Yehoshua Perl

Publication Activity (10 Years)

Years Active: 1975-2024
Publications (10 Years): 46

Top Venues

J. Biomed. Informatics

BIBM

AMIA

BMC Medical Informatics Decis. Mak.

Publications

Mahshad Koohi H. Dehkordi, Navya Martin Kollapally, Yehoshua Perl, James Geller, Fadi P. Deek, Hao Liu, Vipina Kuttichi Keloth, Gai Elhanan, Andrew J. Einstein
Skimming of Electronic Health Records Highlighted by an Interface Terminology Curated with Machine Learning Mining. BIOSTEC (2) (2024)
Michael Halper, Larisa N. Soldatova, Mathias Brochhausen, Fatima Sabiu Maikore, Christopher Ochs, Yehoshua Perl
Guidelines for the reuse of ontology content. Appl. Ontology 18 (1) (2023)
Ling Zheng, Yehoshua Perl, Yongqun He
Big knowledge visualization of the COVID-19 CIDO ontology evolution. BMC Medical Informatics Decis. Mak. 23 (1) (2023)
Mahshad Koohi H. Dehkordi, Andrew J. Einstein, Shuxin Zhou, Gai Elhanan, Yehoshua Perl, Vipina Kuttichi Keloth, James Geller, Hao Liu
Using annotation for computerized support for fast skimming of cardiology electronic health record notes. BIBM (2023)
Vipina Kuttichi Keloth, Shuxin Zhou, Luke Lindemann, Ling Zheng, Gai Elhanan, Andrew J. Einstein, James Geller, Yehoshua Perl
Mining of EHR for interface terminology concepts for annotating EHRs of COVID patients. BMC Medical Informatics Decis. Mak. 23 (1) (2023)
Yongqun He, Hong Yu, Anthony Huffman, Asiyah Yu Lin, Darren A. Natale, John Beverley, Ling Zheng, Yehoshua Perl, Zhigang Wang, Yingtong Liu, Edison Ong, Yang Wang, Philip Huang, Long Tran, Jinyang Du, Zalan Shah, Easheta Shah, Roshan Desai, Hsin-Hui Huang, Yujia Tian, Eric Merrell, William D. Duncan, Sivaram Arabandi, Lynn M. Schriml, Jie Zheng, Anna Maria Masci, Liwei Wang, Hongfang Liu, Fatima Zohra Smaili, Robert Hoehndorf, Zoë May Pendlington, Paola Roncaglia, Xianwei Ye, Jiangan Xie, Yi-Wei Tang, Xiaolin Yang, Suyuan Peng, Luxia Zhang, Luonan Chen, Junguk Hur, Gilbert S. Omenn, Brian D. Athey, Barry Smith
A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. J. Biomed. Semant. 13 (1) (2022)
Ling Zheng, Yehoshua Perl, Yongqun He, Christopher Ochs, James Geller, Hao Liu, Vipina Kuttichi Keloth
Visual comprehension and orientation into the COVID-19 CIDO ontology. J. Biomed. Informatics 120 (2021)
Vipina Kuttichi Keloth, Shuxin Zhou, Andrew J. Einstein, Gai Elhanan, Yan Chen, James Geller, Yehoshua Perl
Generating Training Data for Concept-Mining for an 'Interface Terminology' Annotating Cardiology EHRs. BIBM (2020)
Ling Zheng, Hua Min, Yan Chen, Vipina Kuttichi Keloth, James Geller, Yehoshua Perl, George Hripcsak
Outlier concepts auditing methodology for a large family of biomedical ontologies. BMC Medical Informatics Decis. Mak. (10) (2020)
Hao Liu, Yehoshua Perl, James Geller
Concept placement using BERT trained by transforming and summarizing biomedical ontology structure. J. Biomed. Informatics 112 (2020)
Vipina Kuttichi Keloth, Shuxin Zhou, Luke Lindemann, Gai Elhanan, Andrew J. Einstein, James Geller, Yehoshua Perl
Mining Concepts for a COVID Interface Terminology for Annotation of EHRs. IEEE BigData (2020)
Ling Zheng, Zhe He, Duo Helen Wei, Vipina Kuttichi Keloth, Jung-Wei Fan, Luke Lindemann, Xinxin Zhu, James J. Cimino, Yehoshua Perl
