Lead Software Engineer
Biomedical Text Mining Group [link]
Center for Computational Pharmacology [link]
University of Colorado School of Medicine [link]
Contact information Email: william [dot] baumgartner [at] uchsc [dot] edu Address: Mail Stop 8303, P.O. Box 6511, Aurora, Colorado 80045
Research interests
Bill's current research interests focus around the development and
evaluation of natural language processing technologies applied in the
biomedical domain, particularly with regard to information extraction,
semantic parsing, and knowledgebase construction.
Software and other resources produced by the Center for Computational Pharmacology can be found at http://bionlp.sourceforge.net
Recent publications
SM Leach, H Tipney, W Feng, WA Baumgartner Jr., P Kasliwal, RP Schuyler, T Williams, RA Spritz, L Hunter. Biomedical Discovery Acceleration, with Applications to Craniofacial Development. PLoS Comput Biol 2009 5(3): e1000215. doi:10.1371/journal.pcbi.1000215 [PubMed][link]
KB Cohen, WA Baumgartner Jr., and L Hunter. Software testing and the naturally occurring data assumption in natural language processing. Software engineering, testing, and quality assurance for natural language processing 2008, pp. 23-30. Association for Computational Linguistics. [link]
AP Gabow, SM Leach, WA Baumgartner Jr., L Hunter, and DS Goldberg. Improving Protein Function Prediction Methods with Integrated Literature Data. BMC Bioinformatics 2008 15;9:198. [PubMed] [link]
F Leitner, M Krallinger, C Rodriguez-Penagos, J Hakenberg, C Plake, C-J Kuo, C-N Hsu, RT-H Tsai, H-C Hung, WW Lau, CA Johnson, R Saetre, K Yoshida, YH Chen, S Kim, S-Y Shin, B-T Zhang, WA Baumgartner Jr., L Hunter, B Haddow, M Matthews, X Wang, P Ruch, F Ehrler, Z Ozgur, G Erkan, DR Radev, M Krauthammer, TB Luong, R Hoffman, C Sander, and A Valencia. Introducing Meta-Services for Biomedical Information Extraction. Genome Biology 2008 9(Suppl 2):S6. [link]
L Smith, LK Tanabe, RJ nee Ando, C-J Kuo, I-F Chung, C-N Hsu, Y-S Lin, R Klinger, CM Friedrich, K Ganchev, M Torii, H Liu, B Haddow, CA Struble, RJ Povinelli, A Vlachos, WA Baumgartner Jr., L Hunter, B Carpenter, RT-H Tsai, H-J Dai, F Liu, Y Chen, C Sun, S Katrenko, P Adriaans, C Blaschke, R Torres, M Neves, P Nakov, A Divoli, M Mana-Lopez, J Mata-Vazquez, and WJ Wilbur. Overview of BioCreative II Gene Mention Recognition. Genome Biology 2008 9(Suppl 2):S2. [link]
WA Baumgartner Jr., Z Lu, HL Johnson, JG Caporaso, J Paquette, A Lindemann, EK White, O Medvedeva, KB Cohen, and L Hunter. Concept recognition for extracting protein interaction relations from biomedical text. Genome Biology 2008 9(Suppl 2):S9. [link]
WA Baumgartner Jr., KB Cohen, and L Hunter. An open-source framework for large-scale, flexible evaluation of biomedical text mining systems. J Biomed Discov Collab 2008, 3:1. [PubMed] [link]
L Hunter, Z Lu, J Firby, WA Baumgartner Jr., HL Johnson, PV Ogren, KB Cohen. OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression. BMC Bioinformatics 9:78. [PubMed] [link]
JG Caporaso, WA Baumgartner Jr., DA Randolph, KB Cohen, and L Hunter. Rapid pattern development for concept recognition systems: application to point mutations. J. Bioinform. Comput. Biol. 2007 Dec;5(6):1233-59. doi:10.1142/S0219720007003144. [PubMed] [link]
HL Johnson, WA Baumgartner Jr., J Lones, LM Fox, Z Voronovich, KB Cohen, and L Hunter. Two Approaches To Principled Query Expansion for Genomics Question-Answering. Proceedings of the Sixteenth Text Retrieval Conference, 2007, National Institute of Standards and Technology. [link]
HL Johnson, WA Baumgartner Jr., M Krallinger, KB Cohen, and L Hunter. Corpus refactoring: a feasibility study. J Biomed Discov Collab 2007, 2:4. [PubMed] [link]
WA Baumgartner Jr., KB Cohen, LM Fox, G Acquaah-Mensah, and L Hunter. Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 2007 23(13):i41-i48. Presented at ISMB 2007. [PubMed] [link]
JG Caporaso, WA Baumgartner Jr., DA Randolph, KB Cohen, and L Hunter. MutationFinder: A high-precision system for extracting point mutations from text. Bioinformatics 2007 15;23(14):1862-5; doi: 10.1093/bioinformatics/btm235. [PubMed] [link]
WA Baumgartner Jr., Z Lu, HL Johnson, JG Caporaso, J Paquette, A Lindemann, EK White, O Medvedeva, LM Fox, KB Cohen, and L Hunter. An integrated approach to concept recognition in biomedical text. Proceedings of the Second BioCreative Challenge Evaluation Workshop, April 2007.
JG Caporaso, WA Baumgartner Jr., H Kim, Z Lu, HL Johnson, O Medvedeva, A Lindemann, L Fox, EK White, KB Cohen, and L Hunter. Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering. Proceedings of the Fifteenth Text Retrieval Conference, 2006, National Institute of Standards and Technology. [link]
HL Johnson, KB Cohen, WA Baumgartner Jr., Z Lu, M Bada, TA Kester, H Kim, L Hunter. Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies. Pacific Symposium on Biocomputing. 2006; 11:28-39. [PubMed] [link]
JG Caporaso, WA Baumgartner Jr., KB Cohen, HL Johnson, J Paquette, and L Hunter. Concept recognition and the TREC Genomics tasks. Proceedings of the Fourteenth Text Retrieval Conference, 2005, National Institute of Standards and Technology. [link]