William A. Baumgartner Jr.

40 papers B 3Misc 4Journal 23Unranked 10
YearRankTypeTitle / Venue / Authors
2023 J jnl
An Open-Source Knowledge Graph Ecosystem for the Life Sciences.
CoRR
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
2023 J jnl
Ontologizing health systems data at scale: making translational discovery a reality.
npj Digit. Medicine
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
2023 J jnl
Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study.
J. Am. Medical Informatics Assoc.
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
2022 J jnl
Knowledge-Driven Mechanistic Enrichment of the Preeclampsia Ignorome.
CoRR
Tiffany J. Callahan, Adrianne L. Stefanski, Jin-Dong Kim, William A. Baumgartner Jr., Jordan M. Wyrwa, Lawrence E. Hunter
2022 J jnl
Ontologizing Health Systems Data at Scale: Making Translational Discovery a Reality.
CoRR
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
2021 J jnl
Concept recognition as a machine translation problem.
BMC Bioinform.
Mayla Boguslav, Negacy D. Hailu, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter
2019 — conf
CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference.
BioNLP-OST@EMNLP-IJNCLP
William A. Baumgartner Jr., Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy D. Hailu, Harrison Pielke-Lombardo, Michael Regan, Lawrence Hunter
2018 Misc conf
Improving precision in concept normalization.
PSB
Mayla Boguslav, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence E. Hunter
2018 Misc conf
OWL-NETS: Transforming OWL representations for improved network inference.
PSB
Tiffany J. Callahan, William A. Baumgartner Jr., Michael Bada, Adrianne L. Stefanski, Ignacio Tripodi, Elizabeth K. White, Lawrence E. Hunter
2017 J jnl
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles.
BMC Bioinform.
K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E. Hunter
2017 J jnl
Gold-standard ontology-based anatomical annotation in the CRAFT Corpus.
Database J. Biol. Databases Curation
Michael Bada, Nicole A. Vasilevsky, William A. Baumgartner Jr., Melissa A. Haendel, Lawrence E. Hunter
2016 J jnl
Coreference resolution improves extraction of Biological Expression Language statements from texts.
Database J. Biol. Databases Curation
Miji Choi, Haibin Liu, William A. Baumgartner Jr., Justin Zobel, Karin Verspoor
2016 B conf
SuperCAT: The (New and Improved) Corpus Analysis Toolkit.
LREC
K. Bretonnel Cohen, William A. Baumgartner Jr., Irina P. Temnikova
2015 J jnl
KaBOB: ontology-based semantic integration of biomedical databases.
BMC Bioinform.
Kevin M. Livingston, Michael Bada, William A. Baumgartner Jr., Lawrence E. Hunter
2014 J jnl
Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters.
BMC Bioinform.
Christopher S. Funk, William A. Baumgartner Jr., Benjamin Garcia, Christophe Roeder, Michael Bada, K. Bretonnel Cohen, Lawrence E. Hunter, Karin Verspoor
2014 B conf
Sublanguage Corpus Analysis Toolkit: A tool for assessing the representativeness and sublanguage characteristics of corpora.
LREC
Irina P. Temnikova, William A. Baumgartner Jr., Negacy D. Hailu, Ivelina Nikolova, Tony McEnery, Adam Kilgarriff, Galia Angelova, K. Bretonnel Cohen
2013 Misc conf
Closure Properties of Bulgarian Clinical Text.
RANLP
Irina P. Temnikova, Ivelina Nikolova, William A. Baumgartner Jr., Galia Angelova, K. Bretonnel Cohen
2012 J jnl
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.
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
2012 J jnl
BioLemmatizer: a lemmatization tool for morphological processing of biomedical text.
J. Biomed. Semant.
Haibin Liu, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor
2012 J jnl
Concept annotation in the CRAFT corpus.
BMC Bioinform.
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
2011 — conf
Fast and simple semantic class assignment for biomedical text.
BioNLP@ACL
K. Bretonnel Cohen, Tom Christiansen, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter
2011 J jnl
High-Precision Biological Event Extraction: Effects of System and of Data.
Comput. Intell.
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
2010 J jnl
A UIMA wrapper for the NCBO annotator.
Bioinform.
Christophe Roeder, Clément Jonquet, Nigam H. Shah, William A. Baumgartner Jr., Karin Verspoor, Lawrence Hunter
2010 J jnl
Exploring Species-Based Strategies for Gene Normalization.
IEEE ACM Trans. Comput. Biol. Bioinform.
Karin Verspoor, Christophe Roeder, Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter
2010 B conf
Test Suite Design for Biomedical Ontology Concept Recognition Systems.
LREC
K. Bretonnel Cohen, Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter, Karin Verspoor
2010 — conf
Visualization and Language Processing for Supporting Analysis across the Biomedical Literature.
KES (4)
Carsten Görg, Hannah J. Tipney, Karin Verspoor, William A. Baumgartner Jr., K. Bretonnel Cohen, John T. Stasko, Lawrence Hunter
2009 J jnl
Biomedical Discovery Acceleration, with Applications to Craniofacial Development.
PLoS Comput. Biol.
Sonia M. Leach, Hannah J. Tipney, Weiguo Feng, William A. Baumgartner Jr., Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter
2009 — conf
High-precision biological event extraction with a concept recognizer.
BioNLP@HLT-NAACL (Shared Task)
K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth K. White, Lawrence Hunter
2009 J jnl
U-Compare: share and compare text mining tools with UIMA.
Bioinform.
Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, Jun'ichi Tsujii
2008 J jnl
Improving protein function prediction methods with integrated literature data.
BMC Bioinform.
Aaron Gabow, Sonia M. Leach, William A. Baumgartner Jr., Lawrence Hunter, Debra Goldberg
2008 — conf
Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP.
BioLINK@ISMB/ECCB
Andrew D. Fox, William A. Baumgartner Jr., Helen L. Johnson, Lawrence E. Hunter, Donna K. Slonim
2008 J jnl
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.
Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen
2008 — conf
Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing.
SETQALNLP
K. Bretonnel Cohen, William A. Baumgartner Jr., Lawrence Hunter
2007 — conf
Manual curation is not sufficient for annotation of genomic databases.
ISMB/ECCB (Supplement of Bioinformatics)
William A. Baumgartner Jr., K. Bretonnel Cohen, Lynne M. Fox, George K. Acquaah-Mensah, Lawrence Hunter
2007 J jnl
MutationFinder: a high-performance system for extracting point mutation mentions from text.
Bioinform.
J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter
2007 J jnl
Rapid Pattern Development for Concept Recognition Systems: Application to Point mutations.
J. Bioinform. Comput. Biol.
J. Gregory Caporaso, William A. Baumgartner Jr., David A. Randolph, K. Bretonnel Cohen, Lawrence Hunter
2006 — conf
Concept Recognition, Information Retrieval, and Machine Learning in Genomics Question-Answering.
TREC
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
2006 Misc conf
Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies.
Pacific Symposium on Biocomputing
Helen L. Johnson, K. Bretonnel Cohen, William A. Baumgartner Jr., Zhiyong Lu, Michael Bada, Todd Kester, Hyunmin Kim, Lawrence Hunter
2006 — conf
Refactoring Corpora.
BioNLP@NAACL-HLT
Helen L. Johnson, William A. Baumgartner Jr., Martin Krallinger, K. Bretonnel Cohen, Lawrence Hunter
2005 — conf
Concept Recognition and the TREC Genomics Tasks.
TREC
J. Gregory Caporaso, William A. Baumgartner Jr., K. Bretonnel Cohen, Helen L. Johnson, Jesse Paquette, Lawrence Hunter