TY - GEN
T1 - Transformation from Publications to Diabetes Ontology using Topic-based Assertion Discovery
AU - Nagulapati, Rohithkumar
AU - Chandrashekar, Mayanka
AU - Lee, Yugyung
N1 - Publisher Copyright:
© 2018 IEEE.
PY - 2018/7/16
Y1 - 2018/7/16
N2 - During the last decade, we have seen an explosive growth in the number of bio-medical publications. In this paper, we present an Assertion Discovery framework that aims to transform from PubMed publications (diabetes domain) to an ontology, called Diabetes Publication Ontology (DPO). The assertions in the DPO ontology were mapped and integrated with ones in existing diabetes ontologies. The Assertion Discovery framework consists of three main components: (i) Assertion Discovery, (ii) Assertion Alignment, and (iii) Assertion Integration. The proposed approach for ontology generation was based on Stanford CoreNLP for Natural Language Processing, OpenIE (Open Information Extraction) for relation extraction, LDA (Latent Dirichlet Allocation) for topic modeling, and OWL API for ontology generation on the Spark parallel engine. We presented a web-based application for searching diabetes publications as well as retrieving the assertions from the diabetes publications through the DPO ontology.
AB - During the last decade, we have seen an explosive growth in the number of bio-medical publications. In this paper, we present an Assertion Discovery framework that aims to transform from PubMed publications (diabetes domain) to an ontology, called Diabetes Publication Ontology (DPO). The assertions in the DPO ontology were mapped and integrated with ones in existing diabetes ontologies. The Assertion Discovery framework consists of three main components: (i) Assertion Discovery, (ii) Assertion Alignment, and (iii) Assertion Integration. The proposed approach for ontology generation was based on Stanford CoreNLP for Natural Language Processing, OpenIE (Open Information Extraction) for relation extraction, LDA (Latent Dirichlet Allocation) for topic modeling, and OWL API for ontology generation on the Spark parallel engine. We presented a web-based application for searching diabetes publications as well as retrieving the assertions from the diabetes publications through the DPO ontology.
KW - Assertion Discovery
KW - Diabetes ontologies
KW - Latent Dirichlet Allocation
KW - NLP
KW - Open Information Extraction
KW - PubMed
UR - http://www.scopus.com/inward/record.url?scp=85051001203&partnerID=8YFLogxK
U2 - 10.1109/ICHI-W.2018.00009
DO - 10.1109/ICHI-W.2018.00009
M3 - Conference contribution
AN - SCOPUS:85051001203
T3 - Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018
SP - 9
EP - 18
BT - Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 6th IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018
Y2 - 4 June 2018 through 7 June 2018
ER -