A review of auditing techniques for the Unified Medical Language System. J. Am. Medical Informatics Assoc. 27 (10) (2020)
Ling Zheng, Yan Chen, Hua Min, P. Lloyd Hildebrand, Hao Liu, Michael Halper, James Geller, Sherri de Coronado, Yehoshua Perl
Missing lateral relationships in top-level concepts of an ontology. BMC Medical Informatics Decis. Mak. (10) (2020)
Ling Zheng, Hao Liu, Yehoshua Perl, James Geller
Training Convolutional Neural Network with Terminology Summarization Data Improves SNOMED CT Enrichment. AMIA (2019)
Hasan Yumak, Ling Zheng, Ling Chen, Michael Halper, Yehoshua Perl, Gareth Owen
Quality assurance of complex ChEBI concepts based on number of relationship types. Appl. Ontology 14 (3) (2019)
Hao Liu, Yehoshua Perl, James Geller
Transfer Learning from BERT to Support Insertion of New Concepts into SNOMED CT. AMIA (2019)
James Geller, Yehoshua Perl, Licong Cui, Guo-Qiang Zhang
Quality assurance of biomedical terminologies and ontologies. J. Biomed. Informatics 86 (2018)
Hao Liu, James Geller, Michael Halper, Yehoshua Perl
Using Convolutional Neural Networks to Support Insertion of New Concepts into SNOMED CT. AMIA (2018)
Ling Zheng, Yan Chen, Yehoshua Perl, Michael Halper, James Geller, Sherri de Coronado
Quality Assurance of Concept Roles in the National Cancer Institute thesaurus. BIBM (2018)
Hao Liu, Ling Zheng, Yehoshua Perl, James Geller, Gai Elhanan
Can a Convolutional Neural Network Support Auditing of NCI Thesaurus Neoplasm Concepts? ICBO (2018)
Hao Liu, P. Lloyd Hildebrand, Yehoshua Perl, James Geller
Enrichment of SNOMED CT Ophthalmology Component to Support EHR Coding. BIBM (2018)
Hao Liu, Ling Chen, Ling Zheng, Yehoshua Perl, James Geller
A Quality Assurance Methodology for ChEBI Ontology Focusing on Uncommonly Modeled Concepts. ICBO (2018)
Michael Halper, Christopher Ochs, Yehoshua Perl, Sivaram Arabandi, Mark A. Musen
Quality Assurance of Ontology Content Reuse. ICBO (2018)
Ling Zheng, Hao Liu, Yehoshua Perl, James Geller, Christopher Ochs, James T. Case
Overlapping Complex Concepts Have More Commission Errors, Especially in Intensive Terminology Auditing. AMIA (2018)
Ling Zheng, Yan Chen, Gai Elhanan, Yehoshua Perl, James Geller, Christopher Ochs
Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies. J. Biomed. Informatics 83 (2018)
Christopher Ochs, James Geller, Yehoshua Perl
Applications of the Ontology Abstraction Framework. AMIA (2017)
Ling Zheng, Yehoshua Perl, Gai Elhanan, Christopher Ochs, James Geller, Michael Halper
Summarizing an Ontology: A "Big Knowledge" Coverage Approach. MedInfo (2017)
Ling Zheng, Hua Min, Yehoshua Perl, James Geller
Discovering additional complex NCIt gene concepts with high error rate. BIBM (2017)
Zhe He, Yehoshua Perl, Gai Elhanan, Yan Chen, James Geller, Jiang Bian
Auditing the assignments of top-level semantic types in the UMLS semantic network to UMLS concepts. BIBM (2017)
Christopher Ochs, James Geller, Mark A. Musen, Yehoshua Perl
Real Time Summarization and Visualization of Ontology Change in Protégé. VOILA@ISWC (2017)
Ling Zheng, Hua Min, Yan Chen, Julia Xu, James Geller, Yehoshua Perl
