A randomized double-blind controlled trial of automated term dissection. - Peter L. Elkin; Kent R. Bailey; Philip V. Ogren; Brent A. Bauer; Christopher G. Chute (AMIA, 1999)

A large-scale evaluation of terminology integration characteristics. - Furman S. McDonald; Christopher G. Chute; Philip V. Ogren; Dietlind Wahner-Roedler; Peter L. Elkin (AMIA, 1999)

Barriers to the clinical implementation of compositionality. - Lawrence K. McKnight; Peter L. Elkin; Philip V. Ogren; Christopher G. Chute (AMIA, 1999)

A randomized controlled trial of concept based indexing of Web page content. - Peter L. Elkin; Alexander Ruggieri; Larry Bergstrom; Brent A. Bauer; Mark Lee; Philip V. Ogren; Christopher G. Chute (AMIA, 2000)

A formal approach to integrating synonyms with a reference terminology. - Harold R. Solbrig; Peter L. Elkin; Philip V. Ogren; Christopher G. Chute (AMIA, 2000)

The Compositional Structure of Gene Ontology Terms. - Philip V. Ogren; K. Bretonnel Cohen; George K. Acquaah-Mensah; Jens Eberlein; Lawrence Hunter (Pacific Symposium on Biocomputing, 2004)

Empirical data on corpus design and usage in biomedical natural language processing. - K. Bretonnel Cohen; Philip V. Ogren; Lynne M. Fox; Lawrence Hunter (AMIA, 2005)

Corpus Design for Biomedical Natural Language Processing. - K. Bretonnel Cohen; Lynne M. Fox; Philip V. Ogren; Lawrence Hunter (LBLODMBS@IDMB, 2005)

Implications of Compositionality in the Gene Ontology for Its Curation and Usage . - Philip V. Ogren; K. Bretonnel Cohen; Lawrence Hunter (Pacific Symposium on Biocomputing, 2005)

BioCreAtIvE Task1A: entity identification with a stochastic tagger. - Shuhei Kinoshita; K. Bretonnel Cohen; Philip V. Ogren; Lawrence Hunter (BMC Bioinform., 2005)

Building and Evaluating Annotated Corpora for Medical NLP Systems. - Philip V. Ogren; Guergana Savova; James D. Buntrock; Christopher G. Chute (AMIA, 2006)

Knowtator: A Protégé plug-in for annotated corpus construction. - Philip V. Ogren (HLT-NAACL, 2006)

Constructing Evaluation Corpora for Automated Clinical Named Entity Recognition. - Philip V. Ogren; Guergana K. Savova; Christopher G. Chute (LREC, 2008)

System Evaluation on a Named Entity Corpus from Clinical Notes. - Karin Schuler; Vinod Kaggal; James J. Masanz; Philip V. Ogren; Guergana K. Savova (LREC, 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)

Technical Brief: Mayo Clinic NLP System for Patient Smoking Status Identification. - Guergana K. Savova; Philip V. Ogren; Patrick H. Duffy; James D. Buntrock; Christopher G. Chute (J. Am. Medical Informatics Assoc., 2008)

Word sense disambiguation across two domains: Biomedical literature and clinical notes. - Guergana K. Savova; Anni Coden; Igor L. Sominsky; Rie Johnson; Philip V. Ogren; Piet C. de Groen; Christopher G. Chute (J. Biomed. Informatics, 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)

An architecture for complex clinical question answering. - Rodney D. Nielsen; James J. Masanz; Philip V. Ogren; Wayne H. Ward; James H. Martin; Guergana K. Savova; Martha Palmer (IHI, 2010)

Improving Syntactic Coordination Resolution using Language Modeling. - Philip V. Ogren (NAACL (Student Research Workshop), 2010)

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications. - Guergana K. Savova; James J. Masanz; Philip V. Ogren; Jiaping Zheng; Sunghwan Sohn; Karin Kipper Schuler; Christopher G. Chute (J. Am. Medical Informatics Assoc., 2010)

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)

ClearTK 2.0: Design Patterns for Machine Learning in UIMA. - Steven Bethard; Philip V. Ogren; Lee Becker (LREC, 2014)

Adaptive Question Answering: Enhancing Language Model Proficiency for Addressing Knowledge Conflicts with Source Citations. - Sagi Shaier; Ari Kobren; Philip V. Ogren (EMNLP, 2024)