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

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
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
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
Tracking the Remodeling of SNOMED CTs Bacterial Infectious Diseases.
Ochs C, Case JT, Perl Y.
AMIA Annual Symposium Proceedings: 974-983
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
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
A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.
Ochs C, Geller J, Perl Y, Musen MA.
J Biomed Inform. 62:90-105
2016
Tracking the Remodeling of SNOMED CTs Bacterial Infectious Diseases.
Ochs C, Case JT, Perl Y.
AMIA Annu Symp Proc. 974-983
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
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
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
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
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
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
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
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

Ⓒ 2017 - 2018
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