William A. Baumgartner Jr.

According to our database, William A. Baumgartner Jr. authored at least 40 papers between 2005 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study.

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

J. Am. Medical Informatics Assoc., April, 2023

Ontologizing health systems data at scale: making translational discovery a reality.

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

npj Digit. Medicine, 2023

An Open-Source Knowledge Graph Ecosystem for the Life Sciences.

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

CoRR, 2023

2022

Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality.

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

CoRR, 2022

Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome.

Tiffany J. Callahan, Adrianne L. Stefanski, Jin-Dong Kim, William A. Baumgartner Jr., Jordan M. Wyrwa, Lawrence E. Hunter

CoRR, 2022

2021

Concept recognition as a machine translation problem.

Mayla Boguslav, Negacy D. Hailu, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter

BMC Bioinform., 2021

2019

CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference.

William A. Baumgartner Jr., Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy D. Hailu, Harrison Pielke-Lombardo, Michael Regan, Lawrence Hunter

Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, 2019

2018

OWL-NETS: Transforming OWL representations for improved network inference.

Tiffany J. Callahan, William A. Baumgartner Jr., Michael Bada, Adrianne L. Stefanski, Ignacio Tripodi, Elizabeth K. White, Lawrence E. Hunter

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

Improving precision in concept normalization.

Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

2017

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

K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E. Hunter

BMC Bioinform., 2017

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus.

Michael Bada, Nicole A. Vasilevsky, William A. Baumgartner Jr., Melissa A. Haendel, Lawrence E. Hunter

Database J. Biol. Databases Curation, 2017

2016

Coreference resolution improves extraction of Biological Expression Language statements from texts.

Miji Choi, Haibin Liu, William A. Baumgartner Jr., Justin Zobel, Karin Verspoor

Database J. Biol. Databases Curation, 2016

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

K. Bretonnel Cohen, William A. Baumgartner Jr., Irina P. Temnikova

Proceedings of the Tenth International Conference on Language Resources and Evaluation LREC 2016, 2016

2015

KaBOB: ontology-based semantic integration of biomedical databases.

Kevin M. Livingston, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter

BMC Bioinform., 2015

2014

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters.

Christopher S. Funk, William A. Baumgartner Jr., Benjamin Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence E. Hunter, Karin Verspoor

BMC Bioinform., 2014

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

Irina P. Temnikova, William A. Baumgartner Jr., Negacy D. Hailu, Ivelina Nikolova, Tony McEnery, Adam Kilgarriff, Galia Angelova, K. Bretonnel Cohen

Proceedings of the Ninth International Conference on Language Resources and Evaluation, 2014

2013

Closure Properties of Bulgarian Clinical Text.

Irina P. Temnikova, Ivelina Nikolova, William A. Baumgartner Jr., Galia Angelova, K. Bretonnel Cohen

Proceedings of the Recent Advances in Natural Language Processing, 2013

2012

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

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

BMC Bioinform., 2012

Concept annotation in the CRAFT corpus.

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

BMC Bioinform., 2012

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

Haibin Liu, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor

J. Biomed. Semant., 2012

2011

High-Precision Biological Event Extraction: Effects of System and of Data.

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

Comput. Intell., 2011

Fast and simple semantic class assignment for biomedical text.

K. Bretonnel Cohen, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter

Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, 2011

2010

Exploring Species-Based Strategies for Gene Normalization.

Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter

IEEE ACM Trans. Comput. Biol. Bioinform., 2010

A UIMA wrapper for the NCBO annotator.

Christophe Roeder, Clément Jonquet, Nigam H. Shah, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter

Bioinform., 2010

Test Suite Design for Biomedical Ontology Concept Recognition Systems.

K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, Karin Verspoor

Proceedings of the International Conference on Language Resources and Evaluation, 2010

Visualization and Language Processing for Supporting Analysis across the Biomedical Literature.

Carsten Görg, Hannah J. Tipney, Karin Verspoor, William A. Baumgartner Jr., K. Bretonnel Cohen, John T. Stasko, Lawrence Hunter

Proceedings of the Knowledge-Based and Intelligent Information and Engineering Systems, 2010

2009

Biomedical Discovery Acceleration, with Applications to Craniofacial Development.

Sonia M. Leach, Hannah J. Tipney, Weiguo Feng, William A. Baumgartner Jr., Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter

PLoS Comput. Biol., 2009

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

Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, Jun'ichi Tsujii

Bioinform., 2009

High-precision biological event extraction with a concept recognizer.

K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth K. White, Lawrence Hunter

Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, BioNLP@HLT-NAACL 2009, 2009

2008

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.

Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen

BMC Bioinform., 2008

Improving protein function prediction methods with integrated literature data.

Aaron Gabow, Sonia M. Leach, William A. Baumgartner Jr., Lawrence Hunter, Debra Goldberg

BMC Bioinform., 2008

Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP.

Andrew D. Fox, William A. Baumgartner Jr., Helen L. Johnson, Lawrence E. Hunter, Donna K. Slonim

Proceedings of the Linking Literature, Information, and Knowledge for Biology, 2008

Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing.

K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter

Proceedings of the Software Engineering, 2008

2007

Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations.

J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter

J. Bioinform. Comput. Biol., 2007

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

J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter

Bioinform., 2007

Manual curation is not sufficient for annotation of genomic databases.

William A. Baumgartner Jr., K. Bretonnel Cohen, Lynne M. Fox, George K. Acquaah-Mensah, Lawrence Hunter

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering.

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

Proceedings of the Fifteenth Text REtrieval Conference, 2006

Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies.

Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter

Proceedings of the Biocomputing 2006, 2006

Refactoring Corpora.

Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter

Proceedings of the Workshop on Linking Natural Language and Biology, 2006

2005

Concept Recognition and the TREC Genomics Tasks.

J. Gregory Caporaso, William A. Baumgartner Jr., K. Bretonnel Cohen, Helen L. Johnson, Jesse Paquette, Lawrence Hunter

Proceedings of the Fourteenth Text REtrieval Conference, 2005