Grants and Funding: Extramural Programs (EP)
Dr. Cui Tao – PECASE Recipient 2014
Patient Medical History Representation, Extraction, and Inference from EHR Data (R01-LM-011829)
National Library of Medicine (NLM) grantee Dr. Cui Tao of the University of Texas is one of the 102 scientists and researchers named by President Obama on January 9, 2017 as recipients of the Presidential Early Career Awards for Scientists and Engineers (PECASE), the highest honor bestowed by the United States Government on science and engineering professionals in the early stages of their independent research careers.
Dr. Tao’s area of expertise is in clinical informatics and computer science, and her research interests include ontologies, standard terminologies, semantic web, information extraction and integration as well as applying ontology and semantic web technologies to clinical and translational studies. Dr. Tao was awarded her first research project (R01) grant from the National Library of Medicine, National Institutes of Health in 2014 to study “Patient Medical History Representation, Extraction, and Inference from EHR Data”. Dr. Tao received her Ph.D. in Computer Science from Brigham Young University and is currently an Associate Professor in the School of Biomedical Informatics at the University of Texas Health Science Center at Houston.
The awards, established by President Clinton in 1996, are coordinated by the Office of Science and Technology Policy within the Executive Office of the President. Awardees are selected for their pursuit of innovative research at the frontiers of science and technology and their commitment to community service as demonstrated through scientific leadership, public education, or community outreach.
What do you think the impact of this award will have on your research career?
I am extremely honored and grateful to be a recipient of the PECASE award. This award will provide important impetus for me to continue my research in biomedical informatics. It is not only a recognition of my own research, but also an achievement of the whole NLM community. Health IT and biomedical informatics now play a very significant role to improve patient care in many ways.
Dr. Cui Tao
What is your best career advice to young investigators?
Stay focused and be persistent. Your hard work today will pay back tomorrow one way or another.
What do you think might be the most likely (and meaningful) discovery to emerge in your field in the next five? Ten years?
Big Data solutions from data normalization, data integration, data analysis will provide significant impact to healthcare systems.
Publications supported in part by this grant include:
Rastegar-Mojarad, Majid; Komandur Elayavilli, Ravikumar; Liu, Hongfang. BELTracker: evidence sentence retrieval for BEL statements. Database: the Journal of Biological Databases and Curation. 2016.
Madkour, Mohcine; Benhaddou, Driss; Tao, Cui. Temporal Data Representation, Normalization, Extraction, and Reasoning: A review from Clinical Domain. Computer methods and programs in biomedicine. 2016 May; 128: 52-68.
Liang, Chen; Sun, Jingchun; Tao, Cui. Semantic Web Ontology and Data Integration: A Case Study in Aiding Psychiatric Drug Repurposing. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2016; 2016:132-9.
Liu, Sijia; Liu, Hongfang; Chaudhary, Vipin; Li, Dingcheng. An Infinite Mixture Model for Coreference Resolution in Clinical Notes. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2016; 2016:428-37
Legaz-García, María del Carmen; Menárguez-Tortosa, Marcos; Fernández-Breis, Jesualdo Tomás; Chute, Christopher G; Tao, Cui. Transformation of Standardized Clinical Models based on OWL Technologies: from CEM to OpenEHR Archetypes. Journal of the American Medical Informatics Association: JAMIA. 2015 May; 22 (3):536-44.
Mehrabi, Saeed; Krishnan, Anand; Sohn, Sunghwan; Roch, Alexandra M; Schmidt, Heidi; Kesterson, Joe; Beesley, Chris; Dexter, Paul; Max Schmidt, C; Liu, Hongfang; Palakal, Mathew. DEEPEN: A Negation Detection System for Clinical Text Incorporating Dependency Relation into NegEx. Journal of biomedical informatics. 2015 Apr; 54:213-9.
Tao, Cui; Sun, Jingchun; Zheng, W Jim; Chen, Junjie; Xu, Hua. Colorectal Cancer Drug Target Prediction using Ontology-based Inference and Network Analysis. Database: The Journal of Biological Databases and Curation. 2015; 2015.