Auditing National Cancer Institute thesaurus neoplasm concepts in groups of high error concentration. Appl. Ontology 12 (2) (2017)
Ling Zheng, Christopher Ochs, James Geller, Hao Liu, Yehoshua Perl, Sherri de Coronado
Multi-layer Big Knowledge Visualization Scheme for Comprehending Neoplasm Ontology Content. ICBK (2017)
Christopher Ochs, James T. Case, Yehoshua Perl
Analyzing structural changes in SNOMED CT's Bacterial infectious diseases using a visual semantic delta. J. Biomed. Informatics 67 (2017)
Christopher Ochs, Yehoshua Perl, James Geller, Sivaram Arabandi, Tania Tudorache, Mark A. Musen
An empirical analysis of ontology reuse in BioPortal. J. Biomed. Informatics 71 (2017)
Gai Elhanan, Christopher Ochs, José L. V. Mejino Jr., Hao Liu, Christopher J. Mungall, Yehoshua Perl
From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies. Artif. Intell. Medicine 79 (2017)
Ling Zheng, Hasan Yumak, Ling Chen, Christopher Ochs, James Geller, Joan Kapusnik-Uner, Yehoshua Perl
Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology. J. Biomed. Informatics 73 (2017)
Hao Liu, Ling Zheng, Yehoshua Perl, Yan Chen, Gai Elhanan
Correcting Ontology Errors Simplifies Visual Complexity. MedInfo (2017)
Christopher Ochs, Yehoshua Perl, Gai Elhanan, James T. Case
A Descriptive Delta for Identifying Changes in SNOMED CT. ICBO/BioCreative (2016)
Christopher Ochs, Zhe He, Ling Zheng, James Geller, Yehoshua Perl, George Hripcsak, Mark A. Musen
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. J. Biomed. Informatics 61 (2016)
Christopher Ochs, James Geller, Yehoshua Perl, Mark A. Musen
A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies. J. Biomed. Informatics 62 (2016)
Yehoshua Perl, Christopher Ochs, Sherri de Coronado, Nicole Thomas
Visualizing the "Big Picture" of Change in NCIt's Biological Processes. ICBO/BioCreative (2016)
Hasan Yumak, Ling Chen, Michael Halper, Ling Zheng, Yehoshua Perl, Gai Elhanan
A Quality-Assurance Study of ChEBI. ICBO/BioCreative (2016)
Christopher Ochs, Yehoshua Perl, Michael Halper, James Geller, Jane Lomax
Quality assurance of the gene ontology using abstraction networks. J. Bioinform. Comput. Biol. 14 (3) (2016)
Ankur Agrawal, Yehoshua Perl, Christopher Ochs, Gai Elhanan
A contextual auditing method for SNOMED CT concepts. Int. J. Data Min. Bioinform. 15 (4) (2016)
Ling Zheng, Yehoshua Perl, James Geller, Gai Elhanan
How to Summarize Big Knowledge Subjects. ICBO/BioCreative (2016)
Christopher Ochs, James T. Case, Yehoshua Perl
Tracking the Remodeling of SNOMED CT's Bacterial Infectious Diseases. AMIA (2016)
Ankur Agrawal, Yehoshua Perl, Christopher Ochs, Gai Elhanan
Algorithmic detection of inconsistent modeling among SNOMED CT concepts by combining lexical and structural indicators. BIBM (2015)
Christopher Ochs, Yehoshua Perl, James Geller, Mark A. Musen
Using aggregate taxonomies to summarize SNOMED CT evolution. BIBM (2015)
Duo Helen Wei, Huanying Helen Gu, Yehoshua Perl, Michael Halper, Christopher Ochs, Gai Elhanan, Yan Chen
Structural measures to track the evolution of SNOMED CT hierarchies. J. Biomed. Informatics 57 (2015)
