Using contextual information to clarify gene normalization ambiguity

Po Ting Lai, Yue Yang Bow, Chi Hsin Huang, Hong Jie Dai, Richard Tzong Han Tsai, Wen Lian Hsu

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

7 Scopus citations

Abstract

The goal of Gene Normalization (GN) is to identify the unique database identifiers of genes and proteins mentioned in biomedical literature. A major difficulty in GN comes from inter-species gene ambiguity. That is, the same gene name can refer to different database identifiers depending on the species in question. In this paper, we introduce a method to exploit contextual information in an abstract, like tissue type, chromosome location, etc., to tackle this problem. Using this technique, we have been able to improve system performance (F-score) by 14.3% on the BioCreAtIvE-II GN task test set.

Original languageEnglish
Title of host publication2009 IEEE International Conference on Information Reuse and Integration, IRI 2009
Pages1-5
Number of pages5
DOIs
StatePublished - 2009
Event2009 IEEE International Conference on Information Reuse and Integration, IRI 2009 - Las Vegas, NV, United States
Duration: 10 Aug 200912 Aug 2009

Publication series

Name2009 IEEE International Conference on Information Reuse and Integration, IRI 2009

Conference

Conference2009 IEEE International Conference on Information Reuse and Integration, IRI 2009
Country/TerritoryUnited States
CityLas Vegas, NV
Period10/08/0912/08/09

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