Yehoshua Perl

Zheng, Ling, & Min, Hua, & Chen, Yan, & Keloth, Vipina K, & Geller, James, & Perl, Yehoshua, & Hripcsak, George (2020). Outlier concepts auditing methodology for a large family of biomedical ontologies. BMC Medical Informatics and Decision Making, 20(296),

Liu, Hao, & Perl, Yehoshua, & Geller, James (2020). Concept placement using BERT trained by transforming and summarizing biomedical ontology structure. Journal of Biomedical Informatics, 112,

Zheng, Ling, & He, Zhe, & Wei, Duo, & Keloth, Vipina, & Fan, Jung-Wei, & Lindermann, Luke, & Zhu, Xinxin, & Cimino, James J, & Perl, Yehoshua (2020). A review of auditing techniques for the Unified Medical Language System. Journal of the American Medical Informatics Association, 27(10), 1625-1638.

Yumak, Hasan, & Zheng, Ling, & Chen, Ling, & Halper, Michael H., & Perl, Yehoshua, & Owen, Gareth (2019). Quality assurance of complex ChEBI concepts based on number of relationship types. Applied Ontology/IOSpress, 14(3), 199-214.

Geller, James, & Perl, Yehoshua, & Cui, Licong, & Zhang, Guo-Qiang (2018). Quality assurance of biomedical terminologies and ontologies. Journal of Biomedical Informatics, 86, 106-108.

Zheng, Ling, & Chen, Yan, & Elhanan, Gai, & Perl, Yehoshua, & Geller, James, & Ochs, Christopher (2018). Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies. Journal of Biomedical Informatics, 83, 135-149.

Zheng, Ling, & Min, Hua, & Chen, Yan, & Xu, Julia, & Geller, James, & Perl, Yehoshua (2017). Auditing National Cancer Institute thesaurus neoplasm concepts in groups of high error concentration. Applied Ontology, 12, 113-130.

Halper, Michael H., & Perl, Yehoshua, & Ochs, Christopher, & Zheng, Ling (2017). Taxonomy-based approaches to quality assurance of ontologies. Journal of Healthcare Engineering, 2017, 11.

Zheng, Ling, & Yumak, Hasan, & Chen, Ling, & Ochs, Christopher, & Geller, James, & Kapusnik-Uner, Joan, & Perl, Yehoshua (2017). Quality assurance of chemical ingredient classification for the National Drug File–Reference Terminology. Journal of Biomedical Informatics, 73, 30-42.

Elhanan, Gai, & Ochs, Christopher, & Mejino, Jose, & Liu, Hao, & Mungall, Christopher, & Perl, Yehoshua (2017). From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies. Artificial Intelligence in Medicine, 79, 9-14.

Ochs, Christopher, & Perl, Yehoshua, & Geller, James, & Arabandi, Sivaram, & Tudorache, Tania, & Musen, Mark (2017). An empirical analysis of ontology reuse in BioPortal. Journal of Biomedical Informatics, 71, 165-177.

Min, Hua, & Zheng, Ling, & Perl, Yehoshua, & Halper, Michael H., & de Coronado, Sherri, & Ochs, Christopher (2017). Relating complexity and error rates of ontology concepts: more complex NCIt concepts have more errors. Methods of Information in Medicine, 56(3),

Ochs, Christopher, & Case, James T, & Perl, Yehoshua (2017). Analyzing structural changes in SNOMED CTs Bacterial infectious diseases using a visual semantic delta. Journal of Biomedical Informatics, 67(C), 101-116.

Perl, Yehoshua, & Geller, James, & Halper, Michael H., & Ochs, Christopher, & Zheng, Ling, & Kapusnik-Uner, Joan (2017). Introducing the Big Knowledge to Use (BK2U) challenge. Annals of the New York Academy of Sciences, 1387, 12-24.

Ochs, Christopher, & Geller, James, & Perl, Yehoshua, & Musen, Mark (2016). A Unified Software Framework for Deriving, Visualizing, and Exploring Abstraction Networks for Ontologies. Journal of Biomedical Informatics, 62, 90-105.

Ochs, Christopher, & Perl, Yehoshua, & Halper, Michael H., & Geller, James, & Lomax, Janet (2016). Quality assurance of the Gene Ontology using Abstraction Networks. Journal of Bioinformatics and Computational Biology, 14(3),

Ochs, Christopher, & He, Zhe, & Zheng, Ling, & Geller, James, & Perl, Yehoshua, & Hripcsak, George, & Musen, Mark (2016). Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies. Journal of Biomedical Informatics , 61, 63-76.

Agrawal, Ankur, & Perl, Yehoshua, & Ochs, Christopher, & Elhanan, Gai (2016). A contextual auditing method for SNOMED CT concepts. International Journal of Data Mining and Bioinformatics, 15, 372-391.

