GENOME: Georgia Tech - Emory Object Management Environment for managing Human Genome Databases

We have been developing information systems for managing Human Genome

Project (HGP) data for the last three years. Our focus is on mitochondrial DNA (mtDNA) information from humans which is limited to about 16K base pairs of DNA information (A,C,T,G) and has been fully sequenced already. As such, we have an advantage of being able to harness this information fully and combine it with locus specific details for mtDNA collected over last several decades at Emory University as well as other centers in the world. These details involve different information on genes, mutations, diseases, gene-gene interactions, functional information about genes etc. It is planned to combine anthropological data about the origin of certain mutations and haplotypes into this database as well as disease data coming from actual patients.

As such, our task encompasses modeling and managing complex, heterogeneous data in a flexible manner as well as sharing this data across multiple sites. With the implementation of such systems, we will be better prepared for the onslaught of data being generated by the HGP, and we will be ready to more fully use databases to analyze and understand relationships in HGP data. There are databases such as Genbank or GDB which already use relational technology. We have experimented with commercial OODBMSs as well and have concluded that current commercial DBMS solutions are too rigid and we are better off developing our own solutions by developing a prototype system. We are currently making a limited version of our system called MITOMAP available for browsing and querying over the web (http://www.gen.emory.edu/mitomap.html).

This work draws on technologies from the database area, user interfaces, networking, and computational biology. We are continuously enhancing the system and are planning to create a resource for worldwide use of the mtDNA information. The database server is the key component of the system. We hope that commercial grade systems such as the Universal Servers can be utilized in our next generation of development called GENOME: Georgia tech - Emory Object Management Environment. That will facilitate a wider use of the database structure and applications we plan to develop. In the long term, we would also accept entries for inclusion in this database via the web after some local scrutiny.

Those interested in knowing more about the project, please contact Andy Kogelnik at kogelnik@cc.gatech.edu or Prof. Navathe at sham@cc.gatech.edu.

PUBLICATIONS:

  1. Kogelnik A.M., MT Lott, MD Brown, SB Navathe, and DC Wallace. " MITOMAP: A human mitochondrial genome database," In Nucleic Acid Research, Vol 24 (1), Jan 1996.

  2. Kogelnik AM, MT Lott, MD Brown, S. B. Navathe, and DC Wallace. " MITOMAP: An update of the human mitochondrial genome database," In Nucleic Acid Research, Vol 25 (1), Jan 1997.

  3. Kogelnik AM, "Biological Information Management with application to Human Genome Data," Ph.D. dissertation, Biomedical Engineering, Georgia Institute of Technology, 1998 (forthcoming).