Chen, Guocai; Zhao, Jieyi; Cohen, Trevor; Tao, Cui; Sun, Jingchun; Xu, Hua; Bernstam, Elmer V; Lawson, Andrew; Zeng, Jia; Johnson, Amber M; Holla, Vijaykumar; Bailey, Ann M; Lara-Guerra, Humberto; Litzenburger, Beate; Meric-Bernstam, Funda; Jim Zheng, W. Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature. Database: The Journal of Biological Databases and Curation. 2015; 2015:bav034.
Amith, Muhammad; Gong, Yang; Cunningham, Rachel; Boom, Julie; Tao, Cui. Developing VISO: Vaccine Information Statement Ontology for Patient Education. Journal of biomedical semantics. 2015; 6:23.
Zhu, Kevin; Liu, Qi; Zhou, Yubo; Tao, Cui; Zhao, Zhongming; Sun, Jingchun; Xu, Hua. Oncogenes and Tumor Suppressor Genes: Comparative Genomics and Network Perspectives. BMC Genomics. 2015; 16 Suppl 7:S8.
Myneni, Sahiti; Amith, Muhammad; Geng, Yimin; Tao, Cui. Towards an Ontology-driven Framework to Enable Development of Personalized mHealth Solutions for Cancer Survivors' Engagement in Healthy Living. Studies in health technology and informatics. 2015; 216:113-7.
Mehrabi, Saeed; Krishnan, Anand; Roch, Alexandra M; Schmidt, Heidi; Li, DingCheng; Kesterson, Joe; Beesley, Chris; Dexter, Paul; Schmidt, Max; Palakal, Mathew; Liu, Hongfang. Identification of Patients with Family History of Pancreatic Cancer-Investigation of an NLP System Portability. Studies in health technology and informatics. 2015; 216:604-8.
Li, Dingcheng; Rastegar Mojarad, Majid; Li, Yanpeng; Sohn, Sunghwan; Mehrabi, Saeed; Komandur Elayavilli, Ravikumar; Yu, Yue; Liu, Hongfang.
A Frequency-based Strategy of Obtaining Sentences from Clinical Data Repository for Crowdsourcing. Studies in Health Technology and Informatics. 2015; 216:1033-4.
Tao, Cui; Du, Jingcheng; Cai, Yi; Chen, Yong. Trivalent Influenza Vaccine Adverse Event Analysis Based On MedDRA System Organ Classes using VAERS Data. Studies in health technology and informatics. 2015; 216:1076.
Zhang, Yuji; Wu, Puqiang; Luo, Yi; Tao, Cui. Identification of Sex-associated Network Patterns in Vaccine-Adverse Event Association Network in VAERS. Journal of Biomedical Semantics. 2015; 6:33.
Crowe, Christopher L; Tao, Cui. Designing Ontology-based Patterns for the Representation of the Time-Relevant Eligibility Criteria of Clinical Protocols. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2015; 2015:173-7.
Li, Yanpeng; Liu, Hongfang. Learning Semantic Tags from Big Data for Clinical Text Representation. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science. 2015; 2015:461-5.
Zhang, Yuji; Tao, Cui. Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns. Cancer informatics. 2014; 13 (Suppl 3):45-51.
Zhang, Yuji; Tao, Cui. Correction to "Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns". Cancer informatics. 2014; 13 (Suppl 3):89.
Clark, Kim; Sharma, Deepak; Qin, Rui; Chute, Christopher G; Tao, Cui. A Use Case Study on Late Stent Thrombosis for Ontology-based Temporal Reasoning and Analysis. Journal of biomedical semantics. 2014; 5 (1):49.
Tao, Cui; Wu, Puqiang; Luo, Yi; Zhang, Yuji. Linked Vaccine Adverse Event Data from VAERS for Biomedical Data Analysis and Longitudinal Studies. BioData mining. 2014; 7:36.