Jyotishman Pathak

Summary

Affiliation: Mayo Clinic
Country: USA

Publications

  1. pmc Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Semantics 3:10. 2012
  2. ncbi request reprint Validation and discovery of genotype-phenotype associations in chronic diseases using linked data
    Jyotishman Pathak
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    Stud Health Technol Inform 180:549-53. 2012
  3. pmc LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublime
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 1 Street SW, Rochester, MN 55905, USA
    J Am Med Inform Assoc 16:305-15. 2009
  4. pmc Analyzing categorical information in two publicly available drug terminologies: RxNorm and NDF-RT
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota 55905, USA
    J Am Med Inform Assoc 17:432-9. 2010
  5. pmc Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota 55905, USA
    J Am Med Inform Assoc 17:714-9. 2010
  6. pmc Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
    J Am Med Inform Assoc 18:376-86. 2011
  7. 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
  8. 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
  9. ncbi request reprint Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol
    Suzette J Bielinski
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN Electronic address
    Mayo Clin Proc 89:25-33. 2014
  10. pmc Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL
    Qian Zhu
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Inform 46:690-6. 2013

Detail Information

Publications27

  1. pmc Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Semantics 3:10. 2012
    ..abstract:..
  2. ncbi request reprint Validation and discovery of genotype-phenotype associations in chronic diseases using linked data
    Jyotishman Pathak
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    Stud Health Technol Inform 180:549-53. 2012
    ....
  3. pmc LexGrid: a framework for representing, storing, and querying biomedical terminologies from simple to sublime
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 1 Street SW, Rochester, MN 55905, USA
    J Am Med Inform Assoc 16:305-15. 2009
    ..Existing LexGrid implementations include the LexBIG API as well as a reference implementation of the HL7 Common Terminology Services (CTS) specification providing programmatic access via Java, Web, and Grid services...
  4. pmc Analyzing categorical information in two publicly available drug terminologies: RxNorm and NDF-RT
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota 55905, USA
    J Am Med Inform Assoc 17:432-9. 2010
    ..Analyzing how different drug products described in these terminologies are categorized into drug classes will help in their better organization and classification of pharmaceutical information...
  5. pmc Comparing and evaluating terminology services application programming interfaces: RxNav, UMLSKS and LexBIG
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota 55905, USA
    J Am Med Inform Assoc 17:714-9. 2010
    ..Knowledge about such discrepancies helps inform the choice of an API for a given use case...
  6. pmc Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience
    Jyotishman Pathak
    Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
    J Am Med Inform Assoc 18:376-86. 2011
    ....
  7. 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...
  8. 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...
  9. ncbi request reprint Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol
    Suzette J Bielinski
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN Electronic address
    Mayo Clin Proc 89:25-33. 2014
    ....
  10. pmc Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL
    Qian Zhu
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    J Biomed Inform 46:690-6. 2013
    ..Finally, we used the detailed drug and disease relationship information from NDF-RT and the SPLs to annotate and disambiguate the more general PharmGKB drug and disease associations. ..
  11. pmc Mining the human phenome using semantic web technologies: a case study for Type 2 Diabetes
    Jyotishman Pathak
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    AMIA Annu Symp Proc 2012:699-708. 2012
    ..Our study highlights the potential of Web-scale data federation techniques to execute complex queries...
  12. pmc Using RxNorm and NDF-RT to classify medication data extracted from electronic health records: experiences from the Rochester Epidemiology Project
    Jyotishman Pathak
    Mayo Clinic, Rochester, MN, USA
    AMIA Annu Symp Proc 2011:1089-98. 2011
    ..We further conclude that the Web service APIs developed by the NLM provide useful functionalities for such activities...
  13. 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...
  14. pmc The SHARPn project on secondary use of Electronic Medical Record data: progress, plans, and possibilities
    Christopher G Chute
    Mayo Clinic, Dept Health Sciences Research, Rochester, MN, USA
    AMIA Annu Symp Proc 2011:248-56. 2011
    ..The project is one of the four Strategic Health IT Advanced Research Projects (SHARP) projects funded by the Office of the National Coordinator in 2010...
  15. 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...
  16. pmc Modeling and executing electronic health records driven phenotyping algorithms using the NQF Quality Data Model and JBoss® Drools Engine
    Dingcheng Li
    Mayo Clinic, Rochester, MN, USA
    AMIA Annu Symp Proc 2012:532-41. 2012
    ..To the best of our knowledge, this is the first study illustrating a framework and an approach for executing phenotyping criteria modeled in QDM using the Drools business rules management system...
  17. 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...
  18. pmc Evaluating Phenotypic Data Elements for Genetics and Epidemiological Research: Experiences from the eMERGE and PhenX Network Projects
    Jyotishman Pathak
    Mayo Clinic, Rochester, MN
    AMIA Summits Transl Sci Proc 2011:41-5. 2011
    ....
  19. ncbi request reprint Some experiences and opportunities for big data in translational research
    Christopher G Chute
    Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
    Genet Med 15:802-9. 2013
    ..Meaningful Use data standards in particular have already simplified the task of identifying clinical phenotyping patterns in electronic health records...
  20. ncbi request reprint Using linked data for mining drug-drug interactions in electronic health records
    Jyotishman Pathak
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
    Stud Health Technol Inform 192:682-6. 2013
    ..Our results from the proof-of-concept study demonstrate the potential of applying such a methodology to study patient health outcomes as well as enabling genome-guided drug therapies and treatment interventions. ..
  21. pmc Analyzing the heterogeneity and complexity of Electronic Health Record oriented phenotyping algorithms
    Mike Conway
    Mayo Clinic, Rochester, MN, USA
    AMIA Annu Symp Proc 2011:274-83. 2011
    ..Insights gained from the study will be used to augment the CDISC Protocol Representation Model...
  22. pmc Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels
    Suzette J Bielinski
    Division of Epidemiology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
    Mayo Clin Proc 86:606-14. 2011
    ....
  23. pmc Using semantic web technologies for cohort identification from electronic health records for clinical research
    Jyotishman Pathak
    Department of Health Sciences Research, Mayo Clinic, Rochester, MN
    AMIA Summits Transl Sci Proc 2012:10-9. 2012
    ..Our study highlights the potential of using Web-scale data federation approaches to execute complex queries...
  24. pmc Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease
    Iftikhar J Kullo
    Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
    J Am Med Inform Assoc 17:568-74. 2010
    ..There is significant interest in leveraging the electronic medical record (EMR) to conduct genome-wide association studies (GWAS)...
  25. doi request reprint Electronic health record surveillance algorithms facilitate the detection of transfusion-related pulmonary complications
    Leanne Clifford
    Mayo Clinic, Rochester, Minnesota 55905, USA
    Transfusion 53:1205-16. 2013
    ..We aimed to develop accurate electronic health record-based screening algorithms for improved detection of TRALI/transfused acute lung injury (ALI) and TACO...
  26. doi request reprint Hospitalizations and emergency department use in Mayo Clinic Biobank participants within the employee and community health medical home
    Paul Y Takahashi
    Division of Primary Care Internal Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
    Mayo Clin Proc 88:963-9. 2013
    ..To evaluate the participants in the Mayo Clinic Biobank for their representativeness to the entire Employee and Community Health program (ECH) primary care population with regard to hospital utilization...
  27. doi request reprint Formalizing ICD coding rules using Formal Concept Analysis
    Guoqian Jiang
    Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
    J Biomed Inform 42:504-17. 2009
    ....