Publications

  1. Shen F, Li D, Liu H, Lee Y, Pathak J, Chute CG, Tao C. Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data. 2014 IEEE-EMBS International Conference on Biomedical and Health Informatics, BHI 2014. 2014; (3):531-4.
  2. Zhu Q, Tao C, Shen F, Chute CG. Exploring the pharmacogenomics knowledge base (PharmGKB) for repositioning breast cancer drugs by leveraging Web ontology language (OWL) and cheminformatics approaches. Pac Symp Biocomput. 2014; 172-82.
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  3. Zhang Y, Tao C, Jiang G, Nair AA, Su J, Chute CG, Liu H. Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network. J Biomed Semantics. 2014; 5:33. Epub 2014 Aug 6
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  4. Pathak J, Bailey KR, Beebe CE, Bethard S, Carrell DC, Chen PJ, Dligach D, Endle CM, Hart LA, Haug PJ, Huff SM, Kaggal VC, Li D, Liu H, Marchant K, Masanz J, Miller T, Oniki TA, Palmer M, Peterson KJ, Rea S, Savova GK, Stancl CR, Sohn S, Solbrig HR, Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium. J Am Med Inform Assoc. 2013 Dec; 20(e2):e341-8. Epub 2013 Nov 04.
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  5. Tao C, Song D, Sharma D, Chute CG. Semantator: semantic annotator for converting biomedical text to linked data. J Biomed Inform. 2013 Oct; 46(5):882-93. Epub 2013 Jul 15.
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  6. Sohn S, Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Komandur Elayavilli R, Liu H. Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. J Am Med Inform Assoc. 2013 Sep-Oct; 20(5):836-42. Epub 2013 Apr 04.
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  7. 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 electronic health records data. J Am Med Inform Assoc. 2013 May 1; 20(3):554-62. Epub 2012 Dec 25.
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  8. 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. 2013 Apr; 46(2):286-93. Epub 2012 Nov 29.
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  9. Tao C, Pathak J, Solbrig HR, Wei WQ, Chute CG. Terminology representation guidelines for biomedical ontologies in the semantic web notations. J Biomed Inform. 2013 Feb; 46(1):128-38. Epub 2012 Sep 28.
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  10. Zhang Y, Tao C, He Y, Kanjamala P, Liu H. Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology. J Biomed Semantics. 2013; 4(1):33. Epub 2013 Nov 11.
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  11. Hulse NC, Long J, Tao C. Combining infobuttons and semantic web rules for identifying patterns and delivering highly-personalized education materials. AMIA Annu Symp Proc. 2013; 2013:638-47. Epub 2013 Nov 16.
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  12. Zhang Y, Li D, Tao C, Shen F, Liu H. An integrative computational approach to identify disease-specific networks from PubMed literature information. Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. 2013; 72-5.
  13. Tao C, Li D, Shen F, Lian Z, Pathak J, Liu H, Chute CG. Phenotyping on EHR data using OWL and semantic web technologies. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2013; 8040 LNCS:31-2.
  14. Martinez-Costa C, Bosca D, Legaz-Garcia MC, Tao C, Fernandez Breis JT, Schulz S, Chute CG. Isosemantic rendering of clinical information using formal ontologies and RDF. Stud Health Technol Inform. 2013; 192:1085.
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  15. Zhu Q, Tao C, Ding Y, Chute CG. Time-related patient data retrieval for the case studies from the pharmacogenomics research network. J Med Syst. 2012 Nov; 36 Suppl 1:S37-42. Epub 2012 Oct 18.
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  16. 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.
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  17. 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.
  18. 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; 19(e1):e149-56. Epub 2012 Apr 04.
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  19. Li D, Tao C, Liu H, Chute C. Ontology-based temporal relation modeling with map-reduce latent dirichlet allocations for big EHR data. Proceedings - 2nd International Conference on Cloud and Green Computing and 2nd International Conference on Social Computing and Its Applications, CGC/SCA 2012. 2012; 708-15.
  20. 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 Biomed Semantics. 2012; 3(1):13. Epub 2012 Dec 20.
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  21. He Y, Toldo L, Burns G, Tao C, Abernethy DR. A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012). J Biomed Semantics. 2012; 3(1):12. Epub 2012 Dec 18.
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  22. 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.
  23. 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.