Wei, Duo, & Gu, Huanying, & Perl, Yehoshua, & Halper, Michael H., & Ochs, Christopher, & Elhanan, Gai, & Chen, Yan (2015). Structural measures to track the evolution of SNOMED CT hierarchies. Journal of Biomedical Informatics, 57, 278-287.

Ochs, Christopher, & Perl, Yehoshua, & Geller, James, & Haendel, Melissa, & Brush, Matthew, & Arabandi, Sivaram, & Tu, Samson (2015). Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network. J Biomedical Informatics, 56, 127-144.

Wei, Duo, & Gu, Huanying, & Perl, Yehoshua, & Halper, Michael H., & Ochs, Christopher, & Elhanan, Guy, & Chen, Yan (2015). Structural measures to track the evolution of SNOMED CT hierarchies. J Biomed Informatics, doi: 10.1016/j.jbi.2015.08.001. [Epub ahead of print],

Ochs, Christopher, & Geller, James, & Perl, Yehoshua, & Chen, Yan, & Agrawal, Ankur, & Case, James T, & Hripcsak, George (2015). A tribal abstraction network for SNOMED CT target hierarchies without attribute relationships.. J American Medical Informatics Association, 22(3), 628-639.

Halper, Michael H., & Gu, Huanying, & Perl, Yehoshua, & Ochs, Christopher (2015). Abstraction networks for terminologies: Supporting management of big knowledge. Artificial Intelligence in Medicine, 64(1), 1-16.

Ochs, Christopher, & Geller, James, & Perl, Yehoshua, & Chen, Yan, & Xu, Julia, & Min, Hua, & Case, James T, & Wei, Zhi (2015). Scalable quality assurance for large SNOMED CT hierarchies using subject-based subtaxonomies. J American Medical Informatics Association, 22(3), 507-518.

He, Zhe, & Morrey, Paul, & Perl, Yehoshua, & Elhanan, Gai, & Chen, Ling, & Chen, Yan, & Geller, James (2014). Sculpting the UMLS Refined Semantic Network. Online J Public Health Inform, 6(2),

Agrawal, Ankur, & He, Zhe, & Perl, Yehoshua, & Wei, Duo, & Halper, Michael H., & Elhanan, Gai, & Chen, Yan (2013). The readiness of SNOMED problem list concepts for meaningful use of electronic health records.. Artificial Intelligence in Medicine, 58(2), 73-80.

Geller, James, & He, Zhe, & Perl, Yehoshua, & Morrey, Paul, & Xu, Julia (2013). Rule-based support system for multiple UMLS semantic type assignments. Journal of Biomedical Informatics, 46(1), 97-110.

Gu, Huanying, & Elhanan, Gai, & Perl, Yehoshua, & Hripcsak, George, & Cimino, James J, & Xu, Julia, & Chen, Yan, & Geller, James, & Morrey, Paul (2012). A study of terminology auditors' performance for UMLS semantic type assignments. Journal of Biomedical Informatics, 45(6), 1042-1048.

Morrey, C. P., & Perl, Yehoshua, & Halper, Michael H., & Chen, Ling, & Gu, Huanying (2012). A chemical specialty semantic network for the Unified Medical Language System. Journal of Cheminformatics, 4:9,

Wang, Yue, & Halper, Michael H., & Wei, Duo, & Perl, Yehoshua, & Geller, James (2012). Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED. Journal of Biomedical Informatics, 45(1), 15-29.

Wang, Yue, & Halper, Michael H., & Wei, Duo, & Perl, Yehoshua, & Geller, James (2012). Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED. Journal of Biomedical Informatics, 45(1), 15-29.

Chen, Yan, & Gu, Huanying, & Perl, Yehoshua, & Geller, James (2012). Overcoming an obstacle in expanding a UMLS semantic type extent. Journal of Biomedical Informatics, 45(1), 61-70.

Ochs, Christopher, & Geller, James, & Perl, Yehoshua (2011). A Relationship-Centric Hybrid Interface for Browsing and Auditing the UMLS. Transactions of the Society for Design and Process Scienc, 15(4), 3-25.

Elhanan, Gai, & Perl, Yehoshua, & Geller, James (2011). A survey of SNOMED CT direct users, 2010: impressions and preferences regarding content and quality. Journal of the American Medical Informatics Association, 18(Suppl 1), i36-44.

Huang, Kuo-chuan, & Geller, James, & Halper, Michael H., & Elhanan, Gai, & Perl, Yehoshua (2011). Scalability of piecewise synonym identification in integration of SNOMED into the UMLS. International Journal of Computational Models and Algorithms in Medicine, 2(3), 26-45.

