Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective

Yuan Luo; Peter Szolovits

doi:10.1109/BIBM.2018.8621521

Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective

Yuan Luo, Peter Szolovits

Preventive Medicine

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Scopus citations

Abstract

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.

Original language	English (US)
Title of host publication	Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
Editors	Harald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	461-466
Number of pages	6
ISBN (Electronic)	9781538654880
DOIs	https://doi.org/10.1109/BIBM.2018.8621521
State	Published - Jan 21 2019
Event	2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain Duration: Dec 3 2018 → Dec 6 2018

Publication series

Name	Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

Conference

Conference	2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
Country/Territory	Spain
City	Madrid
Period	12/3/18 → 12/6/18

Keywords

Common Data Model
Computational Phenotyping
Lisp
Portable NLP
Relation Extraction

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics

Access to Document

10.1109/BIBM.2018.8621521

Cite this

Luo, Y., & Szolovits, P. (2019). Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective. In H. Schmidt, D. Griol, H. Wang, J. Baumbach, H. Zheng, Z. Callejas, X. Hu, J. Dickerson, & L. Zhang (Eds.), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 (pp. 461-466). Article 8621521 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2018.8621521

Luo, Yuan ; Szolovits, Peter. / Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. editor / Harald Schmidt ; David Griol ; Haiying Wang ; Jan Baumbach ; Huiru Zheng ; Zoraida Callejas ; Xiaohua Hu ; Julie Dickerson ; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. pp. 461-466 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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title = "Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective",

abstract = "This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.",

keywords = "Common Data Model, Computational Phenotyping, Lisp, Portable NLP, Relation Extraction",

author = "Yuan Luo and Peter Szolovits",

note = "Publisher Copyright: {\textcopyright} 2018 IEEE.; 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 ; Conference date: 03-12-2018 Through 06-12-2018",

year = "2019",

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doi = "10.1109/BIBM.2018.8621521",

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Luo, Y & Szolovits, P 2019, Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective. in H Schmidt, D Griol, H Wang, J Baumbach, H Zheng, Z Callejas, X Hu, J Dickerson & L Zhang (eds), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018., 8621521, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Institute of Electrical and Electronics Engineers Inc., pp. 461-466, 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018, Madrid, Spain, 12/3/18. https://doi.org/10.1109/BIBM.2018.8621521

Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective. / Luo, Yuan; Szolovits, Peter.
Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. ed. / Harald Schmidt; David Griol; Haiying Wang; Jan Baumbach; Huiru Zheng; Zoraida Callejas; Xiaohua Hu; Julie Dickerson; Le Zhang. Institute of Electrical and Electronics Engineers Inc., 2019. p. 461-466 8621521 (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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AU - Szolovits, Peter

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N2 - This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.

AB - This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.

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A2 - Baumbach, Jan

A2 - Zheng, Huiru

A2 - Callejas, Zoraida

A2 - Hu, Xiaohua

A2 - Dickerson, Julie

A2 - Zhang, Le

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

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Luo Y, Szolovits P. Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective. In Schmidt H, Griol D, Wang H, Baumbach J, Zheng H, Callejas Z, Hu X, Dickerson J, Zhang L, editors, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Institute of Electrical and Electronics Engineers Inc. 2019. p. 461-466. 8621521. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018). doi: 10.1109/BIBM.2018.8621521

Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective

Abstract

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Keywords

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