Cui Tao, PhD

Assistant Professor

Cui Tao, PhDCui Tao, PhD, joined the SBMI faculty on July 22, 2013 as an assistant professor of biomedical informatics. She came to SBMI from the Division of Biomedical Statistics and Informatics at Mayo Clinic. Tao’s background 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.

Tao is currently involved in several federally funded research projects including projects that she's leading. These projects focus on temporal-relation modeling, extraction and reasoning; secondary use of electronic health record data for clinical and translational studies; ontology-based analysis for cancer drug repurposing; vaccine adverse event analysis; and ontology-based personalized decision support systems. Tao is the principal investigator of the Clinical Narrative Temporal Relation Ontology (CNTRO) project, in which she leverages ontology and semantic web technologies to model, extract and infer temporal relations from clinical data. She’s also leading the research efforts on common ontology guidelines for semantic representations, which is funded by NIH through the National Center of Biomedical Ontologies. Additionally, she is applying semantic web technologies on normalized electronic data for clinical decision support, which is funded by the Office of the National Coordinator for Health IT through the Strategic Health IT Advanced Research Projects (SHARP) program.

In the coming semesters, Tao will teach an ontology and terminology course. When asked where informatics is headed, Tao said, “I believe the future of biomedical informatics will focus on big data analysis with data standardization and normalization.”

Education

  • PhD, 2008, Computer Science, Brigham Young University 
  • MS, 2004, Computer Science, Brigham Young University  
  • BS, 1997, Biology and Computer Science, Beijing Normal University

Research Interests

  • Applying semantic web and ontology technologies to clinical and biomedical applications
  • Ontology generation and conceptual modeling
  • Common terminology and ontology services
  • Information extraction and integration

Research Projects

  • Temporal relation modeling, extraction and reasoning
  • Secondary use of EHR data for clinical and translational studies
  • Ontology-based analysis for cancer drug repurposing
  • Vaccine adverse event analysis
  • Ontology-based personalized decision support systems

Contact

Cui.Tao@uth.tmc.edu
7000 Fannin St., Suite 600
Houston, TX 77030
Phone: 713.500.3981
Fax: 713.500.3929