Morrey, C P, & Chen, Ling, & Halper, Michael H., & Perl, Yehoshua (2011). Resolution of redundant semantic type assignments for organic chemicals in the UMLS. Artificial Intelligence in Medicine, 52(3), 141-151.

Elhanan, Gai, & Huang, Kuo-Chuan, & Perl, Yehoshua (2010). Source authenticity in the UMLS - A case study of the Minimal Standard Terminology. Journal of Biomedical Informatics, 43(6), 988-997.

Chen, Yan, & Gu, Huanying, & Perl, Yehoshua, & Halper, Michael, & Xu, Julia (2009). Expanding the extent of a UMLS semantic type via group neighborhood auditing. J Am Med Inform Assoc, 16(5), 746-757.

Geller, James, & Perl, Yehoshua, & Halper, Michael, & Cornet, Ronald (2009). Guest Editorial: Special Issue on Auditing of Terminologies. Journal of Biomedical Informatics/Elsevier, 42(3), 407-411 (Special Issue: 407-580).

Chen, Yan, & Gu, Huanying, & Perl, Yehoshua, & Geller, James (2009). Structural group- based auditing of missing hierarchical relationships in UMLS. Journal of Biomedical Informatics/Elsevier, 42(3), 452-467.

Morrey, Charles Paul, & Geller, James, & Halper, Michael, & Perl, Yehoshua (2009). The Neighborhood Auditing Tool: A hybrid interface for auditing the UMLS. Journal of Biomedical Informatics/Elsevier, 42(3), 468-489.

Huang, Kuo-Chuan, & Geller, James, & Halper, Michael, & Perl, Yehoshua, & Xu, Junchuan (2009). Using WordNet synonym substitution to enhance UMLS source integration. Artificial Intelligence in Medicine/Elsevier, 46(2), 97-109.

Chen, Yan, & Gu, Huanying, & Perl, Yehoshua, & Geller, James, & Halper, Michael (2009). Structural group auditing of a UMLS semantic type's extent. Journal of Biomedical Informatics/Elsevier, 42(1), 41-52.

Chen, Ling, & Morrey, Charles Paul, & Gu, Huanying, & Halper, Michael, & Perl, Yehoshua (2009). Modeling multi-typed structurally viewed chemicals with the UMLS Refined Semantic Network. J Am Med Inform Assoc., 16(1), 116-131.

Cohen, Barry, & Oren, Mark, & Min, Hua, & Perl, Yehoshua, & Halper, Michael (2008). Automated comparative auditing of NCIT genomic roles using NCBI. Journal of Biomedical Informatics, 41(6), 904-913.

Min, Hua, & Cohen, Barry, & Halper, Michael, & Oren, Mark, & Perl, Yehoshua (2008). Detecting Role Errors in the Gene Hierarchy of the NCI Thesaurus. Cancer Inform., 6, 293-313.

Geller, James, & Perl, Yehoshua, & Lee, Jintae (2004). Ontology challenges: A thumbnail historical perspective. Knowledge and Information Systems, 6(4), 375.

Gu, Huanying, & Perl, Yehoshua, & Halper, Michael H., & Geller, James, & Neuhold, Erich J. (2004). Contextual partitioning for comprehension of OODB schemas. Knowledge and Information Systems, 6(3), 315-344.

Perl, Yehoshua, & Geller, James (2003). Unified Medical Language System. Journal of Biomedical Informatics, 36(6),

Quality assurance of concept roles in the National Cancer Institute thesaurus
Proceedings of the BIBM'18 1st Int'l Workshop on Quality Assurance of Biological and Biomedical Ontologies and Terminologies, December 2018

Overlapping complex concepts have more commission errors, especially in intensive terminology auditing
AMIA, November 2018

Using convolutional neural networks to support insertion of new concepts into SNOMED CT
Proceedings of the 2018 AMIA Annual Symposium, November 2018

Quality Assurance of Ontology Content Reuse
8th International Conference on Biomedical Ontology (ICBO 2018), August 2018

Can a convolutional neural network support auditing of NCI Thesaurus Neoplasm Concepts?
8th International Conference on Biomedical Ontology (ICBO BioCreative 2018), July (3rd Quarter/Summer) 2018

Quality Assurance Methodology for ChEBI Ontology Focusing on Uncommonly Modeled Concepts
8th International Conference on Biomedical Ontology (ICBO BioCreative 2018), July (3rd Quarter/Summer) 2018

Correcting ontology errors simplifies visual complexity
Studies in Health Technology Information, 2017

Auditing the assignments of top-level semantic types in the UMLS semantic network to UMLS concepts
IEEE BIBM 2017, November 2017

Discovering additional complex NCIt gene concepts with high error rate
IEEE BIBM 2017, November 2017

System Demonstration: Applications of the Ontology Abstraction Framework
American Medical Informatics Association Annual Symposium, November 2017

