TransMiner: Mining Transitive Associations among Biological Objects from TextNarayanasamy 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
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.
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 firstname.lastname@example.org
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
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