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Grant Details

Grant Number: 5U01CA078266-05 Interpret this number
Primary Investigator: Nadkarni, Prakash
Organization: Yale University
Project Title: Delivery of the Cgn Information Resource Database
Fiscal Year: 2002
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Abstract

DESCRIPTION: (Applicant's Description) This applicant undertakes to deliver and maintain the Cancer Genetics Network (CGN) information resource database (i.e., objective 3 as specified in the RFA). The sub-objectives include: 1. Centralized data management, and ready access of the data to authorized users. 2. Quality assurance of the contents of the database. 3. Tracking of biospecimens such as tissue samples, as part of an inventory management system. This proposal does not address the tasks of subject recruitment coordination, primary collection of information, study design and statistical analysis, all of which are part of objective 3. The investigators will provide informatics support to other ITG investigators who are funded to carry out these tasks as and when needed. Creation of the database will involve integration and porting from other Internet-accessible, client-server systems that the investigators have previously built to address the management of clinical data, gene characterization data and biospecimen inventory. The database will be accessible over the World-Wide through a standard browser. The advantages of a Web solution include lower distribution costs, simplified setup and maintenance, and end-user hardware platform independence. The database will incorporate security measures to limit unauthorized access, and restrict viewing and editing of data from individual studies only to the users who are appropriately authorized. Input of data into the system will come primarily through periodic bulk import of data that is maintained locally at individual nodes in the CGN. 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.

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Publications

Guidelines for the effective use of entity-attribute-value modeling for biomedical databases.
Authors: Dinu V. , Nadkarni P. .
Source: International journal of medical informatics, 2007 Nov-Dec; 76(11-12), p. 769-79.
EPub date: 2006-11-13.
PMID: 17098467
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Pivoting approaches for bulk extraction of Entity-Attribute-Value data.
Authors: Dinu V. , Nadkarni P. , Brandt C. .
Source: Computer methods and programs in biomedicine, 2006 Apr; 82(1), p. 38-43.
EPub date: 2006-03-23.
PMID: 16556470
Related Citations

Informatics tools to improve clinical research study implementation.
Authors: Brandt C.A. , Argraves S. , Money R. , Ananth G. , Trocky N.M. , Nadkarni P.M. .
Source: Contemporary clinical trials, 2006 Apr; 27(2), p. 112-22.
EPub date: 2006-01-04.
PMID: 16388990
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The Common Data Elements for cancer research: remarks on functions and structure.
Authors: Nadkarni P.M. , Brandt C.A. .
Source: Methods of information in medicine, 2006; 45(6), p. 594-601.
PMID: 17149500
Related Citations

Metadata-driven Delphi rating on the Internet.
Authors: Deshpande A.M. , Shiffman R.N. , Nadkarni P.M. .
Source: Computer methods and programs in biomedicine, 2005 Jan; 77(1), p. 49-56.
PMID: 15639709
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Managing complex change in clinical study metadata.
Authors: Brandt C.A. , Gadagkar R. , Rodriguez C. , Nadkarni P.M. .
Source: Journal of the American Medical Informatics Association : JAMIA, 2004 Sep-Oct; 11(5), p. 380-91.
EPub date: 2004-06-07.
PMID: 15187070
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Integration of Web-based and PC-based clinical research databases.
Authors: Brandt C.A. , Sun K. , Charpentier P. , Nadkarni P.M. .
Source: Methods of information in medicine, 2004; 43(3), p. 287-95.
PMID: 15227559
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Approaches and informatics tools to assist in the integration of similar clinical research questionnaires.
Authors: Brandt C.A. , Cohen D.B. , Shifman M.A. , Miller P.L. , Nadkarni P.M. , Frawley S.J. .
Source: Methods of information in medicine, 2004; 43(2), p. 156-62.
PMID: 15136865
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Temporal query of attribute-value patient data: utilizing the constraints of clinical studies.
Authors: Deshpande A.M. , Brandt C. , Nadkarni P.M. .
Source: International journal of medical informatics, 2003 Apr; 70(1), p. 59-77.
PMID: 12706183
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The challenges of recording phenotype in a generalizable and computable form.
Authors: Nadkarni P.M. .
Source: The pharmacogenomics journal, 2003; 3(1), p. 8-10.
PMID: 12629577
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Integrating query of relational and textual data in clinical databases: a case study.
Authors: Fisk J.M. , Mutalik P. , Levin F.W. , Erdos J. , Taylor C. , Nadkarni P. .
Source: Journal of the American Medical Informatics Association : JAMIA, 2003 Jan-Feb; 10(1), p. 21-38.
PMID: 12509355
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Metadata-driven creation of data marts from an EAV-modeled clinical research database.
Authors: Brandt C.A. , Morse R. , Matthews K. , Sun K. , Deshpande A.M. , Gadagkar R. , Cohen D.B. , Miller P.L. , Nadkarni P.M. .
Source: International journal of medical informatics, 2002-11-12; 65(3), p. 225-41.
PMID: 12414020
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Designing and implementing special-purpose databases: lessons from the pharmacogenetic network.
Authors: Nadkarni P. , Sun K. , Wiepert M. .
Source: Pharmacogenomics, 2002 Sep; 3(5), p. 687-96.
PMID: 12223053
Related Citations

Metadata-driven ad hoc query of patient data: meeting the needs of clinical studies.
Authors: Deshpande A.M. , Brandt C. , Nadkarni P.M. .
Source: Journal of the American Medical Informatics Association : JAMIA, 2002 Jul-Aug; 9(4), p. 369-82.
PMID: 12087118
Related Citations

An introduction to information retrieval: applications in genomics.
Authors: Nadkarni P.M. .
Source: The pharmacogenomics journal, 2002; 2(2), p. 96-102.
PMID: 12049181
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UMLS concept indexing for production databases: a feasibility study.
Authors: Nadkarni P. , Chen R. , Brandt C. .
Source: Journal of the American Medical Informatics Association : JAMIA, 2001 Jan-Feb; 8(1), p. 80-91.
PMID: 11141514
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Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods.
Authors: Brandt C. , Nadkarni P. .
Source: Computer methods and programs in biomedicine, 2001 Jan; 64(1), p. 37-43.
PMID: 11084231
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Exploring performance issues for a clinical database organized using an entity-attribute-value representation.
Authors: Chen R.S. , Nadkarni P. , Marenco L. , Levin F. , Erdos J. , Miller P.L. .
Source: Journal of the American Medical Informatics Association : JAMIA, 2000 Sep-Oct; 7(5), p. 475-87.
PMID: 10984467
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Clinical patient record systems architecture: an overview.
Authors: Nadkarni P.M. .
Source: Journal of postgraduate medicine, 2000 Jul-Sep; 46(3), p. 199-204.
PMID: 11298472
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WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases.
Authors: Nadkarni P.M. , Brandt C.M. , Marenco L. .
Source: Journal of the American Medical Informatics Association : JAMIA, 2000 Jul-Aug; 7(4), p. 343-56.
PMID: 10887163
Related Citations

Information retrieval in medicine: overview and applications.
Authors: Nadkarni P.M. .
Source: Journal of postgraduate medicine, 2000 Apr-Jun; 46(2), p. 116-22.
PMID: 11013482
Related Citations

Organization of heterogeneous scientific data using the EAV/CR representation.
Authors: Nadkarni P.M. , Marenco L. , Chen R. , Skoufos E. , Shepherd G. , Miller P. .
Source: Journal of the American Medical Informatics Association : JAMIA, 1999 Nov-Dec; 6(6), p. 478-93.
PMID: 10579606
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