William A. Baumgartner Jr.

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 13

Top Topics

Closure Properties

Biomedical Data

Top Venues

Database J. Biol. Databases Curation

Publications

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)
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) (2023)
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 (2023)
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 Reese, Jessica Sinclair, Sanya Bathla Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew E. Williams, Xingman A. Zhang, Peter N. Robinson, Patrick Ryan, George Hripcsak, Tellen D. Bennett, Lawrence E. Hunter, Michael G. Kahn
Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality. CoRR (2022)
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 (2022)
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) (2021)
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)
Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter
Improving precision in concept normalization. PSB (2018)
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)
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 (2017)
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) (2017)
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)
K. Bretonnel Cohen, William A. Baumgartner Jr., Irina P. Temnikova
SuperCAT: The (New and Improved) Corpus Analysis Toolkit. LREC (2016)
Kevin M. Livingston, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter
KaBOB: ontology-based semantic integration of biomedical databases. BMC Bioinform. 16 (2015)
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)
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 (2014)
Irina P. Temnikova, Ivelina Nikolova, William A. Baumgartner Jr., Galia Angelova, K. Bretonnel Cohen
Closure Properties of Bulgarian Clinical Text. RANLP (2013)
Haibin Liu, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor
BioLemmatizer: a lemmatization tool for morphological processing of biomedical text. J. Biomed. Semant. 3 (2012)
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 (2012)
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 (2012)
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)
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) (2011)
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)
K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, Karin Verspoor
Test Suite Design for Biomedical Ontology Concept Recognition Systems. LREC (2010)
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) (2010)
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) (2010)
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) (2009)
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)
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)
K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter
Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing. SETQALNLP (2008)
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)
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)
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)
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) (2007)
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)
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) (2007)
Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter
Refactoring Corpora. BioNLP@NAACL-HLT (2006)
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)
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)
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)