Publications
Below is a complete list of publications associated with our current family-based ontology QA project.
Publications
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 |
|
Using annotation for computerized support for fast skimming of cardiology electronic health record notes. |
2023 |
| An Ontology for the Social Determinants of Health Domain. Kollapally, N. M., Chen, Y., Xu, J., & Geller, J. (2022). arXiv. IEEE BIBM 2022 |
2022 |
|
Public Health Policy Monitoring through Public Perceptions: A Case of COVID-19 Tweet Analysis. |
2022 |
| Visual comprehension and orientation into the COVID-19 CIDO ontology. Zheng, L., Perl, Y., He, Y., Ochs, C., Geller, J., Liu, H., & Keloth, V. K. (2021). Journal of biomedical informatics, 120, 103861. |
2022 |
|
Virtual Reality Ontology Object Manipulation (VROOM). |
2022 |
|
A review of auditing techniques for the Unified Medical Language System. |
2020 |
| Concept placement using BERT trained by transforming and summarizing biomedical ontology structure. Hao Liu, Yehoshua Perl, James Geller. J. Biomed. Informatics 112: 103607 |
2020 |
| Extending import detection algorithms for concept import from two to three biomedical terminologies. Vipina Kuttichi Keloth, James Geller, Yan Chen, Julia Xu. BMC Medical Informatics Decis. Mak. 20-S(10): 272 |
2020 |
|
Missing lateral relationships in top-level concepts of an ontology. BMC Medical Informatics Decis. |
2020 |
|
Outlier concepts auditing methodology for a large family of biomedical ontologies. |
2020 |
| Desiderata for High Quality AMIA Presentation Files. James Geller, Yarou Ding. AMIA 2020 |
2020 |
| Generating Training Data for Concept-Mining for an 'Interface Terminology' Annotating Cardiology EHRs. Vipina Kuttichi Keloth, Shuxin Zhou, Andrew J. Einstein, Gai Elhanan, Yan Chen, James Geller, Yehoshua Perl. BIBM 2020: 1728-1735 |
2020 |
|
Mining Concepts for a COVID Interface Terminology for Annotation of EHRs. |
2020 |
| 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 |