  24. Song D, Chute CG, Tao C. Semantator: annotating clinical narratives with semantic web ontologies. AMIA Jt Summits Transl Sci Proc. 2012; 2012:20-9. Epub 2012 Mar 19.
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  25. Bouamrane M, Tao C, Mair F. Quality Assessement of Electronic Health Information Management Systems International Conference on Information and Knowledge Management, Proceedings. 2012.
  26. 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.
  27. Tao C, Bouamrane MM. Managing interoperability and compleXity in health systems - MIXHS'12. ACM International Conference Proceeding Series. 2012; 2758-9.
  28. Bouamrane MM, Mair FS, Tao C. An overview of electronic health information management systems quality assessment. International Conference on Information and Knowledge Management, Proceedings. 2012; 37-46.
  29. Tao C, Zhang Y, Jiang G, Bouamrane MM, Chute CG. Optimizing semantic MEDLINE for translational science studies using semantic web technologies. International Conference on Information and Knowledge Management, Proceedings. 2012:53-7.
  30. Liu H, Wu S, Tao C, Chute C. Modeling UIMA type system using web ontology language - Towards interoperability among UIMA-based NLP tools. International Conference on Information and Knowledge Management, Proceedings. 2012:31-6.
  31. Song D, Chute CG, Tao C. Semantator: A Semi-automatic Semantic Annotation Tool for Clinical Narratives. International Semantic Web Conference (ISWC). 2011 Oct.
  32. 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.
  33. Clark KK, Sharma DK, Chute CG, Tao C. Application of a temporal reasoning framework tool in analysis of medical device adverse events. AMIA Annu Symp Proc. 2011; 2011:1366-71. Epub 2011 Oct 22.
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  34. Embley DW, Liddle SW, Tao C. A Web of Knowledge: A Conceptual-Modeling Perspective Lecture Note in Computer Science. 2011; 6520:137-60.
  35. Tao C, Solbrig HR, Chute CG. CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. AMIA Jt Summits Transl Sci Proc. 2011; 2011:64-8. Epub 2011 Mar 07.
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  36. 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 Jt Summits Transl Sci Proc. 2011; 2011:59-63. Epub 2011 Mar 07.
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  37. Bouamrane MM, Mair F, Tao C. Managing complexity in pre-operative information management systems. International Conference on Information and Knowledge Management, Proceedings. 2011:3-10.
  38. Bouamrane MM, Tao C. MIXHS'11 foreword: Managing interoperability and compleXity in health systems. International Conference on Information and Knowledge Management, Proceedings. 2011; iii-iv.
  39. 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, Proceedings. 2011:75-8.
  40. Bouamrane MM, Tao C. Managing interoperability and complexity inhealth systems: MIXHS'11 workshop summary. International Conference on Information and Knowledge Management, Proceedings. 2011; 2635-6.
  41. Tao C, Parker CG, Oniki TA, Pathak J, Huff SM, Chute CG. An OWL meta-ontology for representing the Clinical Element Model. AMIA Annu Symp Proc. 2011; 2011:1372-81. Epub 2011 Oct 22.
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  42. Tao C, Jiang G, Clark K, Sharma D, Chute CG. Toward answering time-related questions from adverse event reports using ontology-based approaches. CEUR Workshop Proceedings. 2011; 833:332-4.
  43. 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.
  44. Tao C, Solbrig HR, Sharma DK, Wei WQ, Savova GK, Chute CG. Time-Oriented Question Answering from Clinical Narratives Using Semantic-Web Techniques. Lect Notes Comput Sci. 2010; 6497:241-56.
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  45. 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 Annu Symp Proc. 2010; 2010:857-61. Epub 2010 Nov 13.
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  46. Tao C, Wei WQ, Solbrig HR, Savova G, Chute CG. CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. AMIA Annu Symp Proc. 2010; 2010:787-91. Epub 2010 Nov 13.
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  47. 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.
  48. 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.
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  49. 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.
  50. Tao C, Embley DW. Automatic Hidden-Web Table Interpretation, Conceptualization, and Semantic Annotation. Journal of Data & Knowledge Engineering. 2009; 68(7):683-703.
  51. 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.
  52. 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.
  53. 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.
  54. 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.
  55. 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.
  56. 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.
  57. 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.
  58. 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.