Publications

Found 81 results
2017
South BR, Christensen L, Mowery DL, Castine M, Vali M, Carter M, Conway M, Gundlapalli A, Chapman WW, Keyhani S. Automatic Extraction of Social Determinants of Health from Veterans Affairs Clinical Documents using Natural Language Processing. Joint Summits on Translational Science. 2017 :TBA.
Cary E, Secrest A, Daniels C, Chapman WW, Conway M, Mowery D. Classifying Sentiment of Free-Text Comments in Patient Satisfaction Surveys. Joint Summits on Translational Science. 2017 :TBA.
Mowery DL, Castine M, Madden E, Keyhani S, Chapman W. Developing and Assessing the Complexity of a Knowledge Base for Extracting Indications from Carotid Ultrasounds for the Veterans Health Administration . Joint Summits on Translational Science. 2017 :TBA.
Mowery DL, Bryan C, Conway M. Feature Studies to Inform the Classification of Depressive Symptoms from Twitter Data for Population Health. WSDM 2017 Workshop on Mining Online Health Reports [Internet]. 2017 . Available from: https://arxiv.org/abs/1701.08229
Mowery D, South B, Patterson O, Zhu SH, Conway M. Investigating the Documentation of Electronic Cigarette Use in the Veteran Affairs Electronic Health Record: A Pilot Study. BioNLP. 2017 .
Bucher B, Mowery D, Castine M, Chapman WW. Towards Automatic Detection of Surgical Site Infections. Joint Summits on Translational Science. 2017 :TBA.
Mowery D, Smith H, Cheney T, Stoddard G, Coppersmith G, Bryan C, Conway M. Understanding Depressive Symptoms and Psychosocial Stressors on Twitter: A Corpus-based Study. J Med Internet Res. Special Issue: Computing and Mental Health. 2017 ;19(2).
2016
Patel J, Siddiqui Z, Mowery DL, Thyvalikakath TP. Annotating Patient’s Smoking Status From Electronic Dental Record Histories. AMIA Annu Symp. 2016 :1547.
Patel N, Narasimhan E, Mowery DL, Chapman WW, Chapman BE, Heilbrun ME. Annotation of critical findings from radiology reports: towards automated communication through the electronic health record. In: Portland, OR: Society for Imaging Informatics in Medicine; 2016.
Chapman BE, Mowery DL, Narasimhan E, Patel N, Chapman WW, Heilbrun ME. Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiograph Reports to Referring Physicians. Proceedings of the 15th Workshop on Biomedical Natural Language Processing,. 2016 :181-185.
Mowery DL, Doing-Harris K, Chapman WW, Daniels C, Conway M. A Characterization of Emotional Valence to Support Review of Free-Text Press-Ganey Patient Satisfaction Survey Responses. AMIA Annu Symp. 2016 :1524.
Conway M, Khojoyan A, Fana F, Scuba W, Castine M, Mowery D, Chapman W, Jupp S. Developing a web-based SKOS editor. J Biomed Semantics. 2016 ;7:5.
South BR, Kramer H, Castine M, Mowery DL, Jones B, Chapman WW. Extending an Uncertainty Taxonomy for Suspected Pneumonia Case Review. In: Vol. 8. Denver, CO: International Society for Disease Surveillance; 2016.
Mowery DL, Chapman BE, Conway M, South BR, Madden E, Keyhani S, Chapman WW. Extracting a stroke phenotype risk factor from Veteran Health Administration clinical reports: an information content analysis. J Biomed Semantics. 2016 ;7:26.
Mowery DL, Smith HA, Cheney T, Bryan C, Conway M. Identifying Depression-related Tweets from Twitter Public Health Monitoring. In: Vol. 8. Denver, CO: International Society for Disease Surveillance; 2016.
Scuba W, Tharp M, Mowery D, Tseytlin E, Liu Y, Drews FA, Chapman WW. Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction. J Biomed Semantics. 2016 ;7(1):42.
Mowery DL, South BR, Christensen L, Leng J, Peltonen LM, Salanterä S, Suominen H, Martinez D, Velupillai S, Elhadad N, et al. Normalizing acronyms and abbreviations to aid patient understanding of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2. Journal of Biomedical Semantics. 2016 ;7(143).
