Philip Ogren

I live in Boulder, CO and I am a Ph.D. student at the University of Colorado at Boulder in the Computer Science Department. My research advisor, Larry Hunter, is the director for the Center for Computational Pharmacology at the University of Colorado Denver at the Anschutz Medical Campus. I participate in both the Biomedical Text Mining Group and the Center for Computational Language and EducAtion Research.

My dissertation topic focuses on syntactic coordination resolution in the biomedical domain using machine learning, language modeling, and sequence alignment. I am also interested in open source solutions for natural language processing tasks and am a primary contributor to three projects: ClearTK, Knowtator, and uimaFIT.

Contact Information

• email: philip@ogren.info
• phone: (720) 563-7679
• professional/resume webpage

Software

• ClearTK - a toolkit for developing natural language processing (NLP) components on top of UIMA.
• Knowtator - a general-purpose text annotation tool that is integrated with the Protégé knowledge representation system.
• uimaFIT - provides factories, injection, and testing utilities for UIMA components.
• cTAKES - (secondary contributor) cTAKES processes clinical notes and identifies types of clinical named entities - drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures.

Publications

2010

• Philip V. Ogren (2010) Improving Syntactic Coordination Resolution Using Language Modeling. Proceedings of Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics, Companion Volume: Student Research Workshop and Doctoral Consortium.
• Guergana K. Savova, James Masanz, Philip V. Ogren, Jiaping Zheng, Sunghwan Sohn, Karin Kipper-Schuler and Christopher Chute. (in press). Mayo Clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications. JAMIA.
• Rodney D. Nielsen, James Masanz, Philip V. Ogren, Wayne Ward, James Martin, Martha Palmer, Guergana K. Savova. (under review). An architecture for complex clinical question answering. Submitted to the 1st Annual ACM International Conference on Health Informatics (IHI 2010).

2009

• Philip V. Ogren, Philipp G. Wetzler, Steven J. Bethard (2009) ClearTK : A Framework for Statistical Natural Language Processing. In Proceedings of the Biannual Conference of the German Society for Computational Linguistics and Language Technology. Gunter Narr Verlag, September 2009. ISBN 978-3823365112.
• Philip V. Ogren, Steven J. Bethard (2009) Building Test Suites for UIMA Components Proceedings of the Workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing (SETQA-NLP 2009). June 2009.
• K. Bretonnel Cohen, Karin Verspoor, Helen L. Johnson, Chris Roeder, Philip V. Ogren, William A. Baumgartner Jr., Elizabeth White, Hannah Tipney, and Lawrence Hunter (2009) High-precision biological event extraction with a concept recognizer. BioNLP 2009 Companion Volume: Shared Task on Event Extraction, pp. 50-58.

2008

• Philip V. Ogren, Guergana K. Savova and Christopher G. Chute (2008) Constructing Evaluation Corpora for Automated Clinical Named Entity Recognition. Proceedings of the Sixth International Language Resources and Evaluation (LREC'08).
• Philip V. Ogren, Philipp G. Wetzler, Steven J. Bethard (2008) ClearTK: A UIMA Toolkit for Statistical Natural Language Processing. Towards Enhanced Interoperability for Large HLT Systems: UIMA for NLP. LREC. May 31, 2008;32-38.
• Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, and K. Bretonnel Cohen (2008) OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression. BMC Bioinformatics 9(78).
• Karin Schuler, Vinod Kaggal, James Masanz, Philip Ogren and Guergana Savova (2008) System Evaluation on a Named Entity Corpus from Clinical Notes. Proceedings of the Sixth International Language Resources and Evaluation (LREC'08).
• Guergana K. Savova and Anni R. Coden and Igor L. Sominsky and Rie Johnson and Philip V. Ogren and Piet C. de Groen and Christopher G. Chute (2008) Word sense disambiguation across two domains: Biomedical literature and clinical notes. Journal of Biomedical Informatics. Volume 41, Issue 6, December 2008, Pages 1088-1100.
• Guergana K. Savova, Philip V. Ogren, Patrick H. Duffy, James D. Buntrock, and Christopher G. Chute (2008) Mayo Clinic NLP System for Patient Smoking Status Identification. Journal of the American Medical Informatics Association 2008;15:25-28.

