Call for Papers – Quality Assurance of Biomedical Terminologies and Ontologies

in Special Issue   Posted on August 13, 2017 

Information for the Special Issue

Submission Deadline: Sun 01 Oct 2017
Journal Impact Factor : 3.526
Journal Name : Journal of Biomedical Informatics
Journal Publisher:
Website for the Special Issue:
Journal & Submission Website:

Special Issue Call for Papers:

Due date for submissions: October 1, 2017

The subject of quality assurance for ontologies and terminologies, also known as “auditing,” has a long history in biomedical informatics. This special issue follows up on a previous special issue in JBI [1] and attempts to ascertain what progress has been made in the meantime. Auditing of terminologies is essential, because terminologies may form the basis of clinical decision-support systems, patient-record management systems, health care administrative systems, etc. Any terminology errors could propagate to errors in these systems, which may result in severe negative outcomes for the involved patients.

The purpose of this special issue is to capture the state-of-the-art of research on auditing biomedical ontologies and terminologies. Auditing large terminologies “by hand” is impractical. Therefore, papers on software tools that support quality assurance (QA), curation of ontologies or collaboration between ontology creators/editors/curators are especially encouraged. Those tools may be diagram/graph-based, textual, or hybrid software systems [2,5].

Four kinds of papers are invited for this special issue:

  1. Original research papers on auditing of ontologies and terminologies that report recent, previously unpublished, advances and insights that are transferable to other terminologies and contexts. Of particular interest are multi-criteria methods that increase the QA yield (e.g. [3]);

  2. Methodology review papers that collect, summarize and systematize the existing state-of-the-art in this area (e.g., see the paper by Zhu et al. [4]);

  3. Experience papers by curators, managers, auditors or editors of biomedical terminologies;

  4. Tool-centric papers on software tools for auditing and visualization of biomedical ontologies. Such papers should describe how auditing methods and quality assurance software tools for biomedical terminologies have advanced in the past decade.

We specifically encourage papers that reveal practical and scalable methods (e.g., [6]) that are used successfully within organizations, but are often not accessible to a wider audience.

The topics of this special issue include, but are not limited to, the following:

  • Descriptions of novel approaches for ontology auditing, editing, and versioning
  • Descriptions of auditing methodologies that are applicable to multiple ontologies
  • Structural, lexical and semantic methods in ontology auditing
  • Algorithms for detecting differences between two versions of one ontology and between two ontologies in the same domain
  • Multi-criteria methods to enhance quality assurance yield
  • Standardization of ontologies as a process of “auditing by committee”
  • Success stories of crowd-based auditing and error discovery by laymen
  • Collaborative and team-based auditing methods
  • Internal quality assurance processes and techniques
  • Algorithms for modularization applied to biomedical ontologies
  • Algorithms for automated error detection
  • Algorithms for semantically faithful automated summarization of ontologies
  • Automated severity rating of ontology inconsistencies and errors
  • Approaches to evaluate the performance of ontology auditing methods and tools
  • Descriptions of novel software tools for creating, authoring, auditing and curating biomedical ontologies
  • Descriptions of novel software tools for visualization of ontologies
  • User interface studies and usability studies of software tools for biomedical ontologies

Peer-review process

All submitted papers must be original and will go through a rigorous peer-review process with at least two reviewers. All submissions should follow the guidelines for authors available through a link on the Journal of Biomedical Informatics web site (

JBI’s editorial policy is also outlined on that page and will be strictly followed by special issue reviewers. Note in particular that JBI emphasizes the publication of papers that introduce innovative and generalizable methods of interest to the informatics community.

Specific applications can be described to motivate the methodology being introduced, but papers that focus solely on a specific application are not suitable for JBI.


Authors must submit their papers via the online Elsevier Editorial System (EES) at by October 1, 2017. Authors can register and upload their text, tables, and figures as well as subsequent revisions through this website. Potential authors may contact the Publishing Services Coordinator in the journal’s editorial office ([email protected]) for questions regarding this process.

Authors are also welcome to discuss their potential submissions with the editors by sending an email to James Geller ([email protected]) regarding the potential fit of their submission with this special issue.


  1. Geller J, Perl Y, Halper M, Cornet R, Guest Editorial: Special Issue on Auditing of Terminologies. Journal of Biomedical Informatics, 42(3), 407-411, June 2009.

  2. Morrey CP, Geller J, Halper M, Perl Y, The Neighborhood Auditing Tool: A hybrid interface for auditing the UMLS. Journal of Biomedical Informatics, 42(3), 468–489, June 2009.

  3. Agrawal A, Perl Y, Chen Y, Elhanan G, Liu M, Identifying inconsistencies in SNOMED CT problem lists using structural indicators. AMIA Annu Symp Proc. 2013 Nov 16;2013:17-26.

  4. Zhu X, Fan JW, Baorto DM, Weng C, Cimino JJ, A review of auditing methods applied to the content of controlled biomedical terminologies. J Biomed Inform. 2009 Jun;42(3):413-25.

  5. Zhang GQ, Bodenreider O. Large-scale, exhaustive lattice-based structural auditing of SNOMED CT. AMIA Annu Symp Proc. 2010:922-6.

  6. Cui L, Tao S, Zhang GQ. Biomedical Ontology Quality Assurance Using a Big Data Approach. ACM Transactions on Knowledge Discovery from Data. 2016;10(4):41.

Guest Editors

James Geller
Department of Computer Science
Structural Analysis of Biomedical Ontologies Center (SABOC)
New Jersey Institute of Technology (NJIT)
E-mail address: [email protected]

Licong Cui
Department of Computer Science and
Institute for Biomedical Informatics
University of Kentucky
E-mail address: [email protected]

Christopher Ochs
Department of Computer Science
Structural Analysis of Biomedical Ontologies Center (SABOC)
New Jersey Institute of Technology (NJIT)
E-mail address: [email protected]

GQ Zhang
Institute for Biomedical Informatics and Department of Computer Science
University of Kentucky
E-mail address: [email protected]

Yehoshua Perl
Department of Computer Science
Structural Analysis of Biomedical Ontologies Center (SABOC)
New Jersey Institute of Technology (NJIT)
E-mail address: [email protected]

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