P Nadkarni

Summary

Affiliation: Yale University
Country: USA

Publications

  1. ncbi request reprint Metadata-driven creation of data marts from an EAV-modeled clinical research database
    Cynthia A Brandt
    Center for Medical Informatics, Yale University School of Medicine, P O Box 208009, New Haven, CT 06520 8009, USA
    Int J Med Inform 65:225-41. 2002
  2. pmc An eUtils toolset and its use for creating a pipeline to link genomics and proteomics analyses to domain-specific biomedical literature
    Prakash M Nadkarni
    Department of Medicine, Program of Applied Translational Research, Yale University School of Medicine, New Haven, CT, USA
    J Clin Bioinforma 2:9. 2012
  3. pmc Requirements for guidelines systems: implementation challenges and lessons from existing software-engineering efforts
    Hemant Shah
    Henry Ford Health System, Detroit, USA
    BMC Med Inform Decis Mak 12:16. 2012
  4. pmc Web-browser encryption of personal health information
    Richard E Morse
    MGH Biostatistics Center, Massachusetts General Hospital, 50 Staniford St, Ste 560, Boston, MA 02114, USA
    BMC Med Inform Decis Mak 11:70. 2011
  5. pmc The challenges of recording phenotype in a generalizable and computable form
    P M Nadkarni
    Yale University School of Medicine, New Haven, CT 06520, USA
    Pharmacogenomics J 3:8-10. 2003
  6. ncbi request reprint Mapdiff: determining differences between two genomic maps
    P M Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06510, USA
    Comput Appl Biosci 13:217-25. 1997
  7. pmc The Common Data Elements for cancer research: remarks on functions and structure
    P M Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, PO Box 208009, New Haven, CT 06520 8009, USA
    Methods Inf Med 45:594-601. 2006
  8. pmc Migrating existing clinical content from ICD-9 to SNOMED
    Prakash M Nadkarni
    Yale University School of Medicine, USA
    J Am Med Inform Assoc 17:602-7. 2010
  9. pmc Drug safety surveillance using de-identified EMR and claims data: issues and challenges
    Prakash M Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06511, USA
    J Am Med Inform Assoc 17:671-4. 2010
  10. pmc Determining correspondences between high-frequency MedDRA concepts and SNOMED: a case study
    Prakash M Nadkarni
    Geisinger Health Systems, Danville, PA, USA
    BMC Med Inform Decis Mak 10:66. 2010

Research Grants

  1. ROBUST QUERY OF HETEROGENEOUS CLINICAL DATABASES
    Prakash Nadkarni; Fiscal Year: 2002
  2. DESIGN AND IMPLEMENTATION OF PHARMACOGENETIC DATABASE
    Prakash Nadkarni; Fiscal Year: 2002
  3. DELIVERY OF THE CGN INFORMATION RESOURCE DATABASE
    Prakash Nadkarni; Fiscal Year: 2006

