Cui Tao

Summary

Affiliation: Mayo Clinic
Country: USA

Publications

  1. pmc CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives
    Cui Tao
    Mayo Clinic College of Medicine, Rochester, MN
    AMIA Summits Transl Sci Proc 2011:64-8. 2011
  2. pmc A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012)
    Yongqun He
    Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
    J Biomed Semantics 3:12. 2012
  3. pmc A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data
    Cui Tao
    Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
    J Am Med Inform Assoc 20:554-62. 2013
  4. pmc Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis
    Cui Tao
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Semantics 3:13. 2012
  5. pmc Terminology representation guidelines for biomedical ontologies in the semantic web notations
    Cui Tao
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
    J Biomed Inform 46:128-38. 2013
  6. pmc Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study
    Qian Zhu
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Inform 46:286-93. 2013
  7. doi request reprint Semantator: semantic annotator for converting biomedical text to linked data
    Cui Tao
    School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, United States Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, United States Electronic address
    J Biomed Inform 46:882-93. 2013
  8. pmc Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification
    Sunghwan Sohn
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
    J Am Med Inform Assoc 20:836-42. 2013
  9. pmc An OWL meta-ontology for representing the Clinical Element Model
    Cui Tao
    Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
    AMIA Annu Symp Proc 2011:1372-81. 2011
  10. pmc Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium
    Jyotishman Pathak
    Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
    J Am Med Inform Assoc 20:e341-8. 2013

Detail Information

Publications18

  1. pmc CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives
    Cui Tao
    Mayo Clinic College of Medicine, Rochester, MN
    AMIA Summits Transl Sci Proc 2011:64-8. 2011
    ..This paper introduces CNTRO 2.0, which tries to harmonize CNTRO 1.0 and a list of existing time ontologies or top-level ontologies into a unified model-an OWL based ontology of temporal relations for clinical research...
  2. pmc A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012)
    Yongqun He
    Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
    J Biomed Semantics 3:12. 2012
    ....
  3. pmc A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data
    Cui Tao
    Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
    J Am Med Inform Assoc 20:554-62. 2013
    ..A panel evaluation has been conducted, and the results show that the OWL modeling can faithfully represent the CEM specification and represent patient data...
  4. pmc Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis
    Cui Tao
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Semantics 3:13. 2012
    ..abstract:..
  5. pmc Terminology representation guidelines for biomedical ontologies in the semantic web notations
    Cui Tao
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, United States
    J Biomed Inform 46:128-38. 2013
    ..formal ontologies. We then evaluate the guidelines with a spectrum of widely used terminologies and ontologies to examine how the lexical guidelines are implemented, and whether our proposed guidelines would enhance interoperability...
  6. pmc Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: a case study
    Qian Zhu
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Inform 46:286-93. 2013
    ..This represents a critical first step toward identifying and creating data standards for pharmacogenomics studies...
  7. doi request reprint Semantator: semantic annotator for converting biomedical text to linked data
    Cui Tao
    School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, United States Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, United States Electronic address
    J Biomed Inform 46:882-93. 2013
    ....
  8. pmc Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification
    Sunghwan Sohn
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
    J Am Med Inform Assoc 20:836-42. 2013
    ..Temporal information detection systems have been developed by the Mayo Clinic for the 2012 i2b2 Natural Language Processing Challenge...
  9. pmc An OWL meta-ontology for representing the Clinical Element Model
    Cui Tao
    Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
    AMIA Annu Symp Proc 2011:1372-81. 2011
    ..These OWL representation specifications have been reviewed by CEM experts to ensure they capture the intended meaning of the model faithfully...
  10. pmc Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium
    Jyotishman Pathak
    Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
    J Am Med Inform Assoc 20:e341-8. 2013
    ..To develop scalable informatics infrastructure for normalization of both structured and unstructured electronic health record (EHR) data into a unified, concept-based model for high-throughput phenotype extraction...
  11. pmc A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes
    Wei Qi Wei
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
    AMIA Annu Symp Proc 2010:857-61. 2010
    ..Current research on high throughput identification of patients with a specific phenotype is in its infancy. There is an urgent need to develop a general automatic approach for patient identification...
  12. pmc Towards Semantic-Web Based Representation and Harmonization of Standard Meta-data Models for Clinical Studies
    Cui Tao
    Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN
    AMIA Summits Transl Sci Proc 2011:59-63. 2011
    ..We consider such a harmonization would provide computable semantics of the models, thus facilitate the model reuse, model harmonization and data integration.1...
  13. ncbi request reprint Exploring the pharmacogenomics knowledge base (pharmgkb) for repositioning breast cancer drugs by leveraging web ontology language (owl) and cheminformatics approaches
    Qian Zhu
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
    Pac Symp Biocomput 19:172-82. 2014
    ..Our results demonstrate that combination of pharmacogenomics data and Semantic Web technology/Cheminformatics approaches yields better performance of new indication and possible adverse effects prediction for breast cancer drugs. ..
  14. pmc Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis
    Stephen T Wu
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
    J Am Med Inform Assoc 19:e149-56. 2012
    ..To characterise empirical instances of Unified Medical Language System (UMLS) Metathesaurus term strings in a large clinical corpus, and to illustrate what types of term characteristics are generalisable across data sources...
  15. pmc Application of a temporal reasoning framework tool in analysis of medical device adverse events
    Kimberly K Clark
    Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA
    AMIA Annu Symp Proc 2011:1366-71. 2011
    ..This results in an overall accuracy of 89%. This system should be pursued further to continue assessing its potential benefits in temporal analysis of medical device adverse events...
  16. pmc Time-related patient data retrieval for the case studies from the pharmacogenomics research network
    Qian Zhu
    Mayo Clinic, Rochester, MN, USA
    J Med Syst 36:S37-42. 2012
    ..The SPARQL query builder has been evaluated with a simulated EHR triple store to ensure its functionalities...
  17. pmc CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives
    Cui Tao
    Mayo Clinic College of Medicine, Rochester, MN
    AMIA Annu Symp Proc 2010:787-91. 2010
    ..More temporal information and relations can then be inferred by Semantic-Web based reasoning tools. Experimental results show that this ontology can represent temporal information in real clinical narratives successfully...
  18. pmc Semantator: annotating clinical narratives with semantic web ontologies
    Dezhao Song
    Division of Biomedical Statistics and Informatics, Mayo Clinic 200 First Street SW, Rochester, MN 55905
    AMIA Summits Transl Sci Proc 2012:20-9. 2012
    ..We present discussions based on user experiences of using Semantator...