Patel JS, Mowery DL, Thyvalikakath TP. Representing and Annotating Coronary Heart Disease from Patient’s Medical History. In: Los Angeles, CA: AADR/CADR; 2016.
Shi J, Mowery D, Doing-Harris K, Hurdle J. RuSH: a Rule-based Segmenting Tool Using Hashing for Extremely Accurate Clinical Text Sentence Segmentation. AMIA Annu Symp. 2016 :1587.
Mowery D, Park A, Bryan C, Conway M. Towards Automatically Classifying Depressive Symptoms from Twitter Data for Population Health. Proceedings of the Workshop on Computational Modeling of People’s Opinions, Personality, and Emotions in Social Media [Internet]. 2016 :182-191. Available from: https://peoples2016.github.io/peoples2016.pdf
Doing-Harris K, Mowery DL, Daniels C, Chapman WW, Conway M. Understanding patient satisfaction with received healthcare services: A natural language processing approach. AMIA Annu Symp. 2016 :524-533.
Velupillai S, Mowery DL, Conway M, Hurdle J, Kious B. Vocabulary Development for Substance Abuse Information Extraction from Psychiatry Notes. Proceedings of the 15th Workshop on Biomedical Natural Language Processing. 2016 :92-101.
2015
Mowery DL, South BR, Garvin J, Franc D, Ashfaq S, Zamora T, Cheng E, Chapman B, Keyhani S, Chapman WW. Adapting a Natural Language Processing Algorithm to Support Stroke Cohort Generation. In: HSR&D/QUERI National Conference meeting. HSR&D/QUERI National Conference meeting. Philadelphia, Pennsylvania; 2015. Available from: http://www.hsrd.research.va.gov/meetings/2015/abstract-display.cfm?RecordID=781
South BR, Christensen L, Mowery DL, Gundlapalli A, Tharp M, Vali M, Carter M, Conway M, Keyhani S, Chapman WW. Annotating Measures of Functional Status in Veteran Affairs Clinical Documents. [Internet]. 2015 . Available from: https://higherlogicdownload.s3.amazonaws.com/ACADEMYHEALTH/beea1490-71df-46d2-8e9a-820cd125d9e2/UploadedImages/South.pdf
Velupillai S, Mowery DL, Abdelrahman S, Christensen L, Chapman W. BluLab: Temporal Information Extraction for the 2015 Clinical TempEval Challenge. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015) [Internet]. 2015 :815--819. Available from: http://www.aclweb.org/anthology/S15-2137
Mowery D, Chapman W, Chapman B, Conway M, South B, Madden E, Keyhani S. Evaluating the Usage of Sections, Structures, and Expressions for Reporting and Extracting a Stroke Phenotype Risk Factor. In: Phenotype Day. Phenotype Day. Dublin, Ireland; 2015. Available from: http://phenoday2015.bio-lark.org/pdf/3.pdf
South BR, Gundlapalli A, Tharp M, Vali M, Mowery D, Conway M, Keyhani S, Chapman WW. Extracting Social History and Functional Status from Veteran Affairs Clinical Documents. In: AMIA 2015 Joint Summits on Translational Science. AMIA 2015 Joint Summits on Translational Science. San Francisco, California; 2015.
Mowery DL, South BR, Madden E, Chapman BE, Chapman WW, Keyhani S. Filtering Negative Reports for a Comparative Effectiveness Study of Stroke. In: AMIA 2015 Joint Summits on Translational Science. (Late Breaking Research Presentation). AMIA 2015 Joint Summits on Translational Science. (Late Breaking Research Presentation). San Francisco, California; 2015.
Velupillai S, Mowery D, South BR, Kvist M, Dalianis H. Recent Advances in Clinical Natural Language Processing in Support of Semantic Analysis. Yearbook of Medical Informatics [Internet]. 2015 ;10(1):183-193. Available from: http://www.schattauer.de/de/magazine/uebersicht/zeitschriften-a-z/imia-yearbook/imia-yearbook-2015/issue/special/manuscript/24707/show.html
Velupillai S, Mowery D, Abdelrahman S, Christensen L, Chapman WW. Toward a Generalizable Time Expression Model for Temporal Reasoning in Clinical Notes. AMIA Annu Symp. 2015 .
