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Grant Details

Grant Number: 5R01CA190779-03 Interpret this number
Primary Investigator: Perl, Yehoshua
Organization: New Jersey Institute Of Technology
Project Title: A Family-Based Framework of Quality Assurance for Biomedical Ontologies
Fiscal Year: 2017
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Abstract

DESCRIPTION (provided by applicant): We will develop a family-based Quality Assurance (QA) framework for biomedical ontologies. Ontology QA is critical for increasing the use of ontologies in interdisciplinary research and in electronic health records (EHRs). We will develop computational techniques for identifying concepts with high probability of errors to improve efficiency and effectiveness of ontology QA. Biomedical ontologies are large, complex knowledge representation systems that enable the integration of knowledge from different fields. The largest, best-known ontology repository is the Bioportal of the National Center for Biomedical Ontologies, containing more than 300 ontologies and tools for editing, browsing, and visualizing these ontologies. However, many errors have been discovered in BioPortal's ontologies. QA in BioPortal has been mostly focused on use-cases and ad hoc techniques. Our computational techniques will automatically identify sets of concepts with a high likelihood of errors to empower ontology QA. In past research, we have designed many QA techniques for single ontologies and have shown that sets of complex and uncommonly classified concepts have significantly higher percentages of errors. The theoretical bases for our QA are Abstraction Networks (AbNs), which summarize ontologies in a compact way. Using AbNs, we identified many error-prone concepts. In this project, we will perform QA for whole families of ontologies. We have already identified seven preliminary families, based on structural properties. If a classification of concepts yields higher than usual error rates in several ontologies of a family F then we hypothesize that this will be true for such classifications for most ontologies of F. We will build a prototype software tool (BLUOWL) for determining AbNs for each family, to support QA of its ontologies. Our primary test beds will be seven cancer-related ontologies, e.g., the National Cancer Institute thesaurus (NCIt), with different properties and purposes. Some non-cancer ontologies will also be included. We have published preliminary QA results for four such ontologies. In evaluation studies, we will formulate and test hypotheses, statistically expressing the error expectations for various kinds of concepts. Ontologies' curators were recruited to review the suspicious concepts we will identify as part of their regular QA efforts (outside of our budget). In summary, we will: Identify families of BioPortal ontologies based on ontology structure and design a unified methodology for deriving their abstraction networks; Build a software tool (BLUOWL) for QA of each family; Investigate concept classifications more likely to be erroneous in each family; Perform evaluation of our QA methodologies and usability studies for BLUOWL.