2007

• Anni R. Coden, Guergana K. Savova, James D. Buntrock, Igor L. Sominsky, Philip V. Ogren, Christopher G. Chute, Peit de Groen Text Analysis Integration into a Medical Information Retrieval System: Challenges Related to Word Sense Disambiguation. Medinfo 2007.

2006

• Philip V. Ogren (2006) (Demonstration) Knowtator: A Protégé plug-in for annotated corpus construction. Proceedings of the Human Language Technology Conference of the NAACL, Companion Volume: Demonstrations. June 2006;273-275.
• Philip V. Ogren, Guergana K. Savova, James D. Buntrock, and Christopher G. Chute (2006) (Poster) Building and Evaluating Annotated Corpora for Medical NLP Systems. AMIA Annual Symposium Proceedings. 2006:1050.
• Zhiyong Lu, Michael Bada, Philip V. Ogren, K. Bretonnel Cohen and Lawrence Hunter (2006) Improving Biomedical Corpus Annotation Guidelines. Proceedings of the Joint BioLINK and 9th Bio-Ontologies Meeting. 2006; 89-92.

2005

• Philip V. Ogren, K. Bretonnel Cohen, and Lawrence Hunter (2005) Implications of Compositionality in the Gene Ontology for its Curation and Usage. Pacific Symposium on Biocomputing 10:174-185(2005)
• K. Bretonnel Cohen, Philip V. Ogren, Lynne Fox, and Lawrence Hunter (2005) Empirical data on corpus design and usage in biomedical natural language processing AMIA Annual Symposium Proceedings. 2005:156–160.
• K. Bretonnel Cohen, Lynne Fox, Philip V. Ogren, and Lawrence Hunter (2005). Corpus design for biomedical natural language processing. Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics June 2005;38-45. Association for Computational Linguistics.
• Shuhei Kinoshita, K. Bretonnel Cohen, Philip V. Ogren, and Lawrence Hunter (2005). BioCreative Task 1A: entity identification with a stochastic tagger. BMC Bioinformatics 6(Suppl. 1):S4.

2004

• Philip V. Ogren, K. Bretonnel Cohen, George K. Acquaah-Mensah, Jens Eberlein, and Lawrence Hunter (2004) The Compositional Structure of Gene Ontology Terms. Pacific Symposium on Biocomputing 9:214-225(2004).

1999-2000

• Harold R. Solbrig, Peter L. Elkin, Philip V. Ogren, and Christopher G. Chute (2000) A formal approach to integrating synonyms with a reference terminology. Proceedings of the AMIA Symposium. 2000:814-818.
• Peter L. Elkin, Alexander Ruggieri, Larry Bergstrom, Brent A. Bauer, Mark Lee, Philip V. Ogren, Christopher G. Chute (2000) A randomized controlled trial of concept based indexing of Web page content. Proceedings of the AMIA Symposium. 2000:220-224.
• Peter L. Elkin, Kent R. Bailey, Philip V. Ogren, Brent A. Bauer, and Christopher. G. Chute (1999) A randomized double-blind controlled trial of automated term dissection. Proceedings of the AMIA Symposium. 1999:62-66.
• F. S. McDonald, C. G. Chute, P. V. Ogren, D. Wahner-Roedler, and P. L. Elkin (1999) A large-scale evaluation of terminology integration characteristics. Proceedings of the AMIA Symposium. 1999:864-867.
• L. K. McKnight, P. L. Elkin, P. V. Ogren, and C. G. Chute (1999) Barriers to the clinical implementation of compositionality. Proceedings of the AMIA Symposium. 1999:320-324.

Courses