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ORCIDWilliam A. Baumgartner Jr.
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2020 – today
- 2023
[j20]Anna Ostropolets
, Yasser Albogami, Mitchell Conover, Juan M. Banda, William A. Baumgartner Jr., Clair Blacketer, Priyamvada Desai, Scott L. DuVall, Stephen P. Fortin, James P. Gilbert, Asieh Golozar, Joshua Ide, Andrew S. Kanter, David M. Kern, Chungsoo Kim, Lana Y. H. Lai, Chenyu Li, Feifan Liu, Kristine E. Lynch, Evan Minty, Maria Inês Neves, Ding Quan Ng, Tontel Obene, Victor Pera, Nicole Pratt, Gowtham Rao, Nadav Rappoport, Ines Reinecke, Paola Saroufim, Azza Shoaibi, Katherine Simon, Marc A. Suchard, Joel N. Swerdel, Erica A. Voss, James Weaver, Linying Zhang, George Hripcsak, Patrick B. Ryan:
Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study. J. Am. Medical Informatics Assoc. 30(5): 859-868 (2023)- [j19]Tiffany J. Callahan, Adrianne L. Stefanski, Jordan M. Wyrwa, Chenjie Zeng, Anna Ostropolets, Juan M. Banda, William A. Baumgartner Jr., Richard D. Boyce, Elena Casiraghi, Ben D. Coleman, Janine H. Collins, Sara J. Deakyne Davies, James A. Feinstein, Asiyah Y. Lin, Blake Martin, Nicolas A. Matentzoglu, Daniella Meeker, Justin T. Reese, Jessica Sinclair, Sanya Bathla Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew E. Williams, Xingmin Aaron Zhang, Joshua C. Denny, Patrick B. Ryan, George Hripcsak, Tellen D. Bennett, Melissa A. Haendel, Peter N. Robinson, Lawrence E. Hunter, Michael G. Kahn:
Ontologizing health systems data at scale: making translational discovery a reality. npj Digit. Medicine 6 (2023) - [i3]Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya Bathla Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin T. Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook E. Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter:
An Open-Source Knowledge Graph Ecosystem for the Life Sciences. CoRR abs/2307.05727 (2023) - 2022
- [i2]Tiffany J. Callahan, Adrianne L. Stefanski, Jin-Dong Kim, William A. Baumgartner Jr., Jordan M. Wyrwa, Lawrence E. Hunter:
Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome. CoRR abs/2207.14294 (2022) - [i1]Tiffany J. Callahan, Adrianne L. Stefanski, Jordan M. Wyrwa, Chenjie Zeng, Anna Ostropolets, Juan M. Banda, William A. Baumgartner Jr., Richard D. Boyce, Elena Casiraghi, Ben D. Coleman, Janine H. Collins, Sara J. Deakyne Davies, James A. Feinstein, Melissa A. Haendel, Asiyah Y. Lin, Blake Martin, Nicolas Matentzoglu, Daniella Meeker, Justin T. Reese, Jessica Sinclair, Sanya Bathla Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew E. Williams, Xingman A. Zhang, Peter N. Robinson, Patrick B. Ryan, George Hripcsak, Tellen D. Bennett, Lawrence E. Hunter, Michael G. Kahn:
Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality. CoRR abs/2209.04732 (2022) - 2021
- [j18]Mayla Boguslav, Negacy D. Hailu, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter:
Concept recognition as a machine translation problem. BMC Bioinform. 22(1): 598 (2021)
2010 – 2019
- 2019
- [c17]William A. Baumgartner Jr., Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy D. Hailu, Harrison Pielke-Lombardo, Michael Regan, Lawrence Hunter:
CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference. BioNLP-OST@EMNLP-IJNCLP 2019: 174-184 - 2018
- [c16]Tiffany J. Callahan, William A. Baumgartner Jr., Michael Bada, Adrianne L. Stefanski, Ignacio Tripodi, Elizabeth K. White, Lawrence E. Hunter:
OWL-NETS: Transforming OWL representations for improved network inference. PSB 2018: 133-144 - [c15]Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter:
Improving precision in concept normalization. PSB 2018: 566-577 - 2017
- [j17]Michael Bada, Nicole A. Vasilevsky, William A. Baumgartner Jr., Melissa A. Haendel, Lawrence E. Hunter:
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. Database J. Biol. Databases Curation 2017: bax087 (2017) - [j16]K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E. Hunter:
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinform. 18(1): 372:1-372:14 (2017) - 2016
- [j15]Miji Choi, Haibin Liu, William A. Baumgartner Jr., Justin Zobel, Karin Verspoor:
Coreference resolution improves extraction of Biological Expression Language statements from texts. Database J. Biol. Databases Curation 2016 (2016) - [c14]K. Bretonnel Cohen, William A. Baumgartner Jr., Irina P. Temnikova:
SuperCAT: The (New and Improved) Corpus Analysis Toolkit. LREC 2016 - 2015
- [j14]Kevin M. Livingston, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter:
KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinform. 16: 126:1-126:21 (2015) - 2014
- [j13]Christopher S. Funk, William A. Baumgartner Jr., Benjamin Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence E. Hunter, Karin Verspoor:
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters. BMC Bioinform. 15: 59 (2014) - [c13]Irina P. Temnikova, William A. Baumgartner Jr., Negacy D. Hailu, Ivelina Nikolova, Tony McEnery, Adam Kilgarriff, Galia Angelova, K. Bretonnel Cohen:
Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora. LREC 2014: 1714-1718 - 2013
- [c12]Irina P. Temnikova, Ivelina Nikolova, William A. Baumgartner Jr., Galia Angelova, K. Bretonnel Cohen:
Closure Properties of Bulgarian Clinical Text. RANLP 2013: 667-675 - 2012
- [j12]Haibin Liu, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor:
BioLemmatizer: a lemmatization tool for morphological processing of biomedical text. J. Biomed. Semant. 3: 3 (2012) - [j11]Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A. Baumgartner Jr., K. Bretonnel Cohen, Karin Verspoor, Judith A. Blake, Lawrence E. Hunter:
Concept annotation in the CRAFT corpus. BMC Bioinform. 13: 161 (2012) - [j10]Karin Verspoor, Kevin Bretonnel Cohen, Arrick Lanfranchi, Colin Warner, Helen L. Johnson, Christophe Roeder, Jinho D. Choi, Christopher S. Funk, Yuriy Malenkiy, Miriam Eckert, Nianwen Xue, William A. Baumgartner Jr., Michael Bada, Martha Palmer, Lawrence E. Hunter:
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinform. 13: 207 (2012) - 2011
- [j9]K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth K. White, Hannah J. Tipney, Lawrence Hunter:
High-Precision Biological Event Extraction: Effects of System and of Data. Comput. Intell. 27(4): 681-701 (2011) - [c11]K. Bretonnel Cohen, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter:
Fast and simple semantic class assignment for biomedical text. BioNLP@ACL 2011: 38-45 - 2010
- [j8]Christophe Roeder, Clément Jonquet, Nigam H. Shah, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter:
A UIMA wrapper for the NCBO annotator. Bioinform. 26(14): 1800-1801 (2010) - [j7]Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter:
Exploring Species-Based Strategies for Gene Normalization. IEEE ACM Trans. Comput. Biol. Bioinform. 7(3): 462-471 (2010) - [c10]Carsten Görg, Hannah J. Tipney, Karin Verspoor, William A. Baumgartner Jr., K. Bretonnel Cohen, John T. Stasko, Lawrence Hunter:
Visualization and Language Processing for Supporting Analysis across the Biomedical Literature. KES (4) 2010: 420-429 - [c9]K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, Karin Verspoor:
Test Suite Design for Biomedical Ontology Concept Recognition Systems. LREC 2010
2000 – 2009
- 2009
- [j6]Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, Jun'ichi Tsujii:
U-Compare: share and compare text mining tools with UIMA. Bioinform. 25(15): 1997-1998 (2009) - [j5]Sonia M. Leach, Hannah J. Tipney, Weiguo Feng, William A. Baumgartner Jr., Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter:
Biomedical Discovery Acceleration, with Applications to Craniofacial Development. PLoS Comput. Biol. 5(3) (2009) - [c8]K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth K. White, Lawrence Hunter:
High-precision biological event extraction with a concept recognizer. BioNLP@HLT-NAACL (Shared Task) 2009: 50-58 - 2008
- [j4]Aaron Gabow, Sonia M. Leach, William A. Baumgartner Jr., Lawrence Hunter, Debra Goldberg:
Improving protein function prediction methods with integrated literature data. BMC Bioinform. 9 (2008) - [j3]Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen:
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. BMC Bioinform. 9 (2008) - [c7]K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter:
Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing. SETQALNLP 2008: 23-30 - [c6]Andrew D. Fox, William A. Baumgartner Jr., Helen L. Johnson, Lawrence E. Hunter, Donna K. Slonim:
Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP. BioLINK@ISMB/ECCB 2008: 43-52 - 2007
- [j2]J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter:
MutationFinder: a high-performance system for extracting point mutation mentions from text. Bioinform. 23(14): 1862-1865 (2007) - [j1]J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter:
Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations. J. Bioinform. Comput. Biol. 5(6): 1233-1259 (2007) - [c5]William A. Baumgartner Jr., K. Bretonnel Cohen, Lynne M. Fox, George K. Acquaah-Mensah, Lawrence Hunter:
Manual curation is not sufficient for annotation of genomic databases. ISMB/ECCB (Supplement of Bioinformatics) 2007: 41-48 - 2006
- [c4]Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter:
Refactoring Corpora. BioNLP@NAACL-HLT 2006: 116-117 - [c3]Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter:
Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. Pacific Symposium on Biocomputing 2006: 28-39 - [c2]J. Gregory Caporaso, William A. Baumgartner Jr., Hyunmin Kim, Zhiyong Lu, Helen L. Johnson, Olga Medvedeva, Anna Lindemann, Lynne M. Fox, Elizabeth K. White, K. Bretonnel Cohen, Lawrence Hunter:
Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering. TREC 2006 - 2005
- [c1]J. Gregory Caporaso, William A. Baumgartner Jr., K. Bretonnel Cohen, Helen L. Johnson, Jesse Paquette, Lawrence Hunter:
Concept Recognition and the TREC Genomics Tasks. TREC 2005
Coauthor Index
aka: Lawrence E. Hunter
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