Publications

Below is a complete list of publications associated with our current family-based ontology QA project. See recent publications on Google Scholar

For publications related to our previous NIH-funded projects (prior to 2015), see Dr. Yehoshua Perl's Google Scholar page and Dr. James Geller's Google Scholar page.

Alternatively, view our publications on PubMed.gov.

Publication Details

Year

Quality assurance of complex ChEBI concepts based on number of relationship types.
Yumak H, Zheng L, Chen L, Halper M, Perl Y, Owen G.
Applied Ontology.1-16.
2019
Alternative Classification of Identical Concepts in Different Terminologies: Different Ways to View the World.
Keloth VK, He Z, Elhanan G, Geller J.
J Biomed Inform. 103193.
2019
Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies.
Zheng L, Chen Y, Elhanan G, Perl Y, Geller J, Ochs C.
J Biomed Inform. 83:135-149.
2018
Quality Assurance of Ontology Content Reuse.
Halper M, Ochs C, Perl Y, Arabandi S, Musen MA.
Proceedings of the 9th International Conference on Biological Ontology
2018
Using Convolutional Neural Networks to Support Insertion of New Concepts into SNOMED CT.
Liu H, Geller J, Halper M, Perl Y.
AMIA Annu Symp Proc. 750-759.
2018
Overlapping Complex Concepts Have More Commission Errors, Especially in Intensive Terminology Auditing.
Zheng L, Liu H, Perl Y, Geller J, Ochs C, Case JT.
AMIA Annu Symp Proc.1157-1166.
2018
Extended Analysis of Topological-Pattern-Based Ontology Enrichment.
He Z, Keloth VK, Chen Y, Geller J.
IEEE Int Conf Bioinformatics Biomed.1641-1648
2018
Leveraging Horizontal Density Differences between Ontologies to Identify Missing Child Concepts: A Proof of Concept.
Keloth VK, He Z, Chen Y, Geller J.
AMIA Annu Symp Proc.644-653.
2018
A Quality Assurance Methodology for ChEBI Ontology Focusing on Uncommonly Modeled Concepts.
Liu H, Chen L, Zheng L, Perl Y, Geller J.
Proceedings of International Conference on Biological Ontology.
2018
Validating UMLS Semantic Type Assignments Using SNOMED CT Semantic Tags.
Gu H, He Z, Wei D, Elhanan G, and Chen Y.
Methods Inf Med. 43–53.
2018
Enrichment of SNOMED CT Ophthalmology Component to Support EHR Coding.
Liu H, Hildebrand PL, Perl Y, Geller J.
IEEE International Conference on Bioinformatics and Biomedicine.
2018
Can a Convolutional Neural Network Support Auditing of NCI Thesaurus Neoplasm Concepts?
Liu H, Zheng L, Perl Y, Geller J, Elhanan G.
Proceedings of International Conference on Biological Ontology
2018
Quality Assurance of Concept Roles in the National Cancer Institute thesaurus.
Zheng L, Chen Y, Perl Y, Halper M, Geller J, de Coronado S.
IEEE International Conference on Bioinformatics and Biomedicine. 2001-2008.
2018
Quality assurance of biomedical terminologies and ontologies.
Geller J, Perl Y, Cui L, Zhang GQ.
J Biomed Inform. 86:106-108.
2018
From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies.
Elhanan, G., Ochs, C., Mejino, J. L., Liu, H., Mungall, C. J., Perl, Y.
Artificial Intelligence in Medicine
2017
Taxonomy-Based Approaches to Quality Assurance of Ontologies.
Halper M, Perl Y, Ochs C, Zheng L.
J Healthc Eng. 3495723.
2017
Auditing National Cancer Institute thesaurus neoplasm concepts in groups of high error concentration.
Zheng L, Min H, Chen Y, Xu J, Geller J, Perl Y.
Applied Ontology.12(2): 113-130
2017
Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology.
Zheng L, Yumak H, Chen L, Ochs C, Geller J, Kapusnik-Uner J, Perl Y.
J Biomed Inform. 73:30-42.
2017
Real Time Summarization and Visualization of Ontology Change in Protégé.
Ochs C, Geller J, Musen MA, Perl Y.
VOILA@ ISWC. 75-86.
2017
Multi-layer Big Knowledge Visualization Scheme for Comprehending Neoplasm Ontology Content.
Zheng L, Ochs C, Geller J, Liu H, Perl Y, De Coronado S.
IEEE International Conference on Big Knowledge.
2017
Correcting Ontology Errors Simplifies Visual Complexity.
Liu H, Zheng L, Perl Y, Chen Y, Elhanan G.
Stud Health Technol Inform. 245:1330.
2017
Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts.
He Z, Perl Y, Elhanan G, Chen Y, Geller J, Bian J.
IEEE Int Conf Bioinformatics Biomed.1262-1269
2017
Perceiving the Usefulness of the National Cancer Institute Metathesaurus for Enriching NCIt with Topological Patterns.
He Z, Chen Y, Geller J.
Stud Health Technol Inform.863-867.
2017
Discovering additional complex NCIt Gene concepts with high error rate.
Zheng L, Min H, Perl Y, Geller J.
IEEE International Conference on Bioinformatics and Biomedicine.
2017
An empirical analysis of ontology reuse in BioPortal.
Ochs, C., Perl, Y., Geller, J., Arabandi, S., Tudorache, T., Musen, M. A.
Journal of Biomedical Informatics, 71: 165-177