Mowery D, Bryan C, Conway M. Toward Developing an Annotation Scheme for Depressive Disorder Symptoms: A Preliminary Study using Twitter Data. In: Denver, CO: Computational Linguistics and Clinical Psychology - From Linguistic Signal to Clinical Reality; 2015.
Mowery DL, Bryan C, Conway M. Towards Developing an Annotation Scheme for Depressive Disorder Symptoms: A Preliminary Study using Twitter Data. Proceedings of the 2nd Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality [Internet]. 2015 :89--98. Available from: http://www.aclweb.org/anthology/W15-1211
2014
Velupillai S, Skeppstedt M, Kvist M, Mowery D, Chapman BE, Dalianis H, Chapman WW. Cue-based assertion classification for Swedish clinical text—Developing a lexicon for pyConTextSwe. Artificial intelligence in medicine. 2014 .
El-Kareh R, Mowery D, Ross MK. Developing A Framework For Detecting Asthma Endotypes From Electronic Health Records. Am J Respir Crit Care Med. 2014 ;189:A5446.
Mowery DL, Franc D, Ashfaq S, Zamora T, Cheng E, Chapman WW, Chapman BE. Developing a Knowledge Base for Detecting Carotid Stenosis with pyConText. AMIA Annu Symp Proc. 2014 :1523.
Velupillai S, Mowery D, Christensen L, Elhadad N, Pradhan S, Savova G, Chapman WW. Disease/Disorder Semantic Template Filling – Information Extraction Challenge in the ShARe/CLEF eHealth Evaluation Lab 2014. AMIA Annu Symp Proc. 2014 :1613.
South BR, Mowery D, Suo Y, Leng J, Ferrández Ó, Meystre SM, Chapman WW. Evaluating the Effects of Machine Pre-Annotation and an Interactive Annotation Interface on Manual De-identification of Clinical Text. Journal of Biomedical Informatics. 2014 .
Pradhan S, Elhadad N, South BR, Martinez D, Christensen L, Vogel A, Suominen H, Chapman WW, Savova G. Evaluating the state of the art in disorder recognition and normalization of the clinical narrative. Journal of the American Medical Informatics Association. 2014 :amiajnl–2013.
Mowery D, Ross M, Velupillai S, Meystre S, Wiebe J, Chapman W. Generating Patient Problem Lists from the ShARe Corpus using SNOMED CT/SNOMED CT CORE Problem List. In: Proceedings of BioNLP 2014. Proceedings of BioNLP 2014. Baltimore, Maryland: Association for Computational Linguistics; 2014. Available from: http://www.aclweb.org/anthology/W/W14/W14-3408
Mowery D, Wiebe J, Ross M, Meystre S, Chapman WW. Generating Patient Problem Lists from the ShARe Corpus using SNOMED CT/SNOMED CT CORE Problem List. In: ACL 2014. ACL 2014. ; 2014.
Scuba W, Tharp M, Tseytlin E, Liu Y, Drews FA, Chapman WW. Knowledge Author: Creating Domain Content for NLP Information Extraction. In: Sixth International Symposium on Semantic Mining in Biomedicine (SMBM 2014). 99-103. Sixth International Symposium on Semantic Mining in Biomedicine (SMBM 2014). 99-103. ; 2014.
Kelly L, Goeuriot L, Suominen H, Schreck T, Leroy G, Mowery DL, Velupillai S, Chapman WW, Martinez D, Zuccon G, et al. Overview of the ShARe/CLEF ehealth Evaluation Lab 2014. In: Information Access Evaluation. Multilinguality, Multimodality, and Interaction. Information Access Evaluation. Multilinguality, Multimodality, and Interaction. Springer International Publishing; 2014. pp. 172–191.
South BR, Mowery DL, Leng J, Meystre SM, Chapman W. A System Usability Study Assessing a Machine-Assisted Interactive Interface to Support Annotation of Protected Health Information in Clinical Texts. AMIA Annu Symp Proc. 2014 .
2013
Mowery DL, South BR, Leng J, Murtola L-M, Danielsson-Ojala R, Salanterä S, Chapman WW. Creating a Reference Standard of Acronym and Abbreviation Annotations for the ShARe/CLEF eHealth Challenge 2013. AMIA Annu Symp Proc. 2013 :1031.
