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Vol. 11, No. 6, 2004
Issue release date: November–December 2004
Section title: Original Paper
J Biomed Sci 2004;11:864–873
(DOI:10.1159/000081834)

TransMiner: Mining Transitive Associations among Biological Objects from Text

Narayanasamy V. · Mukhopadhyay S. · Palakal M. · Potter D.A.
aSchool of Informatics, bDepartment of Computer and Information Science, and cDepartments of Medicine and Biochemistry and Walther Oncology Center, Indiana University School of Medicine, Indiana University Purdue University Indianapolis, Ind., USA

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Article / Publication Details

First-Page Preview
Abstract of Original Paper

Received: 3/31/2004
Accepted: 6/16/2004
Published online: 12/1/2004

Number of Print Pages: 10
Number of Figures: 2
Number of Tables: 5

ISSN: 1021-7770 (Print)
eISSN: 1423-0127 (Online)

For additional information: http://www.karger.com/JBS

Abstract

Associations among biological objects such as genes, proteins, and drugs can be discovered automatically from the scientific literature. TransMiner is a system for finding associations among objects by mining the Medline database of the scientific literature. The direct associations among the objects are discovered based on the principle of co-occurrence in the form of an association graph. The principle of transitive closure is applied to the association graph to find potential transitive associations. The potential transitive associations that are indeed direct are discovered by iterative retrieval and mining of the Medline documents. Those associations that are not found explicitly in the entire Medline database are transitive associations and are the candidates for hypothesis generation. The transitive associations were ranked based on the sum of weight of terms that co-occur with both the objects. The direct and transitive associations are visualized using a graph visualization applet. TransMiner was tested by finding associations among 56 breast cancer genes and among 24 objects in the calpain signal transduction pathway. TransMiner was also used to rediscover associations between magnesium and migraine.


  

Author Contacts

Snehasis Mukhopadhyay
Department of Computer and Information Science, Indiana University
Purdue University Indianapolis, 723 W. Michigan St. SL 280
Indianapolis, IN 46202 (USA)
Tel. +1 317 274 9732, Fax +1 317 274 9742, E-Mail smukhopa@cs.iupui.edu

  

Article Information

Received: March 31, 2004
Accepted: June 16, 2004
Number of Print Pages : 10
Number of Figures : 2, Number of Tables : 5, Number of References : 28

  

Publication Details

Journal of Biomedical Science

Vol. 11, No. 6, Year 2004 (Cover Date: November-December 2004)

Journal Editor: S.H.H. Chan, Kaohsiung
ISSN: 1021–7770 (print), 1423–0127 (Online)

For additional information: http://www.karger.com/jbs


Article / Publication Details

First-Page Preview
Abstract of Original Paper

Received: 3/31/2004
Accepted: 6/16/2004
Published online: 12/1/2004

Number of Print Pages: 10
Number of Figures: 2
Number of Tables: 5

ISSN: 1021-7770 (Print)
eISSN: 1423-0127 (Online)

For additional information: http://www.karger.com/JBS


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Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
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