Publications

  1. Hulse N, Long J, Tao C, Combining Infobuttons and Semantic Web Rules for Identifying Patterns and Delivering Highly-Personalized Education Materials, AMIA Annual Symposium. 2013, accepted
  2. Tao C, Song D, Sharma D, Chute CG. Semantic Annotator for Converting Biomedical Text to Linked Data, Journal of Biomedical Informatics, 2013 pii: S1532-0464(13)00102-0. doi: 10.1016/j.jbi.2013.07.003
  3. Tao C, Li D, Shen F, Pathak J, Liu H, Chute CG, Phenotyping on EHR Data Using OWL and Semantic Web Technologies, Lecture Notes in Computer Science series 8084, International Conference of Smart Health 2013.
  4. Sohn S, Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Elayavilli RK, Liu H. Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. J Am Med Inform Assoc. 2013 Apr. PMID:23558168. DOI:10.1136/amiajnl-2013-001622.
  5. Tao C, Jiang G, Oniki TA, Freimuth RR, Zhu Q, Sharma D, Pathak J, Huff SM, Chute CG, A Semantic-Web Oriented Representation of the Clinical Element Model for Secondary Use of EHR Data, J Am Med Inform Assoc. 2012, PMID:23268487. DOI:10.1136/amiajnl-2012-001326
  6. Tao C, He Y, Yang H, Poland GA, Chute CG, Ontology-based Time Information Representation of Vaccine Adverse Events in VAERS for Temporal Analysis. J Biomedical Semantics. 2012, 3:13
  7. Zhu Q, Freimuth RR, Lian Z, Bauer S, Pathak J, Tao C, Durski MJ, Chute CG, Harmonization and Semantic Annotation of Data Dictionaries from the Pharmacogenomics Research Network:  a case study. J Biomed Inform. 2012 PMID:23201637. DOI:10.1016/j.jbi.2012.11.004.
  8. Tao C, Pathak J, Solbrig HR, Wei W-Q, Chute CG.  Terminology representation guidelines for biomedical ontologies in the semantic web notations.  J Biomed Inform. 2012 Sep 28. pii: S1532-0464(12)00150-5. doi: 10.1016/j.jbi.2012.09.003.
  9. Zhu Q, Tao C, Ding Y, Chute CG, Time-Related Patient Data Retrieval for the Case Studies from the Pharmacogenomics Research Network.  Journal of Medical Systems, 2012 PMID: 23076712
  1. Rea S, Pathak J, Savova G, Oniki TA, Westberg L, Beebe CE, Tao C, Parker CG, Haug PJ, Huff SM, Chute CG.  Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: The SHARPn project.  J Biomed Inform. 2012 Aug; 45(4):763-71. Epub 2012 Feb 04.  PMID:22326800. DOI:10.1016/j.jbi.2012.01.009.
  2. Tao C, He Y, Poland GA, Chute CG.  Time modeling of vaccine adverse events in VAERS for temporal analysis. International Conference on Biomedical Ontology. July 2012.
  3. Wu ST, Liu H, Li D, Tao C, Musen MA, Chute CG, Shah NH.  Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.  J Am Med Inform Assoc. 2012 Jun 1; 19(e1):e149-56. Epub 2012 Apr 04.  PMID:22493050. PMCID:3392861. DOI:10.1136/amiajnl-2011-000744.
  4. Tao C, Zhang Y, Jiang G, Bouamrane M, Chute CG.  Optimizing Semantic MEDLINE for Translational Science Studies Using Semantic Web Technologies. International Conference on Information and Knowledge Management, (CIKM 2012). 2012.
  5. Tao C, Wongsuphasawat K, Clark K, Plaisant C, Shneiderman B, Chute CG.  Towards event sequence representation, reasoning and visualization for EHR data.  IHI'12 - Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium. 2012:801-5.
  6. Tao C, Noy NF, Solbrig HR, Shah NH, Musen MA, Chute CG.  Proposed SKOS extensions for bioportal terminology services.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2012; 7185 LNCS:342-9.
  7. Song D, Chute CG, Tao C. Semantator: annotating clinical narratives with semantic web ontologies.  AMIA Summits Transl Sci Proc. 2012; 2012:20-9. Epub 2012 Mar 19.  PMID:22779043. PMCID:3392053.
  8. Liu H, Wu S, Tao C, Chute CG.  Modeling UIMA Type System Using Web Ontology Language – towards Interoperability among UIMA-based NLP Tools.  International Conference on Information and Knowledge Management (CIKM 2012). 2012.
  9. Li D, Tao C, Liu H, Chute CG.  Ontology-based Temporal Relation Modeling with MapReduce Latent Dirichlet Allocations for Big EHR Data.  International Symposium on Big Data and MapReduce. 2012.
  10. Bouamrane M, Tao C, Mair F.  Quality Assessment of Electronic Health Information Management Systems. International Conference on Information and Knowledge Management (CIKM 2012). 2012.
  11. Song D, Chute CG, Tao C. Semantator: A Semi-automatic Semantic Annotation Tool for Clinical Narratives.  International Semantic Web Conference (ISWC 2011). 2011 OCT.
  12. Tao C, Jiang G, Clark KK, Sharma DK, Chute CG.  Toward Answering Time-Related Questions from Adverse Event Reports Using Ontology-based Approaches.  International Conference on Biomedical Ontologies: Representing Adverse. 2011 Jul.
  13. Tao C, Solbrig HR, Chute CG.  CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives.  AMIA Summits Transl Sci Proc. 2011; 2011:64-8. Epub 2011 Mar 07.  PMID:22211182. PMCID:3248753.
  14. Tao C, Pathak J, Welch SR, Bouamrane MM, Huff SM, Chute CG.  Toward semantic web based knowledge representation and extraction from electronic health records.  International Conference on Information and Knowledge Management (CIKM 2011). 2011:75-8.