Chapman W, Velupillai S, Kvist M, Skeppstedt M, Chapman B, Conway M, Tharp M, Mowery D, Deleger L, Hilert D. Extending the NegEx Lexicon for Multiple Languages. In: Proceedings of the 14th World Congress on Medical and Health Informatics (MedInfo 2013). Proceedings of the 14th World Congress on Medical and Health Informatics (MedInfo 2013). ; 2013.
Suominen H, Salanterä S, Velupillai S, Chapman WW, Savova G, Elhadad N, Pradhan S, South BR, Mowery DL, Jones GJF, et al. Overview of the ShARe/CLEF eHealth Evaluation Lab 2013. In: Forner P, Müller H, Paredes R, Rosso P, Stein B Information Access Evaluation. Multilinguality, Multimodality, and Visualization. Vol. 8138. Information Access Evaluation. Multilinguality, Multimodality, and Visualization. Springer Berlin Heidelberg; 2013. pp. 212-231. Available from: http://dx.doi.org/10.1007/978-3-642-40802-1_24
Velupillai S, Skeppstedt M, Kvist M, Mowery D, Chapman BE, Dalianis H, Chapman WW. Porting a Rule-based Assertion Classifier for Clinical Text from English to Swedish. In: Proceedings of the 4th International Louhi Workshop on Health Document Text Mining and Information Analysis - Louhi 2013. Proceedings of the 4th International Louhi Workshop on Health Document Text Mining and Information Analysis - Louhi 2013. Sydney, Australia; 2013. Available from: http://nicta.com.au/__data/assets/pdf_file/0009/37656/louhi2013_submission_7.pdf
Mowery DL, Jordan P, Wiebe J, Harkema H, Dowling J, Chapman WW. Semantic annotation of clinical events for generating a problem list. AMIA Annu Symp Proc. 2013 ;2013:1032-41.
Pradhan S, Elhadad N, South BR, Martinez D, Christensen L, Vogel A, Suominen H, Chapman WW, Savova G. Task 1: ShARe/CLEF eHealth Evaluation Lab 2013. CLEF [Internet]. 2013 . Available from: http://idash.ucsd.edu/sites/default/files/uploads/Brett%20South%20Poster.pdf
Mowery DL, South BR, Murtola LM, Salanterä S, Suominen H, Elhadad N, Pradhan S, Savova GK, Chapman WW. Task 2: ShARe/CLEF eHealth Evaluation Lab 2013. CLEF. 2013 .
Myslín M, Zhu S-H, Chapman W, Conway M. Using twitter to examine smoking behavior and perceptions of emerging tobacco products. J Med Internet Res. 2013 ;15(8):e174.
2012
Mowery DL, Wiebe JM, Visweswaran S, Harkema H, Chapman WW. Building an Automated SOAP Classifier for Emergency Department Reports. J Biomed Inform. 2012 ;45:71-81.
Conway M, Chapman W. Discovering Lexical Instantiations of Clinical Concepts using Web Services, WordNet and Corpus Resources. In: American Medical Informatics Association Symposium. American Medical Informatics Association Symposium. ; 2012.
Mowery DL, Jordan PW, Wiebe JM, Liu L, Chapman WW. The Effect of Setting Default Values in Problem Assertion Annotation. In: Proceedings of HISB NLP Annotation Workshop. Proceedings of HISB NLP Annotation Workshop. ; 2012.
South BR, Mowery DL, Suo Y, Levy E, Ashfaq S, Shevi E, Wang L, Zhang M, Meystre SM, Chapman WW. Ensuring Adequate Coverage to Build a Publicly Available Corpus of De-identfied Clinical Documents. NLP Annotation Workshop. 2012 .
Mowery DL, Velupillai S, Chapman WW. Medical diagnosis lost in translation: analysis of uncertainty and negation expressions in English and Swedish clinical texts. In: Proceedings of the 2012 Workshop on Biomedical Natural Language Processing. Proceedings of the 2012 Workshop on Biomedical Natural Language Processing. Stroudsburg, PA, USA: Association for Computational Linguistics; 2012.
South BR, Mowery DL, Ferrandez O, Shen S, Suo Y, Zhang M, Chen A, Wang L, Meystre SM, Chapman WW. On the Road Towards Developing a Publicly Available Corpus of De-identified Clinical Texts. American Medical Informatics Association Annual Symposium. 2012 .