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Publications

Statin Use and Breast Cancer Prognosis in Black and White Women.
Authors: Leiter A. , Bickell N.A. , LeRoith D. , Nayak A. , Feldman S.M. , Friedman N.B. , Estabrook A. , King T.A. , Fei K. , Franco R. , et al. .
Source: Hormones & Cancer, 2018 Feb; 9(1), p. 55-61.
EPub date: 2017-10-19 00:00:00.0.
PMID: 29052171
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Elevated tumor LDLR expression accelerates LDL cholesterol-mediated breast cancer growth in mouse models of hyperlipidemia.
Authors: Gallagher E.J. , Zelenko Z. , Neel B.A. , Antoniou I.M. , Rajan L. , Kase N. , LeRoith D. .
Source: Oncogene, 2017-11-16 00:00:00.0; 36(46), p. 6462-6471.
EPub date: 2017-07-31 00:00:00.0.
PMID: 28759039
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Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology.
Authors: Zheng L. , Yumak H. , Chen L. , Ochs C. , Geller J. , Kapusnik-Uner J. , Perl Y. .
Source: Journal Of Biomedical Informatics, 2017 Sep; 73, p. 30-42.
EPub date: 2017-07-16 00:00:00.0.
PMID: 28723580
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An empirical analysis of ontology reuse in BioPortal.
Authors: Ochs C. , Perl Y. , Geller J. , Arabandi S. , Tudorache T. , Musen M.A. .
Source: Journal Of Biomedical Informatics, 2017 Jul; 71, p. 165-177.
EPub date: 2017-06-02 00:00:00.0.
PMID: 28583809
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From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies.
Authors: Elhanan G. , Ochs C. , Mejino J.L.V. , Liu H. , Mungall C.J. , Perl Y. .
Source: Artificial Intelligence In Medicine, 2017-05-19 00:00:00.0; , .
EPub date: 2017-05-19 00:00:00.0.
PMID: 28532962
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Analyzing Structural Changes In Snomed Ct's Bacterial Infectious Diseases Using A Visual Semantic Delta
Authors: Ochs C. , Case J.T. , Perl Y. .
Source: Journal Of Biomedical Informatics, 2017 Mar; 67, p. 101-116.
PMID: 28215561
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Taxonomy-Based Approaches to Quality Assurance of Ontologies.
Authors: Halper M. , Perl Y. , Ochs C. , Zheng L. .
Source: Journal Of Healthcare Engineering, 2017; 2017, p. 3495723.
EPub date: 2017-10-11 00:00:00.0.
PMID: 29158885
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Perceiving the Usefulness of the National Cancer Institute Metathesaurus for Enriching NCIt with Topological Patterns.
Authors: He Z. , Chen Y. , Geller J. .
Source: Studies In Health Technology And Informatics, 2017; 245, p. 863-867.
PMID: 29295222
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Introducing The Big Knowledge To Use (bk2u) Challenge
Authors: Perl Y. , Geller J. , Halper M. , Ochs C. , Zheng L. , Kapusnik-Uner J. .
Source: Annals Of The New York Academy Of Sciences, 2016-10-17 00:00:00.0; , .
PMID: 27750400
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A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.
Authors: Ochs C. , Geller J. , Perl Y. , Musen M.A. .
Source: Journal Of Biomedical Informatics, 2016 Aug; 62, p. 90-105.
PMID: 27345947
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Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.
Authors: Ochs C. , He Z. , Zheng L. , Geller J. , Perl Y. , Hripcsak G. , Musen M.A. .
Source: Journal Of Biomedical Informatics, 2016 Jun; 61, p. 63-76.
PMID: 26988001
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Preliminary Analysis of Difficulty of Importing Pattern-Based Concepts into the National Cancer Institute Thesaurus.
Authors: He Z. , Geller J. .
Source: Studies In Health Technology And Informatics, 2016; 228, p. 389-93.
PMID: 27577410
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Topological-Pattern-Based Recommendation of UMLS Concepts for National Cancer Institute Thesaurus.
Authors: He Z. , Chen Y. , de Coronado S. , Piskorski K. , Geller J. .
Source: Amia ... Annual Symposium Proceedings. Amia Symposium, 2016; 2016, p. 618-627.
EPub date: 2017-02-10 00:00:00.0.
PMID: 28269858
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Tracking the Remodeling of SNOMED CT's Bacterial Infectious Diseases.
Authors: Ochs C. , Case J.T. , Perl Y. .
Source: Amia ... Annual Symposium Proceedings. Amia Symposium, 2016; 2016, p. 974-983.
EPub date: 2017-02-10 00:00:00.0.
PMID: 28269894
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Structural measures to track the evolution of SNOMED CT hierarchies.
Authors: Wei D. , Helen Gu H. , Perl Y. , Halper M. , Ochs C. , Elhanan G. , Chen Y. .
Source: Journal Of Biomedical Informatics, 2015 Oct; 57, p. 278-87.
PMID: 26260003
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Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.
Authors: Ochs C. , Perl Y. , Geller J. , Haendel M. , Brush M. , Arabandi S. , Tu S. .
Source: Journal Of Biomedical Informatics, 2015 Aug; 56, p. 127-44.
PMID: 26048076
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A tribal abstraction network for SNOMED CT target hierarchies without attribute relationships.
Authors: Ochs C. , Geller J. , Perl Y. , Chen Y. , Agrawal A. , Case J.T. , Hripcsak G. .
Source: Journal Of The American Medical Informatics Association : Jamia, 2015 May; 22(3), p. 628-39.
PMID: 25332354
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Scalable quality assurance for large SNOMED CT hierarchies using subject-based subtaxonomies.
Authors: Ochs C. , Geller J. , Perl Y. , Chen Y. , Xu J. , Min H. , Case J.T. , Wei Z. .
Source: Journal Of The American Medical Informatics Association : Jamia, 2015 May; 22(3), p. 507-18.
PMID: 25336594
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Abstraction networks for terminologies: Supporting management of "big knowledge".
Authors: Halper M. , Gu H. , Perl Y. , Ochs C. .
Source: Artificial Intelligence In Medicine, 2015 May; 64(1), p. 1-16.
PMID: 25890687
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A comparative analysis of the density of the SNOMED CT conceptual content for semantic harmonization.
Authors: He Z. , Geller J. , Chen Y. .
Source: Artificial Intelligence In Medicine, 2015 May; 64(1), p. 29-40.
PMID: 25890688
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Drug-drug Interaction Discovery Using Abstraction Networks for "National Drug File - Reference Terminology" Chemical Ingredients.
Authors: Ochs C. , Zheng L. , Gu H. , Perl Y. , Geller J. , Kapusnik-Uner J. , Zakharchenko A. .
Source: Amia ... Annual Symposium Proceedings. Amia Symposium, 2015; 2015, p. 973-82.
PMID: 26958234
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Quality Assurance Of The Gene Ontology Using Abstraction Networks
Authors: Ochs C. , Perl Y. , Halper M. , Geller J. , Lomax J. .
Source: Journal Of Bioinformatics And Computational Biology, 2016 06; 14(3), p. 1642001.
PMID: 27301779
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