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Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.

Cohen KB, Lanfranchi A, Choi MJ, Bada M, Baumgartner WA Jr, Panteleyeva N, Verspoor K, Palmer M, Hunter LE.

BMC Bioinformatics. 2017 Aug 17;18(1):372. doi: 10.1186/s12859-017-1775-9.


SuperCAT: The (New and Improved) Corpus Analysis Toolkit.

Cohen KB, Baumgartner WA Jr, Temnikova I.

LREC Int Conf Lang Resour Eval. 2016 May;2016:2784-2788.


KaBOB: ontology-based semantic integration of biomedical databases.

Livingston KM, Bada M, Baumgartner WA Jr, Hunter LE.

BMC Bioinformatics. 2015 Apr 23;16:126. doi: 10.1186/s12859-015-0559-3.


Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora.

Temnikova IP, Baumgartner WA Jr, Hailu ND, Nikolova I, McEnery T, Kilgarriff A, Angelova G, Cohen KB.

LREC Int Conf Lang Resour Eval. 2014 May;2014:1714-1718.


A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.

Verspoor K, Cohen KB, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, Baumgartner WA Jr, Bada M, Palmer M, Hunter LE.

BMC Bioinformatics. 2012 Aug 17;13:207. doi: 10.1186/1471-2105-13-207.


Concept annotation in the CRAFT corpus.

Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA Jr, Cohen KB, Verspoor K, Blake JA, Hunter LE.

BMC Bioinformatics. 2012 Jul 9;13:161. doi: 10.1186/1471-2105-13-161.


BioLemmatizer: a lemmatization tool for morphological processing of biomedical text.

Liu H, Christiansen T, Baumgartner WA Jr, Verspoor K.

J Biomed Semantics. 2012 Apr 1;3:3. doi: 10.1186/2041-1480-3-3.



Cohen KB, Verspoor K, Johnson HL, Roeder C, Ogren PV, Baumgartner WA Jr, White E, Tipney H, Hunter L.

Comput Intell. 2011 Nov;27(4):681-701.


Exploring species-based strategies for gene normalization.

Verspoor K, Roeder C, Johnson HL, Cohen KB, Baumgartner WA Jr, Hunter LE.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep;7(3):462-71. doi: 10.1109/TCBB.2010.48.


A UIMA wrapper for the NCBO annotator.

Roeder C, Jonquet C, Shah NH, Baumgartner WA Jr, Verspoor K, Hunter L.

Bioinformatics. 2010 Jul 15;26(14):1800-1. doi: 10.1093/bioinformatics/btq250. Epub 2010 May 26.


U-Compare: share and compare text mining tools with UIMA.

Kano Y, Baumgartner WA Jr, McCrohon L, Ananiadou S, Cohen KB, Hunter L, Tsujii J.

Bioinformatics. 2009 Aug 1;25(15):1997-8. doi: 10.1093/bioinformatics/btp289. Epub 2009 May 4.


Concept recognition for extracting protein interaction relations from biomedical text.

Baumgartner WA Jr, Lu Z, Johnson HL, Caporaso JG, Paquette J, Lindemann A, White EK, Medvedeva O, Cohen KB, Hunter L.

Genome Biol. 2008;9 Suppl 2:S9. doi: 10.1186/gb-2008-9-s2-s9. Epub 2008 Sep 1.


Introducing meta-services for biomedical information extraction.

Leitner F, Krallinger M, Rodriguez-Penagos C, Hakenberg J, Plake C, Kuo CJ, Hsu CN, Tsai RT, Hung HC, Lau WW, Johnson CA, Saetre R, Yoshida K, Chen YH, Kim S, Shin SY, Zhang BT, Baumgartner WA Jr, Hunter L, Haddow B, Matthews M, Wang X, Ruch P, Ehrler F, Ozgür A, Erkan G, Radev DR, Krauthammer M, Luong T, Hoffmann R, Sander C, Valencia A.

Genome Biol. 2008;9 Suppl 2:S6. doi: 10.1186/gb-2008-9-s2-s6. Epub 2008 Sep 1.


Overview of BioCreative II gene mention recognition.

Smith L, Tanabe LK, Ando RJ, Kuo CJ, Chung IF, Hsu CN, Lin YS, Klinger R, Friedrich CM, Ganchev K, Torii M, Liu H, Haddow B, Struble CA, Povinelli RJ, Vlachos A, Baumgartner WA Jr, Hunter L, Carpenter B, Tsai RT, Dai HJ, Liu F, Chen Y, Sun C, Katrenko S, Adriaans P, Blaschke C, Torres R, Neves M, Nakov P, Divoli A, Maña-López M, Mata J, Wilbur WJ.

Genome Biol. 2008;9 Suppl 2:S2. doi: 10.1186/gb-2008-9-s2-s2. Epub 2008 Sep 1.


OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression.

Hunter L, Lu Z, Firby J, Baumgartner WA Jr, Johnson HL, Ogren PV, Cohen KB.

BMC Bioinformatics. 2008 Jan 31;9:78. doi: 10.1186/1471-2105-9-78.


An open-source framework for large-scale, flexible evaluation of biomedical text mining systems.

Baumgartner WA Jr, Cohen KB, Hunter L.

J Biomed Discov Collab. 2008 Jan 29;3:1. doi: 10.1186/1747-5333-3-1.


Corpus refactoring: a feasibility study.

Johnson HL, Baumgartner WA Jr, Krallinger M, Cohen KB, Hunter L.

J Biomed Discov Collab. 2007 Sep 13;2:4.


Manual curation is not sufficient for annotation of genomic databases.

Baumgartner WA Jr, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L.

Bioinformatics. 2007 Jul 1;23(13):i41-8.


MutationFinder: a high-performance system for extracting point mutation mentions from text.

Caporaso JG, Baumgartner WA Jr, Randolph DA, Cohen KB, Hunter L.

Bioinformatics. 2007 Jul 15;23(14):1862-5. Epub 2007 May 11.


Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.

Johnson HL, Cohen KB, Baumgartner WA Jr, Lu Z, Bada M, Kester T, Kim H, Hunter L.

Pac Symp Biocomput. 2006:28-39.

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