency Inverse Document Frequency) for feature extraction, OpenIE (Open Information Extraction) for relation extraction, K-Means clustering for topic discovery and OWL API for ontology generation. We have shown that the ontology generated may be very effective in biomedical applications (such as paper search and summarization) with scientific publications.
UR - https://www.scopus.com/pages/publications/85046001049
U2 - 10.1109/BIBM.2017.8217715
DO - 10.1109/BIBM.2017.8217715
M3 - Conference contribution
AN - SCOPUS:85046001049
T3 - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
SP - 581
EP - 584
BT - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
A2 - Yoo, Illhoi
A2 - Zheng, Jane Huiru
A2 - Gong, Yang
A2 - Hu, Xiaohua Tony
A2 - Shyu, Chi-Ren
A2 - Bromberg, Yana
A2 - Gao, Jean
A2 - Korkin, Dmitry
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Y2 - 13 November 2017 through 16 November 2017
ER -