Philip Ogren

For information on where I am and what I am doing please see my resume page.

I live in Boulder, CO and I am a Ph.D. student at CU Boulder in the Computer Science Department. My interests include natural language processing, machine learning, and applications of these two research areas to the biomedical domain.

Software

• Knowtator - a general-purpose text annotation tool that is integrated with the Protégé knowledge representation system.
• ClearTK - a toolkit for developing natural language processing (NLP) components on top of UIMA.

Courses

Publications

first author
• Constructing Evaluation Corpora for Automated Clinical Named Entity Recognition. P.V. Ogren, G.K. Savova, C.G. Chute. LREC 2008.
• ClearTK: A UIMA Toolkit for Statistical Natural Language Processing. P.V. Ogren, P.G. Wetzler, S.J. Bethard. LREC 2008.
• Implications of Compositionality in the Gene Ontology for its Curation and Usage. P.V. Ogren, K.B. Cohen, L. Hunter PSB 2005.
• The Compositional Structure of Gene Ontology Terms. P.V. Ogren, K.B. Cohen, G.K. Acquaah-Mensah, J. Eberlein, L. Hunter. PSB 2004.

secondary author
• Word sense disambiguation across two domains: Biomedical literature and clinical notes. Savova GK, Coden AR, Sominsky IL, Johnson R, Ogren PV, Groen PC, Chute CG. J Biomed Inform 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. Hunter L, Lu Z, Firby J, Baumgartner WA Jr, Johnson HL, Ogren PV, Cohen KB. BMC Bioinformatics 2008.
• Mayo clinic NLP system for patient smoking status identification. Savova GK, Ogren PV, Duffy PH, Buntrock JD, Chute CG. J Am Med Inform Assoc. 2008
• Improving biomedical corpus annotation guidelines. Zhiyong Lu, Michael Bada, Philip V. Ogren, K. Bretonnel Cohen and Lawrence Hunter. BioLINK 2006.
• BioCreAtIvE Task1A: Entity Identification with a stochastic tagger. S. Kinoshita, K.B. Cohen, P.V. Ogren, L. Hunter. BMC Bioinformatics 2005.
• Empirical data on corpus design and usage in biomedical natural language processing. Cohen KB, Fox L, Ogren PV, Hunter L. AMIA Annu Symp Proc. 2005.