Christopher Ochs, James Geller, Yehoshua Perl, Yan Chen, Junchuan Xu, Hua Min, James T. Case, Zhi Wei
Scalable quality assurance for large SNOMED CT hierarchies using subject-based subtaxonomies. J. Am. Medical Informatics Assoc. 22 (3) (2015)
Christopher Ochs, Ling Zheng, Huanying Gu, Yehoshua Perl, James Geller, Joan Kapusnik-Uner, Aleksandr Zakharchenko
Drug-drug Interaction Discovery Using Abstraction Networks for "National Drug File - Reference Terminology" Chemical Ingredients. AMIA (2015)
Christopher Ochs, James Geller, Yehoshua Perl, Yan Chen, Ankur Agrawal, James T. Case, George Hripcsak
A tribal abstraction network for SNOMED CT target hierarchies without attribute relationships. J. Am. Medical Informatics Assoc. 22 (3) (2015)
Christopher Ochs, Yehoshua Perl, James Geller, Melissa A. Haendel, Matthew H. Brush, Sivaram Arabandi, Samson W. Tu
Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. J. Biomed. Informatics 56 (2015)
Michael Halper, Huanying Gu, Yehoshua Perl, Christopher Ochs
Abstraction networks for terminologies: Supporting management of "big knowledge". Artif. Intell. Medicine 64 (1) (2015)
Christopher Ochs, Zhe He, Yehoshua Perl, Sivaram Arabandi, Michael Halper, James Geller
Choosing the Granularity of Abstraction Networks for Orientation and Quality Assurance of the Sleep Domain Ontology. ICBO (2013)
Christopher Ochs, Yehoshua Perl, James Geller, Michael Halper, Huanying Helen Gu, Yan Chen, Gai Elhanan
Scalability of Abstraction-Network-Based Quality Assurance to Large SNOMED Hierarchies. AMIA (2013)
Ankur Agrawal, Zhe He, Yehoshua Perl, Duo Helen Wei, Michael Halper, Gai Elhanan, Yan Chen
The readiness of SNOMED problem list concepts for meaningful use of electronic health records. Artif. Intell. Medicine 58 (2) (2013)
Christopher Ochs, Yehoshua Perl, James Geller
BLUSNO: A System for Orientation, Visualization, and Quality Assurance of SNOMED CT Using Abstraction Networks. ICBO (2013)
Ankur Agrawal, Yehoshua Perl, Gai Elhanan
Identifying Problematic Concepts in SNOMED CT using a Lexical Approach. MedInfo (2013)
Zhe He, Christopher Ochs, Ankur Agrawal, Yehoshua Perl, Dimitris Zeginis, Konstantinos A. Tarabanis, Gai Elhanan, Michael Halper, Natasha F. Noy, James Geller
A Family-Based Framework for Supporting Quality Assurance of Biomedical Ontologies in BioPortal. AMIA (2013)
Zhe He, Christopher Ochs, Larisa N. Soldatova, Yehoshua Perl, Sivaram Arabandi, James Geller
Auditing Redundant Import in Reuse of a Top Level Ontology for the Drug Discovery Investigations Ontology. VDOS+DO@ICBO (2013)
Ankur Agrawal, Yehoshua Perl, Yan Chen, Gai Elhanan, Mei Liu
Identifying Inconsistencies in SNOMED CT Problem Lists using Structural Indicators. AMIA (2013)
James Geller, Zhe He, Yehoshua Perl, C. Paul Morrey, Julia Xu
Rule-based support system for multiple UMLS semantic type assignments. J. Biomed. Informatics 46 (1) (2013)
Zhe He, Michael Halper, Yehoshua Perl, Gai Elhanan
Clinical clarity versus terminological order: the readiness of SNOMED CT concept descriptors for primary care. MIX-HS (2012)
David Daudelin, James Geller, Yehoshua Perl
Using Gamification and Crowdsourcing to Enhance Terminology Auditing. AMIA (2012)
