Genealogical-based method for ontology self-extension in MeSH

Yu Wen Guo, Hung Yu Kao

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

Abstract

During the last decade, the advent of Ontologies used for biomedical annotation has had a deep impact on life science. MeSH is a well-known Ontology for the purpose of indexing journal articles in PubMed, improving literature searching on multi-domain topics. Since the explosion of data growth in recent years, there are new terms, concepts that weed through the old and bring forth the new. Automatically extending sets of existing terms will enable bio-curators to systematically improve text-based ontologies level by level. However, most of the related techniques which apply symbolic patterns based on a literature corpus tend to focus on more general but not specific parts of the ontology. Therefore, in this work, we present a novel method for utilizing genealogical information from Ontology itself to find suitable siblings for ontology extension. Based on the breadth and depth dimensions, the sibling generation stage and pruning strategy are proposed in our approach. As a result, on the average, the precision of the genealogical-based method achieved 0.5, with the best 0.83 performance of category "Organisms". We also achieve average precision 0.69 of 229 new terms in MeSH 2013 version.

Original languageEnglish
Title of host publicationProceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
Pages428-433
Number of pages6
DOIs
Publication statusPublished - 2013 Dec 1
Event2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013 - Shanghai, China
Duration: 2013 Dec 182013 Dec 21

Publication series

NameProceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013

Other

Other2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013
CountryChina
CityShanghai
Period13-12-1813-12-21

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Ontology
Explosions

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering

Cite this

Guo, Y. W., & Kao, H. Y. (2013). Genealogical-based method for ontology self-extension in MeSH. In Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013 (pp. 428-433). [6732530] (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013). https://doi.org/10.1109/BIBM.2013.6732530
Guo, Yu Wen ; Kao, Hung Yu. / Genealogical-based method for ontology self-extension in MeSH. Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. 2013. pp. 428-433 (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).
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Guo, YW & Kao, HY 2013, Genealogical-based method for ontology self-extension in MeSH. in Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013., 6732530, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013, pp. 428-433, 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013, Shanghai, China, 13-12-18. https://doi.org/10.1109/BIBM.2013.6732530

Genealogical-based method for ontology self-extension in MeSH. / Guo, Yu Wen; Kao, Hung Yu.

Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. 2013. p. 428-433 6732530 (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).

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

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Guo YW, Kao HY. Genealogical-based method for ontology self-extension in MeSH. In Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. 2013. p. 428-433. 6732530. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013). https://doi.org/10.1109/BIBM.2013.6732530