Linking ontological resources using aggregatable substance identifiers to organize extracted relations

Byron Marshall, Hua Su, Daniel McDonald, Hsinchun Chen

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

2 Scopus citations

Abstract

Systems that extract biological regulatory pathway relations from free-text sources are intended to help researchers leverage vast and growing collections of research literature. Several systems to extract such relations have been developed but little work has focused on how those relations can be usefully organized (aggregated) to support visualization systems or analysis algorithms. Ontological resources that enumerate name strings for different types of biomedical objects should play a key role in the organization process. In this paper we delineate five potentially useful levels of relational granularity and propose the use of aggregatable substance identifiers to help reduce lexical ambiguity. An aggregatable substance identifier applies to a gene and its products. We merged 4 extensive lexicons and compared the extracted strings to the text of five million MEDLINE abstracts. We report on the ambiguity within and between name strings and common English words. Our results show an 89% reduction in ambiguity for the extracted human substance name strings when using an aggregatable substance approach.

Original languageEnglish (US)
Title of host publicationProceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005
Pages162-173
Number of pages12
StatePublished - 2005
Event10th Pacific Symposium on Biocomputing, PSB 2005 - Big Island of Hawaii, United States
Duration: Jan 4 2005Jan 8 2005

Publication series

NameProceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005

Other

Other10th Pacific Symposium on Biocomputing, PSB 2005
CountryUnited States
CityBig Island of Hawaii
Period1/4/051/8/05

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering

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    Marshall, B., Su, H., McDonald, D., & Chen, H. (2005). Linking ontological resources using aggregatable substance identifiers to organize extracted relations. In Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005 (pp. 162-173). (Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005).