2017
Relating Complexity and Error Rates of Ontology Concepts. More Complex NCIt Concepts Have More Errors.
Min H, Zheng L, Perl Y, Halper M, De Coronado S, Ochs C.
Methods Inf Med. 56(3):200-208
2017
Analyzing structural changes in SNOMED CTs Bacterial infectious diseases using a visual semantic delta.
Ochs C, Case JT, Perl Y.
J Biomed Inform. 67:101-116
2017
Introducing the Big Knowledge to Use (BK2U) challenge.
Perl Y, Geller J, Halper M, Ochs C, Zheng L, Kapusnik-Uner J.
Ann N Y Acad Sci. 1387(1):12-24
2017
Summarizing an Ontology: A “Big Knowledge” Coverage Approach.
Zheng L, Perl Y, Elhanan G, Ochs C, Geller J, Halper M.
Stud Health Technol Inform. 245:978-982.
2017
Tracking the Remodeling of SNOMED CTs Bacterial Infectious Diseases.
Ochs C, Case JT, Perl Y.
AMIA Annual Symposium Proceedings: 974-983
2016
A Descriptive Delta for Identifying Changes in SNOMED CT.
Ochs C, Perl Y, Elhanan G, Case JT.
International Conference on Biological Ontology Proceedings
2016
Visualizing the "Big Picture" of Change in NCIts BiologicalProcesses.
Perl Y, Ochs C, de Coronado S, Thomas N.
International Conference on Biological Ontology Proceedings
2016
Topological-Pattern-Based Recommendation of UMLS Concepts for National Cancer Institute Thesaurus.
He Z, Chen Y, de Coronado S, Piskorski K, Geller J
AMIA Annu Symp, pp. 618-627
2016
A quality-assurance study of ChEBI.
Yumak H, Chen L, Halper M, Zheng L, Perl Y, Elhanan G.
Proceedings of International Conference on Biological Ontology
2016
Preliminary Analysis of Difficulty of Importing Pattern-Based Concepts into theNational Cancer Institute Thesaurus.
He Z and Geller J.
Exploring Complexity in Health: An Interdisciplinary Systems Approach. Series Studies in Health Technology and Informatics. Volume 228. pp. 389 - 393.
2016
Quality assurance of the gene ontology using abstraction networks.
Ochs C, Perl Y, Halper M, Geller J, Lomax J.
J Bioinform Comput Biol. 2016 14(3)
2016
Quality Assurance of UMLS Semantic Type Assignments to SNOMED CT Concepts with the Use of SNOMED CT Hierarchies.
Gu H, Chen Y, He Z, Halper M, and Chen L.
Methods Inf Med. 55(2): 158–165.
2016
A contextual auditing method for SNOMED CT concepts.
Agrawal A, Perl Y, Ochs C and Elhanan G.
International Journal of Data Mining and Bioinformatics 15, no. 4: 372-391
2016
Utilizing a structural meta-ontologyfor family-based quality assurance of the BioPortal ontologies.
Ochs C, He Z, Zheng L, Geller J, Perl Y, Hripcsak G and Musen MA.
Journal of Biomedical Informatics 61: 63-76
2016
A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.
Ochs C, Geller J, Perl Y, and Musen MA.
Journal of Biomedical Informatics 62: 90-105
2016
Gene Ontology Summarization to Support Visualization and Quality Assurance.
Ochs C, Perl Y, Halper M, Lomax J, Geller J.
BICoB
2015
Drug-drug Interaction Discovery Using Abstraction Networks for "National Drug File – Reference Terminology" Chemical Ingredients.
Ochs C, Zheng L, Perl Y, Geller J, Gu H, Kapusnik-Uner J.
AMIA Annu Symp
2015
Using Aggregate Taxonomies to Summarize SNOMED CT Evolution.
Ochs C, Perl Y, Geller J, Musen MA.
International Workshop on Biomedical and Health Informatics
2015
Abstraction networks for terminologies: Supporting management of "big knowledge".
Halper M, Gu H, Perl Y, Ochs C.
Artif Intell Med. 64(1):1-16
2015
A comparative analysis of the density of the SNOMED CT conceptual content for semantic harmonization.
He Z, Geller J, Chen Y.
Artif Intell Med. 64(1):29-40
2015
Scalable quality assurance for large SNOMED CT hierarchies using subject-based subtaxonomies.
Ochs C, Geller J, Perl Y, Chen Y, Xu J, Min H, Case JT, Wei Z.
J Am Med Inform Assoc. 22(3):507-18
2015
A tribal abstraction network for SNOMED CT target hierarchies without attribute relationships.
Ochs C, Geller J, Perl Y, Chen Y, Agrawal A, Case JT, Hripcsak G.
J Am Med Inform Assoc. 22(3):628-39
2015
Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.
Ochs C, Perl Y, Geller J, Haendel M, Brush M, Arabandi S, Tu S.
J Biomed Inform. 56:127-44
2015
Structural measures to track the evolution of SNOMED CT hierarchies.
Wei D, Helen Gu H, Perl Y, Halper M, Ochs C, Elhanan G, Chen Y.
J Biomed Inform
2015
Algorithmic Detection of Inconsistent Modeling among SNOMED CT Concepts by Combining Lexical and Structural indicators.
Agrawal A, Perl Y, Ochs C, Elhanan G.
IEEE International Conference on Bioinformatics and Biomedicine
2015

Ⓒ 2017 - 2021
Structural Analysis of Biomedical Ontologies Center (SABOC)
Department of Computer Science, Ying Wu College of Computing
New Jersey Institute of Technology
University Heights, Newark, New Jersey 07102