Yue Wang, Michael Halper, Duo Helen Wei, Huanying Gu, Yehoshua Perl, Junchuan Xu, Gai Elhanan, Yan Chen, Kent A. Spackman, James T. Case, George Hripcsak
Auditing complex concepts of SNOMED using a refined hierarchical abstraction network. J. Biomed. Informatics 45 (1) (2012)
James Geller, Christopher Ochs, Yehoshua Perl, Junchuan Xu
New Abstraction Networks and a New Visualization Tool in Support of Auditing the SNOMED CT Content. AMIA (2012)
Huanying Gu, Gai Elhanan, Yehoshua Perl, George Hripcsak, James J. Cimino, Julia Xu, Yan Chen, James Geller, C. Paul Morrey
A study of terminology auditors' performance for UMLS semantic type assignments. J. Biomed. Informatics 45 (6) (2012)
Yue Wang, Michael Halper, Duo Helen Wei, Yehoshua Perl, James Geller
Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED. J. Biomed. Informatics 45 (1) (2012)
C. Paul Morrey, Yehoshua Perl, Michael Halper, Ling Chen, Huanying Gu
A chemical specialty semantic network for the Unified Medical Language System. J. Cheminformatics 4 (2012)
Christopher Ochs, Ankur Agrawal, Yehoshua Perl, Michael Halper, Samson W. Tu, Simona Carini, Ida Sim, Natalya Fridman Noy, Mark A. Musen, James Geller
Deriving an Abstraction Network to Support Quality Assurance in OCRe. AMIA (2012)
Yan Chen, Huanying Gu, Yehoshua Perl, James Geller
Overcoming an obstacle in expanding a UMLS semantic type extent. J. Biomed. Informatics 45 (1) (2012)
C. Paul Morrey, Ling Chen, Michael Halper, Yehoshua Perl
Resolution of redundant semantic type assignments for organic chemicals in the UMLS. Artif. Intell. Medicine 52 (3) (2011)
Gai Elhanan, Yehoshua Perl, James Geller
A survey of SNOMED CT direct users, 2010: impressions and preferences regarding content and quality. J. Am. Medical Informatics Assoc. 18 (Supplement) (2011)
Kuo-Chuan Huang, James Geller, Michael Halper, Gai Elhanan, Yehoshua Perl
Scalability of Piecewise Synonym Identification in Integration of SNOMED into the UMLS. Int. J. Comput. Model. Algorithms Medicine 2 (3) (2011)
Christopher Ochs, James Geller, Yehoshua Perl
A Relationship-Centric Hybrid Interface for Browsing and Auditing the UMLS. Trans. SDPS 15 (4) (2011)
Gai Elhanan, Kuo-Chuan Huang, Yehoshua Perl
Source authenticity in the UMLS - A case study of the Minimal Standard Terminology. J. Biomed. Informatics 43 (6) (2010)
Ling Chen, C. Paul Morrey, Huanying Gu, Michael Halper, Yehoshua Perl
Research Paper: Modeling Multi-typed Structurally Viewed Chemicals with the UMLS Refined Semantic Network. J. Am. Medical Informatics Assoc. 16 (1) (2009)
Yan Chen, Huanying Helen Gu, Yehoshua Perl, James Geller
Structural group-based auditing of missing hierarchical relationships in UMLS. J. Biomed. Informatics 42 (3) (2009)
C. Paul Morrey, James Geller, Michael Halper, Yehoshua Perl
The Neighborhood Auditing Tool: A hybrid interface for auditing the UMLS. J. Biomed. Informatics 42 (3) (2009)
James Geller, Yehoshua Perl, Michael Halper, Ronald Cornet
Special Issue on Auditing of Terminologies. J. Biomed. Informatics 42 (3) (2009)
James Geller, C. Paul Morrey, Junchuan Xu, Michael Halper, Gai Elhanan, Yehoshua Perl, George Hripcsak
