Yehoshua Perl
Yehoshua Perl
Professor, Computer Science
Guttenberg Information Technologies Center (GITC)
Education
Ph.D.; The Weizmann Institute of Science; ; 1975
M.S.; The Weizmann Institute of Science; ; 1971
B.S.; Bar-Ilan University; ; 1969
M.S.; The Weizmann Institute of Science; ; 1971
B.S.; Bar-Ilan University; ; 1969
2024 Fall Courses
CS 700B - MASTER'S PROJECT
CS 726 - INDEPENDENT STUDY II
CS 792 - PRE-DOCTORAL RESEARCH
CS 725 - INDEPENDENT STUDY I
CS 701B - MASTER'S THESIS
CS 790A - DOCT DISSERTATION & RES
CS 488 - INDEPENDENT STUDY IN CS
CS 726 - INDEPENDENT STUDY II
CS 792 - PRE-DOCTORAL RESEARCH
CS 725 - INDEPENDENT STUDY I
CS 701B - MASTER'S THESIS
CS 790A - DOCT DISSERTATION & RES
CS 488 - INDEPENDENT STUDY IN CS
Past Courses
CS 435: ADV DATA STRUCT-ALG DES
CS 610: DATA STRUCTURE & ALG
CS 698: ST:DEEP WEB & MEDICAL TERMINOLG
CS 786: ST:DEEP WEB
CS 610: DATA STRUCTURE & ALG
CS 698: ST:DEEP WEB & MEDICAL TERMINOLG
CS 786: ST:DEEP WEB
Conference Paper
Skimming of Electronic Health Records Highlighted by an Interface Terminology Curated with Machine Learning Mining
17th International Conference on Health Informatics—HEALTHINF, 2024
Using annotation for computerized support for fast skimming of cardiology electronic health record notes
IEEE, December 2023
17th International Conference on Health Informatics—HEALTHINF, 2024
Using annotation for computerized support for fast skimming of cardiology electronic health record notes
IEEE, December 2023
Journal Article
Zheng, Ling, & Perl, Yehoshua, & He, Yongqun (2023). Big knowledge visualization of the COVID-19 CIDO ontology evolution. BMC Medical Informatics and Decision Making, 23, 1-18.
Keloth, V K, & Zhou, S, & Lindemann, L, & Zheng, L, & Elhanan, G, & Einstein, A J, & Geller, James, & Perl, Yehoshua (2023). Mining of EHR for interface terminology concepts for annotating EHRs of COVID patients.. BMC medical informatics and decision making, 23(Suppl 1), 1-18.
Halper, Michael H., & Soldatova, Larisa Soldatova, & Brochhausen, Matthias, & Maikore, Fatima S., & Ochs, Christopher, & Perl, Yehoshua (2023). Guidelines for the Reuse of Ontology Content. Applied Ontology, 18(1), 5-29.
Liu, Cong, & Lee, Junghwan, & Ta, Casey, & Soroush, Ali, & Rogers, James R, & Kim, Jae Hyun, & Natarajan, Karthik, & Zucker, Jason, & Perl, Yehoshua, & Weng, Chunhua (2022). Risk Factors Associated With SARS-CoV-2 Breakthrough Infections in Fully mRNA-Vaccinated Individuals: Retrospective Analysis. JMIR Health and surveillance, 8(5:e35311),
Zheng, Ling, & Perl, Yehoshua, & He, Yongqun, & Ochs, Christopher, & Geller, James, & Liu, Hao, & Keloth, Vipina K (2021). Visual Comprehension and Orientation into the COVID-19 CIDO Ontology. Journal of Biomedical Informatics. Journal of Biomedical Informatics, 120(C),
Keloth, V K, & Zhou, S, & Lindemann, L, & Zheng, L, & Elhanan, G, & Einstein, A J, & Geller, James, & Perl, Yehoshua (2023). Mining of EHR for interface terminology concepts for annotating EHRs of COVID patients.. BMC medical informatics and decision making, 23(Suppl 1), 1-18.
Halper, Michael H., & Soldatova, Larisa Soldatova, & Brochhausen, Matthias, & Maikore, Fatima S., & Ochs, Christopher, & Perl, Yehoshua (2023). Guidelines for the Reuse of Ontology Content. Applied Ontology, 18(1), 5-29.
Liu, Cong, & Lee, Junghwan, & Ta, Casey, & Soroush, Ali, & Rogers, James R, & Kim, Jae Hyun, & Natarajan, Karthik, & Zucker, Jason, & Perl, Yehoshua, & Weng, Chunhua (2022). Risk Factors Associated With SARS-CoV-2 Breakthrough Infections in Fully mRNA-Vaccinated Individuals: Retrospective Analysis. JMIR Health and surveillance, 8(5:e35311),
Zheng, Ling, & Perl, Yehoshua, & He, Yongqun, & Ochs, Christopher, & Geller, James, & Liu, Hao, & Keloth, Vipina K (2021). Visual Comprehension and Orientation into the COVID-19 CIDO Ontology. Journal of Biomedical Informatics. Journal of Biomedical Informatics, 120(C),
SHOW MORE
Zheng, Ling, & Chen, Yan, & Min, Hua, & Hildebrand, P Lloyd, & Liu, Hao, & Halper, Michael H., & Geller, James, & deCoronado, Sherri, & Perl, Yehoshua (2020). Missing lateral relationships in top-level concepts of an ontology. BMC Medical Informatics and Decision Making, 20(305),
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),
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),
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Conference Proceeding
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MedInfo, August 2017
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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
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IEEE Int. Conference on BioInformatics and BioMedicine (BIBM) , November 2015
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Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA), November 2015
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American Medical Informatics Association (AMIA) Annual Symposium, November 2013
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American Medical Informatics Association (AMIA) Annual Symposium, November 2013
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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
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Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems (MIXHS'12), October (4th Quarter/Autumn) 2012
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A Survey of Direct Users and Uses of SNOMED CT: 2010 Status
American Medical Informatics Association Annu Symp Proc, November 2010
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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
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