Extended Analysis of Topological-Pattern-Based Ontology Enrichment

Zhe He, Vipina Kuttichi Keloth, Yan Chen, James Geller

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Abstract

Maintenance of biomedical ontologies is difficult. We have previously developed a topological-pattern-based method to deal with the problem of identifying concepts in a reference ontology that could be of interest for insertion into a target ontology. Assuming that both ontologies are parts of the Unified Medical Language System (UMLS), the method suggests approximate locations where the target ontology could be extended with new concepts from the reference ontology. However, the final decision about each concept has to be made by a human expert. In this paper, we describe the universe of cross-ontology topological patterns in quantitative terms. We then present a theoretical analysis of the number of potential placements of reference concepts in a path in a target ontology, allowing for new cross-ontology synonyms. This provides a rough estimate of what expert resources need to be allocated for the task. One insight in previous work on this topic was the large percentage of cases where importing concepts was impossible, due to a configuration called 'alternative classification In this paper, we confirm this observation. Our target ontology is the National Cancer Institute thesaurus (NCIt). However, the methods can be applied to other pairs of ontologies with hierarchical relationships from the UMLS.

Original languageEnglish (US)
Title of host publicationProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
EditorsHarald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1641-1648
Number of pages8
ISBN (Electronic)9781538654880
DOIs
StatePublished - Jan 21 2019
Externally publishedYes
Event2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 - Madrid, Spain
Duration: Dec 3 2018Dec 6 2018

Publication series

NameProceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

Conference

Conference2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
CountrySpain
CityMadrid
Period12/3/1812/6/18

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Health Informatics

Keywords

  • Biomedical ontology
  • NCIt
  • concept Insertion
  • ontology maintenance

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