Comparing Inconsistent Relationship Configurations Indicating UMLS Errors. AMIA (2009)
Yan Chen, Huanying Gu, Yehoshua Perl, James Geller, Michael Halper
Structural group auditing of a UMLS semantic type's extent. J. Biomed. Informatics 42 (1) (2009)
Kuo-Chuan Huang, James Geller, Michael Halper, Yehoshua Perl, Junchuan Xu
Using WordNet synonym substitution to enhance UMLS source integration. Artif. Intell. Medicine 46 (2) (2009)
Duo Helen Wei, Michael Halper, Gai Elhanan, Yan Chen, Yehoshua Perl, James Geller, Kent A. Spackman
Auditing SNOMED Relationships Using a Converse Abstraction Network. AMIA (2009)
Yan Chen, Huanying Gu, Yehoshua Perl, Michael Halper, Junchuan Xu
Research Paper: Expanding the Extent of a UMLS Semantic Type via Group Neighborhood Auditing. J. Am. Medical Informatics Assoc. 16 (5) (2009)
Yue Wang, Duo Helen Wei, Junchuan Xu, Gai Elhanan, Yehoshua Perl, Michael Halper, Yan Chen, Kent A. Spackman, George Hripcsak
Auditing Complex Concepts in Overlapping Subsets of SNOMED. AMIA (2008)
Yan Chen, Yehoshua Perl, James Geller, George Hripcsak, Li Zhang
Comparing and consolidating two heuristic metaschemas. J. Biomed. Informatics 41 (2) (2008)
Barry Cohen, Marc Oren, Hua Min, Yehoshua Perl, Michael Halper
Automated comparative auditing of NCIT genomic roles using NCBI. J. Biomed. Informatics 41 (6) (2008)
Duo Helen Wei, Yue Wang, Yehoshua Perl, Junchuan Xu, Michael Halper, Kent A. Spackman
Complexity Measures to Track the Evolution of a SNOMED Hierarchy. AMIA (2008)
Michael Halper, Yue Wang, Hua Min, Yan Chen, George Hripcsak, Yehoshua Perl, Kent A. Spackman
Analysis of Error Concentrations in SNOMED. AMIA (2007)
Huanying Gu, George Hripcsak, Yan Chen, C. Paul Morrey, Gai Elhanan, James J. Cimino, James Geller, Yehoshua Perl
Evaluation of a UMLS Auditing Process of Semantic Type Assignments. AMIA (2007)
Barry Cohen, Yan Chen, Yehoshua Perl
Updating the Genomic Component of the UMLS Semantic Network. AMIA (2007)
Yue Wang, Michael Halper, Hua Min, Yehoshua Perl, Yan Chen, Kent A. Spackman
Structural methodologies for auditing SNOMED. J. Biomed. Informatics 40 (5) (2007)
Yan Chen, Yehoshua Perl, James Geller, James J. Cimino
Analysis of a Study of the Users, Uses, and Future Agenda of the UMLS. J. Am. Medical Informatics Assoc. 14 (2) (2007)
Michael Halper, Li-min Liu, James Geller, Yehoshua Perl
Ownership as a conceptual modeling construct. Data Knowl. Eng. 62 (2) (2007)
Hua Min, Yehoshua Perl, Yan Chen, Michael Halper, James Geller, Yue Wang
Research Paper: Auditing as Part of the Terminology Design Life Cycle. J. Am. Medical Informatics Assoc. 13 (6) (2006)
Xuan Zhou, James Geller, Yehoshua Perl, Michael Halper
An Application Intersection Marketing Ontology. Essays in Memory of Shimon Even (2006)
Li Zhang, Yehoshua Perl, Michael Halper, James Geller, George Hripcsak
A lexical metaschema for the UMLS semantic network. Artif. Intell. Medicine 33 (1) (2005)
Li Zhang, George Hripcsak, Yehoshua Perl, Michael Halper, James Geller
An expert study evaluating the UMLS lexical metaschema. Artif. Intell. Medicine 34 (3) (2005)

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Publication Activity (10 Years)

Top Topics

Top Venues

Yehoshua Perl