2011
Chapman WW, Savova GK, Zheng J, Tharp M, Crowley RS. Anaphoric Reference in Clinical Reports: Characteristics of an Annotated Corpus. J Biomed Inform. 2011 ;45:507-21.
Savova GK, Chapman WW, Zheng J, Crowley RS. Anaphoric Relations in the Clinical Narrative: Corpus Creation. J Am Med Inform Assoc. 2011 ;18:459-65.
Conway M, Dowling J, Chapman W. Developing an Application Ontology for Mining Free Text Clinical Reports: The Extended Syndromic Surveillance Ontology. In: Third International Workshop on Health Document Text Mining and Information Analysis (LOUHI 2011). Third International Workshop on Health Document Text Mining and Information Analysis (LOUHI 2011). ; 2011. pp. 75-82.
Chapman BE, Lee S, Kang HP, Chapman WW. Document-level classification of CT pulmonary angiography reports based on an extension of the ConText algorithm. J Biomed Inform. 2011 ;44:728–737.
Conway M, Dowling J, Chapman W. Evaluating Syndrome Definitions in the Extended Syndromic Surveillance Ontology. In: International Society for Disease Surveillance Annual Conference. International Society for Disease Surveillance Annual Conference. ; 2011. p. 32.
Wang L, Zhang M, Conway M, Haug P, Chapman W. Using cKASS to Facilitate Knowledge Authoring and Sharing for Syndromic Surveillance. In: International Society for Disease Surveillance Annual Conference. International Society for Disease Surveillance Annual Conference. ; 2011. p. 158.
Chen A, Chapman W, Conway M, Chapman B. A Web Based Platform to Support Text Mining of Clinical Reports. In: International Society for Disease Surveillance Annual Conference. International Society for Disease Surveillance Annual Conference. ; 2011. p. 27.
2010
Jordan PW, Mowery DL, Wiebe J, Chapman WW. Annotating Conditions in Clinical Narratives to Support Temporal Classification. In: AMIA Annu Symp Proc. AMIA Annu Symp Proc. ; 2010.
Chapman W, Christensen L, Dowling J, Lee Q, Conway M, Harkema H, Tsui R. Challenges in Adapting an NLP System for Real-time Surveillance. In: International Society for Disease Surveillance Annual Conference. International Society for Disease Surveillance Annual Conference. ; 2010. p. 7.
Conway M, Dowling J, Chapman W. Developing a Biosurveillance Application Ontology for Influenza-Like-Illnes. In: Proceedings of the 6th Workshop on Ontologies and Lexical Resources. Proceedings of the 6th Workshop on Ontologies and Lexical Resources. ; 2010. pp. 58–66. Available from: http://www.aclweb.org/anthology-new/W/W10/W10-3307.pdf
Conway M, Dowling J, Tsui R, Chapman W. Developing an Application Ontology for Mining Clinical Reports: The Extended Syndromic Surveillance Ontology. In: International Society for Disease Surveillance Annual Conference. International Society for Disease Surveillance Annual Conference. ; 2010. p. 15.
Chapman W, Dowling J, Baer A, Buckeridge D, Cochrane D, Conway M, Elkin P, Espino J, Gunn J, Hales C, et al. Developing Syndrome Definitions Based on Consensus and Current Use. Journal of the American Medical Informatics Association. 2010 ;17:595-601.
Conway M, Okhmatovskia A, Buckeridge D, Chapman W. Using Consensus Syndrome Definitions to Classify Chief Complaints –- The Onto-Classifier Web Application. In: American Medical Informatics Association Symposium. American Medical Informatics Association Symposium. ; 2010. p. 1012.
2008
Piwowar HA, Chapman WW, Chapman W. Identifying data sharing in biomedical literature. AMIA Annu Symp Proc. 2008 :596-600.
Mowery DL, Harkema H, Chapman WW. Temporal annotation of clinical text. In: Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing. Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing. Association for Computational Linguistics; 2008.
2007
Chapman WW, Chu D, Dowling JN. ConText: an algorithm for identifying contextual features from clinical text. In: Proc. BioNLP '07. Proc. BioNLP '07. Stroudsburg, PA, USA: Association for Computational Linguistics; 2007.
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