Concept Recognition and the TREC Genomics Tasks. - J. Gregory Caporaso; William A. Baumgartner Jr.; K. Bretonnel Cohen; Helen L. Johnson 001; Jesse Paquette; Lawrence Hunter (TREC, 2005)

Refactoring Corpora. - Helen L. Johnson 001; William A. Baumgartner Jr.; Martin Krallinger; K. Bretonnel Cohen; Lawrence Hunter (BioNLP@NAACL-HLT, 2006)

Evaluation of Lexical Methods for Detecting Relationships Between Concepts from Multiple Ontologies. - Helen L. Johnson 001; K. Bretonnel Cohen; William A. Baumgartner Jr.; Zhiyong Lu; Michael Bada; Todd Kester; Hyunmin Kim; Lawrence Hunter (Pacific Symposium on Biocomputing, 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 001; Olga Medvedeva; Anna Lindemann; Lynne M. Fox; Elizabeth K. White; K. Bretonnel Cohen; Lawrence Hunter (TREC, 2006)

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 (ISMB/ECCB (Supplement of Bioinformatics), 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)

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)

Software Testing and the Naturally Occurring Data Assumption in Natural Language Processing. - K. Bretonnel Cohen; William A. Baumgartner Jr.; Lawrence Hunter (SETQALNLP, 2008)

Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP. - Andrew D. Fox; William A. Baumgartner Jr.; Helen L. Johnson 001; Lawrence E. Hunter; Donna K. Slonim (BioLINK@ISMB/ECCB, 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)

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 001; Philip V. Ogren; K. Bretonnel Cohen (BMC Bioinform., 2008)

High-precision biological event extraction with a concept recognizer. - K. Bretonnel Cohen; Karin Verspoor; Helen L. Johnson 001; Christophe Roeder; Philip V. Ogren; William A. Baumgartner Jr.; Elizabeth K. White; Lawrence Hunter (BioNLP@HLT-NAACL (Shared Task), 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)

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)

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 (KES (4), 2010)

Test Suite Design for Biomedical Ontology Concept Recognition Systems. - K. Bretonnel Cohen; Christophe Roeder; William A. Baumgartner Jr.; Lawrence Hunter; Karin Verspoor (LREC, 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)

Exploring Species-Based Strategies for Gene Normalization. - Karin Verspoor; Christophe Roeder; Helen L. Johnson 001; K. Bretonnel Cohen; William A. Baumgartner Jr.; Lawrence Hunter (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Fast and simple semantic class assignment for biomedical text. - K. Bretonnel Cohen; Tom Christiansen; William A. Baumgartner Jr.; Karin Verspoor; Lawrence Hunter (BioNLP@ACL, 2011)

High-Precision Biological Event Extraction: Effects of System and of Data. - K. Bretonnel Cohen; Karin Verspoor; Helen L. Johnson 001; Christophe Roeder; Philip V. Ogren; William A. Baumgartner Jr.; Elizabeth K. White; Hannah J. Tipney; Lawrence Hunter (Comput. Intell., 2011)

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text. - Haibin Liu; Tom Christiansen; William A. Baumgartner Jr.; Karin Verspoor (J. Biomed. Semant., 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)

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 001; Christophe Roeder; Jinho D. Choi; Christopher S. Funk; Yuriy Malenkiy; Miriam Eckert; Nianwen Xue; William A. Baumgartner Jr.; et al. (BMC Bioinform., 2012)

Closure Properties of Bulgarian Clinical Text. - Irina P. Temnikova; Ivelina Nikolova; William A. Baumgartner Jr.; Galia Angelova; K. Bretonnel Cohen (RANLP, 2013)

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 (LREC, 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)

KaBOB: ontology-based semantic integration of biomedical databases. - Kevin M. Livingston; Michael Bada; William A. Baumgartner Jr.; Lawrence E. Hunter (BMC Bioinform., 2015)

SuperCAT: The (New and Improved) Corpus Analysis Toolkit. - K. Bretonnel Cohen; William A. Baumgartner Jr.; Irina P. Temnikova (LREC, 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)

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)

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)

Improving precision in concept normalization. - Mayla Boguslav; K. Bretonnel Cohen; William A. Baumgartner Jr.; Lawrence E. Hunter (PSB, 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 (PSB, 2018)

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 (BioNLP-OST@EMNLP-IJNCLP, 2019)

PheKnowLator. - TJ Callahan; William A. Baumgartner Jr.; Ignacio J. Tripodi; Adrianne L. Stefanski; Jordan M. Wyrwa; Lawrence Hunter (Zenodo, 2019)

OMOP2OBO Drug Exposure Ingredient Mappings. - Tiffany J. Callahan; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Drug Exposure Ingredient Mappings. - Tiffany J. Callahan; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Drug Exposure Ingredient Mappings. - Tiffany J. Callahan; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Drug Exposure Ingredient Mappings. - Tiffany J. Callahan; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Drug Exposure Ingredient Mappings. - Tiffany J. Callahan; William A. Baumgartner Jr.; Jordan M. Wyrwa; Nicole A. Vasilevsky; Tellen D. Bennett; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Measurement Mappings. - Tiffany J. Callahan; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Measurement Mappings. - Tiffany J. Callahan; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Measurement Mappings. - Tiffany J. Callahan; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Measurement Mappings. - Tiffany J. Callahan; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Measurement Mappings. - Tiffany J. Callahan; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Measurement Mappings. - Tiffany J. Callahan; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Measurement Mappings. - Tiffany J. Callahan; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Measurement Mappings - WRONG DATA FILE UPLOADED IGNORE THIS VERSION. - Tiffany J. Callahan; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Measurement Mappings. - Tiffany J. Callahan; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Condition Occurrence Mappings. - Tiffany J. Callahan; Jordan M. Wyrwa; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Condition Occurrence Mappings. - Tiffany J. Callahan; Jordan M. Wyrwa; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Condition Occurrence Mappings. - Tiffany J. Callahan; Jordan M. Wyrwa; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Condition Occurrence Mappings. - Tiffany J. Callahan; Jordan M. Wyrwa; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Condition Occurrence Mappings. - Tiffany J. Callahan; Jordan M. Wyrwa; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Condition Occurrence Mappings. - Tiffany J. Callahan; Jordan M. Wyrwa; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

OMOP2OBO Condition Occurrence Mappings. - Tiffany J. Callahan; Jordan M. Wyrwa; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2020)

Concept recognition as a machine translation problem. - Mayla Boguslav; Negacy D. Hailu; Michael Bada; William A. Baumgartner Jr.; Lawrence E. Hunter (BMC Bioinform., 2021)

Adapting the Harmonized Data Quality Framework for Ontology Quality Assessment. - Tiffany J. Callahan; William A. Baumgartner Jr.; Nicolas A. Matentzoglu; Nicole A. Vasilevsky; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2021)

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)

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; et al. (CoRR, 2022)

Adapting the Harmonized Data Quality Framework for Ontology Quality Assessment. - Tiffany J. Callahan; William A. Baumgartner Jr.; Nicolas A. Matentzoglu; Nicole A. Vasilevsky; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2022)

OMOP2OBO Condition Occurrence Mappings. - Tiffany J. Callahan; Jordan M. Wyrwa; Nicole A. Vasilevsky; Tellen D. Bennett; Blake Martin; James A. Feinstein; William A. Baumgartner Jr.; Lawrence E. Hunter; Michael G. Kahn (Zenodo, 2022)

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; et al. (CoRR, 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; et al. (npj Digit. Medicine, 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; et al. (J. Am. Medical Informatics Assoc., 2023)