Collaborators

Detail Information

Publications34

  1. ncbi request reprint Metadata-driven creation of data marts from an EAV-modeled clinical research database
    Cynthia A Brandt
    Center for Medical Informatics, Yale University School of Medicine, P O Box 208009, New Haven, CT 06520 8009, USA
    Int J Med Inform 65:225-41. 2002
    ..The metadata, in addition to driving the process, is exported along with the data, in order to facilitate its human interpretation...
  2. pmc An eUtils toolset and its use for creating a pipeline to link genomics and proteomics analyses to domain-specific biomedical literature
    Prakash M Nadkarni
    Department of Medicine, Program of Applied Translational Research, Yale University School of Medicine, New Haven, CT, USA
    J Clin Bioinforma 2:9. 2012
    ..abstract:..
  3. pmc Requirements for guidelines systems: implementation challenges and lessons from existing software-engineering efforts
    Hemant Shah
    Henry Ford Health System, Detroit, USA
    BMC Med Inform Decis Mak 12:16. 2012
    ..During such an analysis, study of examples of existing, software-engineering efforts in non-biomedical fields can provide useful signposts to the implementer of a clinical guideline system...
  4. pmc Web-browser encryption of personal health information
    Richard E Morse
    MGH Biostatistics Center, Massachusetts General Hospital, 50 Staniford St, Ste 560, Boston, MA 02114, USA
    BMC Med Inform Decis Mak 11:70. 2011
    ..However it is important to protect patient confidentiality, as many medical conditions are stigmatized and disclosure could result in personal and/or financial loss...
  5. pmc The challenges of recording phenotype in a generalizable and computable form
    P M Nadkarni
    Yale University School of Medicine, New Haven, CT 06520, USA
    Pharmacogenomics J 3:8-10. 2003
  6. ncbi request reprint Mapdiff: determining differences between two genomic maps
    P M Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06510, USA
    Comput Appl Biosci 13:217-25. 1997
    ..Its usefulness increases in proportion to the percentage of shared objects between the two maps. Mapdiff uses a greedy algorithm to determine differences between shared objects...
  7. pmc The Common Data Elements for cancer research: remarks on functions and structure
    P M Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, PO Box 208009, New Haven, CT 06520 8009, USA
    Methods Inf Med 45:594-601. 2006
    ..We also performed automated checks for certain types of content errors that provided a rough measure of curation quality...
  8. pmc Migrating existing clinical content from ICD-9 to SNOMED
    Prakash M Nadkarni
    Yale University School of Medicine, USA
    J Am Med Inform Assoc 17:602-7. 2010
    ....
  9. pmc Drug safety surveillance using de-identified EMR and claims data: issues and challenges
    Prakash M Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06511, USA
    J Am Med Inform Assoc 17:671-4. 2010
    ..Finally, access to online drug information that includes both a reliable hierarchy of drug families as well as structured information on existing ADEs can improve the focus and predictive ability of surveillance efforts...
  10. pmc Determining correspondences between high-frequency MedDRA concepts and SNOMED: a case study
    Prakash M Nadkarni
    Geisinger Health Systems, Danville, PA, USA
    BMC Med Inform Decis Mak 10:66. 2010
    ..We aimed to identify aspects of MedDRA that complicate mapping to SNOMED CT, determine pattern in unmapped high-frequency MedDRA concepts, and to identify types of integration errors in the mapping of MedDRA to UMLS...
  11. pmc Natural language processing: an introduction
    Prakash M Nadkarni
    Yale University School of Medicine, New Haven, Connecticut, USA
    J Am Med Inform Assoc 18:544-51. 2011
    ..To provide an overview and tutorial of natural language processing (NLP) and modern NLP-system design...
  12. pmc Leveraging a clinical research information system to assist biospecimen data and workflow management: a hybrid approach
    Prakash M Nadkarni
    Yale University School of Medicine, New Haven, CT, USA
    J Clin Bioinforma 1:22. 2011
    ..abstract:..
  13. ncbi request reprint Designing and implementing special-purpose databases: lessons from the pharmacogenetic network
    Prakash Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, PO Box 208009, New Haven, Connecticut, 06520 8009, USA
    Pharmacogenomics 3:687-96. 2002
    ..Where multiple groups face common problems, such as managing genotyping data or clinical study support, we have devised generic software that can be reused in its entirety by individual groups, or customized with modest effort...
  14. pmc An introduction to information retrieval: applications in genomics
    P M Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut 06520 8009, USA
    Pharmacogenomics J 2:96-102. 2002
    ..This article provides an introduction to IR and summarizes various applications of IR and related technologies to genomics...
  15. pmc Managing attribute--value clinical trials data using the ACT/DB client-server database system
    P M Nadkarni
    Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520 8009, USA
    J Am Med Inform Assoc 5:139-51. 1998
    ..It uses a Microsoft Access client running on Windows 95 machines, which communicates with an Oracle server running on a UNIX platform. ACT/DB is being used to manage the data for seven studies in its initial deployment...
  16. pmc UMLS concept indexing for production databases: a feasibility study
    P Nadkarni
    Yale University School of Medicine, New Haven, CT 06520 8009, USA
    J Am Med Inform Assoc 8:80-91. 2001
    ..To quantitatively evaluate this strategy in terms of true positives, false positives (spuriously identified concepts) and false negatives (concepts missed by the identification process)...
  17. ncbi request reprint Mapmerge: merge genomic maps
    P Nadkarni
    Center for Medical Informatics and Department of Anesthesiology, Yale University School of Medicine, 333 Cedar Street, TMP 3, New Haven, CT 06510, USA
    Bioinformatics 14:310-6. 1998
    ..When two or more genomic maps of a chromosomal region are available, it is useful to be able to synthesize them to create a merged map...
  18. pmc Data extraction and ad hoc query of an entity-attribute-value database
    P M Nadkarni
    Yale University, New Haven, Connecticut, USA
    J Am Med Inform Assoc 5:511-27. 1998