Real time summarization and visualization of ontology change in Protege
VOILA 2017: Visualization and Interaction of Ontologies and Linked Data, October (4th Quarter/Autumn) 2017

Summarizing an ontology: a "big knowledge" coverage approach
MedInfo, August 2017

Multi-layer Big Knowledge Visualization Scheme for Comprehending Neoplasm Ontology Content
IEEE International Conference on Big Knowledge (ICBK), August 2017

A Descriptive Delta for Identifying Changes in SNOMED CT
International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016), August 2016

A Quality-Assurance Study of ChEBI
International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016), August 2016

Visualizing the Big Picture of Change in NCIt's Biological Processes
International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016), August 2016

The Big Knowledge to Use (BK2U) Challenge
Data Science, Learning, and Applications to Biomedical and Health Sciences, January (1st Quarter/Winter) 2016

Algorithmic detection of inconsistent modeling among SNOMED CT concepts by combining lexical and structural indicators
IEEE Int. Conference on BioInformatics and BioMedicine (BIBM) , November 2015

Drug-drug Interaction Discovery Using Abstraction Networks for National Drug File - Reference Terminology
Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA), November 2015

Using Aggregate Taxonomies to Summarize SNOMED CT Evolution
Biomedical & Health Informatics (BHI) Workshop at BIBM, November 2015

Gene Ontology Summarization to Support Visualization and Quality Assurance
BICoB 6th international conference on Bioinformatics and Computational Biology, March 2015

A family-based framework for supporting quality assurance of biomedical ontologies in BioPortal
American Medical Informatics Association (AMIA) Annual Symposium, November 2013

Identifying inconsistencies in SNOMED CT problem lists using structural indicators
American Medical Informatics Association (AMIA) Annual Symposium, November 2013

Scalability of abstraction-network-based quality assurance to large SNOMED hierarchies
American Medical Informatics Association (AMIA) Annual Symposium, November 2013

Identifying Problematic Concepts in SNOMED CT using a Lexical Approach
Stud Health Technol Inform.: MEDINFO 2013, August 2013

Auditing Redundant Import in Reuse of a Top Level Ontology for the Drug Discovery Investigations Ontology
Workshop on Vaccine and Drug Ontology Studies (VDOS 2013) collocated with Semantic Trilogy 2013, July (3rd Quarter/Summer) 2013

BLUSNO: A System for Orientation, Visualization, and Quality Assurance of SNOMED CT Using Abstraction Networks
4th International Conference on Biomedical Ontology ICBO 2013, July (3rd Quarter/Summer) 2013

Choosing the Granularity of Abstraction Networks for Orientation and Quality Assurance of the Sleep Domain Ontology
4th International Conference on Biomedical Ontology ICBO 2013, July (3rd Quarter/Summer) 2013

Identifying Inconsistencies in SNOMED-CT Problem Lists using Structural Indicators
American Medical Informatics Association Annual Symposium,

Deriving an Abstraction Network to Support Quality Assurance in OCRe
Proceedings of the American Medical Informatics Association (AMIA) Annual Meeting, November 2012

New Abstraction Networks and a New Visualization Tool in Support of Auditing the SNOMED CT Content
Proceedings of the American Medical Informatics Association (AMIA) Annual Meeting, November 2012

Using Gamification and Crowdsourcing to Enhance Terminology Auditing
Proceedings of the American Medical Informatics Association (AMIA) Annual Meeting, November 2012

Clinical clarity versus terminological order -- the readiness of SNOMED CT concept descriptors for primary care
Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems (MIXHS'12), October (4th Quarter/Autumn) 2012

Auditing hierarchical cycles to locate other inconsistencies in the UMLS
AMIA Annual Symposium Proceedings, October (4th Quarter/Autumn) 2011

A Survey of Direct Users and Uses of SNOMED CT: 2010 Status
American Medical Informatics Association Annu Symp Proc, November 2010

Auditing SNOMED Integration into the UMLS for Duplicate Concepts
American Medical Informatics Association Annu Symp Proc, November 2010

Auditing SNOMED Relationships Using a Converse Abstraction Network
Proceedings of the American Medical Informatics Association, Omnipress, November 2009

Comparing Inconsistent Relationship Configurations Indicating UMLS Errors
Proceedings of the American Medical Informatics Association, Omnipress, November 2009

Semantic Visualization of UMLS Chemical Intersection Types
Proceedings of the American Medical Informatics Association, Omnipress, November 2009

Auditing complex concepts in overlapping subsets of SNOMED
Proceedings of the American Medical Informatics Association, Omnipress, November 2008

Complexity measures to track the evolution of a SNOMED hierarchy
Proceedings of the American Medical Informatics Association, Omnipress, November 2008