title: Nominalization and alternations in biomedical language.
abstract: BACKGROUND
  This paper presents data on alternations in the argument structure of common domain-specific verbs and their associated verbal nominalizations in the PennBioIE corpus. Alternation is the term in theoretical linguistics for variations in the surface syntactic form of verbs, e.g. the different forms of stimulate in FSH stimulates follicular development and follicular development is stimulated by FSH. The data is used to assess the implications of alternations for biomedical text mining systems and to test the fit of the sublanguage model to biomedical texts.
  
  
  RESULTS
  We examined 1,872 tokens of the ten most common domain-specific verbs or their zero-related nouns in the PennBioIE corpus and labelled them for the presence or absence of three alternations. We then annotated the arguments of 746 tokens of the nominalizations related to these verbs and counted alternations related to the presence or absence of arguments and to the syntactic position of non-absent arguments. We found that alternations are quite common both for verbs and for nominalizations. We also found a previously undescribed alternation involving an adjectival present participle.
  
  
  CONCLUSIONS
  We found that even in this semantically restricted domain, alternations are quite common, and alternations involving nominalizations are exceptionally diverse. Nonetheless, the sublanguage model applies to biomedical language. We also report on a previously undescribed alternation involving an adjectival present participle.
authors.affiliation: Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, United States of America. kevin.cohen@gmail.com
authors.forename: K Bretonnel
authors.initials: KB
authors.lastname: Cohen
authors.forename: Martha
authors.initials: M
authors.lastname: Palmer
authors.forename: Lawrence
authors.initials: L
authors.lastname: Hunter
mesh_terms: D005640:Follicle Stimulating Hormone / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D007802:Language; D008037:Linguistics; D009323:Natural Language Processing; D012660:Semantics; D012984:Software; D014705:Verbal Behavior
chemical_list: D005640:Follicle Stimulating Hormone
references.citation: Bioinformatics. 2001 Feb;17(2):155-61
references.pmid: 11238071
references.citation: Pac Symp Biocomput. 2002;:362-73
references.pmid: 11928490
references.citation: BMC Bioinformatics. 2006 Nov 24;7 Suppl 3:S5
references.pmid: 17134478
references.citation: Pac Symp Biocomput. 2002;:350-61
references.pmid: 11928489
references.citation: PLoS Comput Biol. 2005 Jun;1(1):e10
references.pmid: 16103899
references.citation: Bioinformatics. 2005 Jun 1;21(11):2759-65
references.pmid: 15814565
references.citation: Cancer Lett. 1998 Dec 25;134(2):169-76
references.pmid: 10025877
references.citation: Bioinformatics. 2003;19 Suppl 1:i180-2
references.pmid: 12855455
references.citation: J Biomed Inform. 2003 Jun;36(3):145-58
references.pmid: 14615225
references.citation: Bioinformatics. 2006 Jul 1;22(13):1668-9
references.pmid: 16644790
references.citation: Brief Bioinform. 2007 Sep;8(5):358-75
references.pmid: 17977867
references.citation: BMC Bioinformatics. 2004 Oct 19;5:155
references.pmid: 15494078
references.citation: PLoS Comput Biol. 2008 Jan;4(1):e20
references.pmid: 18225946
references.citation: J Biomed Inform. 2002 Aug;35(4):222-35
references.pmid: 12755517
references.citation: J Am Med Inform Assoc. 2005 May-Jun;12(3):296-8
references.pmid: 15684123
references.citation: AMIA Annu Symp Proc. 2005;:410-4
references.pmid: 16779072
references.citation: Bioinformatics. 2005 Jun;21 Suppl 1:i319-27
references.pmid: 15961474