    ..The authors' work does not close the query problem, and they identify several complex subproblems that are still to be solved...
  19. pmc Organization of heterogeneous scientific data using the EAV/CR representation
    P M Nadkarni
    Center for Medical Informatics, Yale University, New Haven, Connecticut 06520 8009, USA
    J Am Med Inform Assoc 6:478-93. 1999
    ..The authors refer to their modification of the basic EAV paradigm as EAV/CR (EAV with classes and relationships). They describe EAV/CR representation with examples from two biomedical databases that use it...
  20. pmc WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases
    P M Nadkarni
    Yale University School of Medicine, New Haven, Connecticut 06520 8009, USA
    J Am Med Inform Assoc 7:343-56. 2000
    ..It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples...
  21. pmc Integration of multidisciplinary sensory data: a pilot model of the human brain project approach
    P L Miller
    Yale University, New Haven, CT 06520 8009, USA
    J Am Med Inform Assoc 8:34-48. 2001
    ....
  22. ncbi request reprint Reengineering a database for clinical trials management: lessons for system architects
    C A Brandt
    Center for Medical Informatics, Yale University School of Medicine, New Haven, CT 06520 8009, USA
    Control Clin Trials 21:440-61. 2000
    ..The lessons learned in the process should prove instructive for system architects as well as managers of electronic patient record systems...
  23. pmc Metadata-driven ad hoc query of patient data: meeting the needs of clinical studies
    Aniruddha M Deshpande
    Yale University School of Medicine, New Haven, Connecticut 06520, USA
    J Am Med Inform Assoc 9:369-82. 2002
    ..The authors describe major revisions of their previously described CSDMS ad hoc query interface to meet CSDMS needs more fully, as well as its porting to a Web-based platform...
  24. ncbi request reprint Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods
    C Brandt
    Yale Center for Medical Informatics, Yale School of Medicine, PO Box 208009, New Haven, CT, 06520 8009, USA
    Comput Methods Programs Biomed 64:37-43. 2001
    ..Alternative, currently available scripting environments for Web development appear to have most of LISP's advantages and few of its disadvantages...
  25. ncbi request reprint Informatics tools to improve clinical research study implementation
    Cynthia A Brandt
    Yale School of Medicine, Center for Medical Informatics, New Haven, CT 06520 8009, USA
    Contemp Clin Trials 27:112-22. 2006
    ..These issues are compounded when studies are multi-site and multiple personnel from different sites are responsible for varying actions from case report form design to primary data collection and data entry...
  26. ncbi request reprint Text mining neuroscience journal articles to populate neuroscience databases
    Chiquito J Crasto
    Center for Medical Informatics, Yale University, New Haven, CT, USA
    Neuroinformatics 1:215-37. 2003
    ..Software that uses the NeuroText approach can facilitate the creation of curated, special-interest, bibliography databases...
  27. pmc Managing complex change in clinical study metadata
    Cynthia A Brandt
    Center for Medical Informatics, Yale School of Medicine, New Haven, CT 06520 8009, USA
    J Am Med Inform Assoc 11:380-91. 2004
    ..We review approaches that have been used for metadata management in other contexts and describe the features, capabilities, and limitations of our system...
  28. pmc Achieving evolvable Web-database bioscience applications using the EAV/CR framework: recent advances
    Luis Marenco
    Center for Medical Informatics, Yale University School of Medicine, PO Box 208009, New Haven, CT 06520 8009, USA
    J Am Med Inform Assoc 10:444-53. 2003
    ....
  29. ncbi request reprint Metadata-driven Delphi rating on the Internet
    Aniruddha M Deshpande
    Center for Medical Informatics, Yale University School of Medicine, PO Box 208009, New Haven, CT 06520 8009, USA
    Comput Methods Programs Biomed 77:49-56. 2005
    ..0), acceptable (median 4.5, IQR 4.0-5.0) and easily accessible (median 5, IQR 4.0-5.0). We conclude that Web-based Delphi rating for consensus development is a convenient and acceptable alternative to the traditional paper-based method...
  30. pmc Exploring the degree of concordance of coded and textual data in answering clinical queries from a clinical data repository
    H D Stein
    Yale University School of Medicine, Center for Medical Informatics, New Haven, Connecticut 06520 8009, USA
    J Am Med Inform Assoc 7:42-54. 2000
    ....
  31. pmc Temporal query of attribute-value patient data: utilizing the constraints of clinical studies
    Aniruddha M Deshpande
    Center for Medical Informatics, Yale University School of Medicine, PO Box 208009, New Haven, CT 06520 8009, USA
    Int J Med Inform 70:59-77. 2003
    ..To apply temporal operators, data for parameters of interest must first be transiently converted into conventional relational form, with one column per parameter...
  32. pmc Implementing description-logic rules for SNOMED-CT attributes through a table-driven approach
    Prakash M Nadkarni
    Center for Health Research, Geisinger Health Systems, Danville, Pennsylvania 17821, USA
    J Am Med Inform Assoc 17:182-4. 2010
    ..This approach, which is tailored to database implementations, is computationally efficient and allows new attribute-definition rules to be created as data while needing minimal or no code modification...
  33. pmc Service-oriented architecture in medical software: promises and perils
    Prakash M Nadkarni
    J Am Med Inform Assoc 14:244-6. 2007
  34. pmc Translating pharmacogenomics discoveries into clinical practice: the role of curated databases
    Prakash M Nadkarni
    Pharmacogenomics 6:451-4. 2005

Research Grants5

  1. ROBUST QUERY OF HETEROGENEOUS CLINICAL DATABASES
    Prakash Nadkarni; Fiscal Year: 2002
    ..In particular, research will be performed on utilization of newer database technologies, such as new indexing methods, as well as parallel database implementations. ..
  2. DESIGN AND IMPLEMENTATION OF PHARMACOGENETIC DATABASE
    Prakash Nadkarni; Fiscal Year: 2002
    ..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..
  3. DELIVERY OF THE CGN INFORMATION RESOURCE DATABASE
    Prakash Nadkarni; Fiscal Year: 2006
    ..Informatics assistance will be provided to the individual nodes to assist the task of data exchange, and when necessary, to assist the design of local data collection systems. ..