title: SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedicine.
abstract: Many text-mining studies have focused on the issue of named entity recognition and normalization, especially in the field of biomedical natural language processing. However, entity recognition is a complicated and difficult task in biomedical text. One particular challenge is to identify and resolve composite named entities, where a single span refers to more than one concept(e.g., BRCA1/2). Most bioconcept recognition and normalization studies have either ignored this issue, used simple ad-hoc rules, or only handled coordination ellipsis, which is only one of the many types of composite mentions studied in this work. No systematic methods for simplifying composite mentions have been previously reported, making a robust approach greatly needed. To this end, we propose a hybrid approach by integrating a machine learning model with a pattern identification strategy to identify the antecedent and conjuncts regions of a concept mention, and then reassemble the composite mention using those identified regions. Our method, which we have named SimConcept, is the first method to systematically handle most types of composite mentions. Our method achieves high performance in identifying and resolving composite mentions for three fundamental biological entities: genes (89.29% in F-measure), diseases (85.52% in F-measure) and chemicals (84.04% in F-measure). Furthermore, our results show that, using our SimConcept method can subsequently help improve the performance of gene and disease concept recognition and normalization.
authors.affiliation: 8600 Rockville Pike, National Center for Biotechnology Information (NCBI), Bethesda, Maryland, USA, 20894.
authors.forename: Chih-Hsuan
authors.initials: CH
authors.lastname: Wei
authors.affiliation: 8600 Rockville Pike, National Center for Biotechnology Information (NCBI), Bethesda, Maryland, USA, 20894.
authors.forename: Robert
authors.initials: R
authors.lastname: Leaman
authors.affiliation: 8600 Rockville Pike, National Center for Biotechnology Information (NCBI), Bethesda, Maryland, USA, 20894.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Lu
keywords: Algorithms; Mention simplification; conditional random field; name entity normalization; name entity recognition; natural language processing
references.citation: J Biomed Inform. 2014 Feb;47:1-10
references.pmid: 24393765
references.citation: BMC Bioinformatics. 2008 Jun 11;9:277
references.pmid: 18547432
references.citation: J Biomed Semantics. 2014 Jan 17;5(1):3
references.pmid: 24438362
references.citation: Bioinformatics. 2003;19 Suppl 1:i180-2
references.pmid: 12855455
references.citation: BMC Bioinformatics. 2011 Oct 03;12 Suppl 8:S1
references.pmid: 22151647
references.citation: Inf Process Manag. 2007 Nov;43(6):1606-1618
references.pmid: 32287938
references.citation: J Biomed Semantics. 2011 Oct 06;2 Suppl 5:S11
references.pmid: 22166494
references.citation: J Biomed Inform. 2012 Oct;45(5):870-8
references.pmid: 22546622
references.citation: Database (Oxford). 2014 May 22;2014:
references.pmid: 24852177
references.citation: Bioinformatics. 2013 Jun 1;29(11):1433-9
references.pmid: 23564842
references.citation: BMC Bioinformatics. 2011 Oct 03;12 Suppl 8:S2
references.pmid: 22151901
references.citation: BMC Bioinformatics. 2011 Oct 03;12 Suppl 8:S3
references.pmid: 22151929
references.citation: Bioinformatics. 2012 Jun 15;28(12):1633-40
references.pmid: 22500000
references.citation: Bioinformatics. 2008 Aug 15;24(16):i126-132
references.pmid: 18689813
references.citation: BMC Bioinformatics. 2005;6 Suppl 1:S16
references.pmid: 15960828
references.citation: J Biomed Inform. 2014 Feb;47:139-52
references.pmid: 24153413
references.citation: BMC Bioinformatics. 2011 Oct 03;12 Suppl 8:S5
references.pmid: 22151999
references.citation: Database (Oxford). 2012 Nov 17;2012:bas041
references.pmid: 23160414
references.citation: Bioinformatics. 2013 Nov 15;29(22):2909-17
references.pmid: 23969135
references.citation: PLoS One. 2012;7(6):e38460
references.pmid: 22679507
references.citation: AMIA Annu Symp Proc. 2010 Nov 13;2010:351-5
references.pmid: 21346999
references.citation: BMC Bioinformatics. 2011 Jun 09;12 Suppl 3:S3
references.pmid: 21658290
references.citation: Nucleic Acids Res. 2013 Jul;41(Web Server issue):W518-22
references.pmid: 23703206
references.citation: J Chem Inf Model. 2011 Mar 28;51(3):739-53
references.pmid: 21384929
references.citation: Bioinformatics. 2009 Mar 15;25(6):815-21
references.pmid: 19188193
references.citation: AMIA Annu Symp Proc. 2012;2012:522-31
references.pmid: 23304324
references.citation: J Biomed Inform. 2011 Apr;44(2):310-8
references.pmid: 21094696
references.citation: Brief Bioinform. 2007 Sep;8(5):358-75
references.pmid: 17977867
references.citation: BMC Bioinformatics. 2008 Jan 31;9:78
references.pmid: 18237434
references.citation: Genome Biol. 2008;9 Suppl 2:S3
references.pmid: 18834494
references.citation: Bioinformatics. 2002 Aug;18(8):1124-32
references.pmid: 12176836
references.citation: Genome Biol. 2008;9 Suppl 2:S9
references.pmid: 18834500
references.citation: BMC Bioinformatics. 2008 Sep 25;9:402
references.pmid: 18817555