  15. Tao C, Parker CG, Oniki TA, Pathak J, Huff SM, Chute CG.  An OWL meta-ontology for representing the Clinical Element Model. AMIA Annual Symposium. 2011; 2011:1372-81. Epub 2011 Oct 22.  PMID:22195200. PMCID:3243162.
  16. Tao C, Jiang G, Wei W, Solbrig HR, Chute CG.  Towards Semantic-Web Based Representation and Harmonization of Standard Meta-data Models for Clinical Studies.  AMIA Summits Transl Sci Proc. 2011; 2011:59-63. Epub 2011 Mar 07.  PMID:22211181. PMCID:3248749.
  17. Embley DW, Liddle SW, Tao C. A Web of Knowledge: A Conceptual-Modeling Perspective.  Lecture Note in Computer Science. 2011; 6520:137-60.  DOI:10.1007/978-3-642-17505-3_7.
  18. Clark KK, Sharma DK, Chute CG, Tao C. Application of a temporal reasoning framework tool in analysis of medical device adverse events. AMIA Annual Symposium. 2011; 2011:1366-71. Epub 2011 Oct 22.  PMID:22195199. PMCID:3243139.
  19. Bouamrane MM, Mair F, Tao C. Managing complexity in pre-operative information management systems.  International Conference on Information and Knowledge Management (CIKM 2011). 2011:3-10.
  20. Wei WQ, Tao C, Jiang G, Chute CG.  A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes. AMIA Annual Symposium. 2010; 2010:857-61. Epub 2010 Nov 13.  PMID:21347100. PMCID:3041302.
  21. Tao C, Wei WQ, Solbrig HR, Savova G, Chute CG.  CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives.  AMIA Annual Symposium. 2010; 2010:787-91. Epub 2010 Nov 13.  PMID:21347086. PMCID:3041418.
  22. Tao C, Solbrig HR, Sharma DK, Wei WQ, Savova GK, Chute CG.  Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques. Lecture Notes in Computer Science. 2010; 6497:241-56.  PMID:22025812. PMCID:3198866. DOI:10.1007/978-3-642-17749-1_16.
  23. Embley DW, Liddle SW, Lonsdale DW, Steward A, Tao C. KBB: A Knowledge-Bundle Builder for Research Studies.  International Workshop on Active Conceptual Modeling of Learning in conjunction with ER 2009, Lecture Notes in Computer Science. 2010; 6413:148-157.  DOI:10.1007/978-3-642-16385-2_19.
  24. Tao C, Embley DW.  FOCIH: Form-based Ontology Creation, Information Harvesting.  International Conference of Conceptual Modeling (ER 2009), Lecture Notes in Computer Science. 2009 Nov; 5829:346-59.  DOI:10.1007/978-3-642-04840-1_26.
  25. Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG.  LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical Ontologies.  CEUR Workshop Proc. 2009 Oct 26; 521:3.  PMID:21804785. PMCID:3146261.
  26. Tao C, Pathak J, Solbrig HR, Chute CG.  LexOWL: A Bridge from LexGrid to OWL.  International Conference of Biomedical Ontology (ICBO 2009). 2009 Jul:131-4.  DOI:1038/npre.2009.3468.1.
  27. Tao C, Embley DW.  Automatic Hidden-Web Table Interpretation, Conceptualization, and Semantic Annotation.  Journal of Data & Knowledge Engineering. 2009; 68(7):683-703.  DOI:10.1016/j.datak.2009.02.010.
  28. Embley DW, Liddle SW, Lonsdale DW, Nagy G, Tijerino Y, Clawson R, Crabtree J, Ding Y, Jha P, Lian Z, Lynn S, Padmanabhan R, Peters J, Tao C, Watts R, Woodbury C, Zitzelberger A.  A Conceptual-Model-Based Computational Alembic for a Web of Knowledge.  International Conference on Conceptual Modeling (ER 2008), Lecture Notes in Computer Science. 2008; 5231:532-3.  DOI:10.1007/978-3-540-87877-3_47.
  29. Tao C, Embley DW.  Seed-based Generation of Personalized Bio-Ontologies for Information Extraction.  International Workshop on Conceptual Modeling for Life Sciences Applications (CMLSA 2007) in conjunction with ER 2007, Lecture Notes In Computer Science. 2007 Nov; 4802:74-84.  DOI:10.1007/978-3-540-76292-8_9.
  30. Tao C, Embley DW.  Automatic Hidden-Web Table Interpretation by Sibling Page Comparison.  International Conference on Conceptual Modeling (ER2007), Lecture Notes in Computer Science, Springer-Verlag, New York. 2007 Nov:566-81.  DOI:10.1007/978-3-540-75563-0_38.
  31. Tao C. Toward Making Online Biological Data Machine Understandable.  International Semantic Web Conference (ISWC 2006), Lecture Notes in Computer Science. 2006 Nov; 4273:992-3.  DOI:10.1007/11926078_83.
  32. Tao C, Ding Y, Lonsdale D.  Automatic Creation of Web Services from Extraction Ontologies.  International Workshop on Semantic Web Applications: Theory and Practice (SWAT 2006) in conjunction with ER 2006, Lecture Notes in Computer Science. 2006 Nov; 4231:415-24.  DOI:10.1007/11908883_49.
  33. Tao C, Embley DW.  HTML Table Interpretation by Sibling Page Comparison in the Molecular Biology Domain.  Proceedings of the 3rd Biotechnology and Bioinformatics Symposium (BIOT 2006) Provo, UT. 2006 Oct:116-9.
  34. Embley DW, Tao C, Liddle SW.  Automating the Extraction of Data from HTML Tables with Unknown Structure.  Journal of Data & Knowledge Engineering. 2005 Jul; 54(1):3-28.  DOI:10.1016/j.datak.2004.10.004.
  35. Embley DW, Tao C, Liddle SW.  Automatically Extracting Ontologically Specified Data from HTML Tables with Unknown Structure.  International Conference on Conceptual Modeling (ER 2002), Lecture Notes in Computer Science. 2002 Oct 7-11(2573):322-27.  DOI:10.1007/3-540-45816-6_32.?