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MiMI - Michigan Molecular Interactions

NAR Molecular Biology Database Collection entry number 942
Jayapandian, M1, Chapman, A.1, Tarcea V.G.1, Yu, C.1, Elkiss, A.1, Ianni, A.1, Liu, B.1, Nandi, A.1, Santos, C.2, Andrews, P.3, Athey, B.4, States, D.5 and Jagadish, H.V.1
1Department of Electrical Engineering and Computer Science, University of Michigan, 2260 Hayward Ave, Ann Arbor, MI, 48109-2121
2Bioinformatics Program, University of Michigan, Palmer Commons 2035B, 100 Washtenaw Road, Ann Arbor, MI, 48109
3 University of Michigan Medical School Department of Biological Chemistry, University of Michigan, 3328 Med Sci I, Ann Arbor, MI, 48109
5Department of Human Genetics and Medical School, University of Michigan, Palmer Commons 2035B, 100 Washtenaw Road, Ann Arbor, MI, 48109, USA

Database Description

MiMI provides a deeply merged view of several popular interaction databases including: BIND, HPRD, IntAct, GRID, and others. MiMI allows scientists to access one cohesive view of molecules found in these databases. Through a unique deep integration process, data that is complementary or conflicting among sites is highlighted.

Recent Developments

The entire database can be downloaded in XML format by following the link provided in the web site (


This work has been supported in part by grants R01 LM008106 and U54 DA021519 from the National Institutes of Health, by grant IIS 0219513 from the National Science Foundation, and by the Michigan Center for Biological Information.


1. Birkland, A. and Yona, G. (2006) The BIOZON database: a hub of heterogeneous biological data. Nucleic Acids Research, 34, D235-242.
2. Davidson, S. B., Crabtree, J., Brunk, B. P., Schug, J., Tannen, V., Overton, G. C., and Stoeckert Jr., C. J. (2001) K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Systems Journal, 40(2), 512-531.
3. Buneman, P., Chapman, A., and Cheney, J. (June, 2006) Provenance management in curated databases. ACM SIGMOD.
4. Peri, S. et al. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Research, 13, 2363-2371.
5. Shannon, P. et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13(11), 2498-504.
6. Jagadish, H. V., Al-Khalifa, S., Chapman, A., Lakshmanan, L. V., Nierman, A., Paparizos, S., Patel, J. M., Srivastava, D., Wiwatwattana, N., Wu, Y., and Yu, C. (2002) Timber: A native XML database. The VLDB Journal, 11(4), 274-291.
7. Bader, G., Betel, D., and Hogue, C. W. (2003) BIND: the biomolecule interaction network database. Nucleic Acids Research, 31(1), 248-250.
8. Xenarios, I., Salwinski, L., Duan, X. J., Higney, P., Kin, S.-M., and Eisenberg, D. (2002) DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Research, 30(1), 303-305.
9. Stark, C., Breitkreutz, B., et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Research, 34. pp. D535-D539.
10. Hermjakob, H. et al. (2004) IntAct - an open source molecular interaction database. Nucleic Acids Research, 32, D452-D455.
11. Han, J. et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430, 88-93.
12. Stelzl, U. et al. (2005) A human protein-protein interaction network: A resource for annotating the proteome. Cell, 122, 957-968.
13. Gene Ontology Consortium (August, 2001) Creating the gene ontology resource: design and implementation. Genome Res, 8, 1425-1433.
14. Mulder, N. et al. (2005) Interpro, progress and status in 2005. Nucleic Acids Research, 33, D201-D205.
15. Kersey, P. et al. (2004) The international protein index: An integrated database for proteomics experiments. Proteomics, 4(7), 1985-1988.
16. Kim, Y. J. et al. (2005) miBLAST: Scalable evaluation of a batch of nucleotide sequence queries with blast. Nucleic Acids Research, 33(13), 4335-4344.
17. Wiwatwattana, N. and Kumar, A. (2005) Organelle DB: a cross-species database of proteinlocalization and function. Nucleic Acids Research, 33, D598-604.
18. Chen, F. et al. (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Research, 34, D363-8.
19. Finn, R. et al. (2006) PFam: clans, web tools and services. Nucleic Acids Research, 34, D247-D251.
20. Sasson, O. et al. (2003) ProtoNet: hierarchical classification of the protein space. Nucleic Acids Research, 31(1), 348-352.
21. Jayapandian, M. and Jagadish, H. V. (2006) Automating the design and construction of query forms. ICDE, p. 125.
22. Joshi-Tope, G. et al. (2005) Reactome: a knowledgebase of biological pathways. Nucleic Acids Research, 33, D428-432.

Go to the abstract in the NAR 2009 Database Issue.
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