Literature DB >> 28723580

Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology.

Ling Zheng1, Hasan Yumak2, Ling Chen3, Christopher Ochs4, James Geller5, Joan Kapusnik-Uner6, Yehoshua Perl7.   

Abstract

The National Drug File - Reference Terminology (NDF-RT) is a large and complex drug terminology consisting of several classification hierarchies on top of an extensive collection of drug concepts. These hierarchies provide important information about clinical drugs, e.g., their chemical ingredients, mechanisms of action, dosage form and physiological effects. Within NDF-RT such information is represented using tens of thousands of roles connecting drugs to classifications. In previous studies, we have introduced various kinds of Abstraction Networks to summarize the content and structure of terminologies in order to facilitate their visual comprehension, and support quality assurance of terminologies. However, these previous kinds of Abstraction Networks are not appropriate for summarizing the NDF-RT classification hierarchies, due to its unique structure. In this paper, we present the novel Ingredient Abstraction Network (IAbN) to summarize, visualize and support the audit of NDF-RT's Chemical Ingredients hierarchy and its associated drugs. A common theme in our quality assurance framework is to use characterizations of sets of concepts, revealed by the Abstraction Network structure, to capture concepts, the modeling of which is more complex than for other concepts. For the IAbN, we characterize drug ingredient concepts as more complex if they belong to IAbN groups with multiple parent groups. We show that such concepts have a statistically significantly higher rate of errors than a control sample and identify two especially common patterns of errors.
Copyright © 2017 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Auditing NDF-RT; Auditing chemical ingredients; Chemical Ingredients hierarchy; Drug terminology; NDF-RT quality assurance; National Drug File – Reference Terminology

Mesh:

Substances:

Year:  2017        PMID: 28723580      PMCID: PMC5652327          DOI: 10.1016/j.jbi.2017.07.013

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  32 in total

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Review 2.  A review of auditing methods applied to the content of controlled biomedical terminologies.

Authors:  Xinxin Zhu; Jung-Wei Fan; David M Baorto; Chunhua Weng; James J Cimino
Journal:  J Biomed Inform       Date:  2009-03-12       Impact factor: 6.317

3.  Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.

Authors:  Christopher Ochs; Yehoshua Perl; James Geller; Melissa Haendel; Matthew Brush; Sivaram Arabandi; Samson Tu
Journal:  J Biomed Inform       Date:  2015-06-03       Impact factor: 6.317

4.  Scalable quality assurance for large SNOMED CT hierarchies using subject-based subtaxonomies.

Authors:  Christopher Ochs; James Geller; Yehoshua Perl; Yan Chen; Junchuan Xu; Hua Min; James T Case; Zhi Wei
Journal:  J Am Med Inform Assoc       Date:  2014-10-21       Impact factor: 4.497

5.  New abstraction networks and a new visualization tool in support of auditing the SNOMED CT content.

Authors:  James Geller; Christopher Ochs; Yehoshua Perl; Junchuan Xu
Journal:  AMIA Annu Symp Proc       Date:  2012-11-03

6.  Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.

Authors:  Christopher Ochs; Zhe He; Ling Zheng; James Geller; Yehoshua Perl; George Hripcsak; Mark A Musen
Journal:  J Biomed Inform       Date:  2016-03-14       Impact factor: 6.317

Review 7.  Pharmacogenomics knowledge for personalized medicine.

Authors:  M Whirl-Carrillo; E M McDonagh; J M Hebert; L Gong; K Sangkuhl; C F Thorn; R B Altman; T E Klein
Journal:  Clin Pharmacol Ther       Date:  2012-10       Impact factor: 6.875

Review 8.  Auditing complex concepts of SNOMED using a refined hierarchical abstraction network.

Authors:  Yue Wang; Michael Halper; Duo Wei; Huanying Gu; Yehoshua Perl; Junchuan Xu; Gai Elhanan; Yan Chen; Kent A Spackman; James T Case; George Hripcsak
Journal:  J Biomed Inform       Date:  2011-09-01       Impact factor: 6.317

9.  A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.

Authors:  Christopher Ochs; James Geller; Yehoshua Perl; Mark A Musen
Journal:  J Biomed Inform       Date:  2016-06-23       Impact factor: 6.317

10.  PharmGKB Drug Data Normalization with NDF-RT.

Authors:  Qian Zhu; Robert R Freimuth; Jyotishman Pathak; Christopher G Chute
Journal:  AMIA Jt Summits Transl Sci Proc       Date:  2013-03-18
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  3 in total

Review 1.  Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.

Authors:  Muhammad Amith; Zhe He; Jiang Bian; Juan Antonio Lossio-Ventura; Cui Tao
Journal:  J Biomed Inform       Date:  2018-02-17       Impact factor: 6.317

2.  InContext: curation of medical context for drug indications.

Authors:  Kody Moodley; Linda Rieswijk; Tudor I Oprea; Michel Dumontier
Journal:  J Biomed Semantics       Date:  2021-02-12

3.  Missing lateral relationships in top-level concepts of an ontology.

Authors:  Ling Zheng; Yan Chen; Hua Min; P Lloyd Hildebrand; Hao Liu; Michael Halper; James Geller; Sherri de Coronado; Yehoshua Perl
Journal:  BMC Med Inform Decis Mak       Date:  2020-12-15       Impact factor: 2.796

  3 in total

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