We proposed to develop a database for storage, retrieval, and graphical display of physical mapping data being produced by several laboratories at the Yale Departments of Human Genetics and Biology. In the near future, large amounts of physical mapping data describing the human genome will be produced at Yale and elsewhere, and will need to be stored in an organized fashion so it can be retrieved and displayed easily. Many different types of data are being produced which characterize the genome at different levels of detail. This information is typically uncertain and incomplete, and data at one level may interact with (reinforce, complement or contradict) data at another level. The routines that retrieve this data should adapt intelligently to the uncertainty, incompleteness and interdependencies of the data. Representation of Physical Mapping Data. The laboratories of Drs. Kenneth Kidd, David Ward, Sherman Weissman, Frank Ruddle, Stephen Reeders, and Allen Bale are currently producing large quantities of physical mapping data, including large scale restriction maps, sets of overlapping cosmids, mapping of yeast artificial chromosomes, and in situ hybridization data. We will develop and refine an appropriate representation for this data. We will focus particularly on how best to represent the inherent uncertainties and interdependencies in the data, and consensus conclusions based on the data. Intelligent Retrieval and Concise Display of the Data. We will develop routines that incorporate several types of knowledge to allow intelligent retrieval of the data. We will also develop routines to display the data graphically at different levels of detail, including the construction of gene maps. Although the data in the database itself will be complex and interrelated, the display routines will be designed to present the data clearly, at an appropriate level of detail. For example, a map of a chromosome or of a large or small chromosomal region will be concise and easily understood.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG000175-02
Application #
3333224
Study Section
Special Emphasis Panel (SRC (B1))
Project Start
1991-01-01
Project End
1993-12-31
Budget Start
1992-01-01
Budget End
1992-12-31
Support Year
2
Fiscal Year
1992
Total Cost
Indirect Cost
Name
Yale University
Department
Type
Schools of Medicine
DUNS #
082359691
City
New Haven
State
CT
Country
United States
Zip Code
06520
Nadkarni, P (1998) Mapmerge: merge genomic maps. Bioinformatics 14:310-6
Nadkarni, P M (1997) Mapdiff: determining differences between two genomic maps. Comput Appl Biosci 13:217-25
Nadkarni, P M; Banks, A; Montgomery, K et al. (1996) CONTIG EXPLORER: interactive marker-content map assembly. Genomics 31:301-10
Nadkarni, P; Cheung, K H; Castiglione, C et al. (1996) DNA workbench: a database package to manage regional physical mapping. J Comput Biol 3:319-29
Miller, P L; Nadkarni, P M; Kidd, K K et al. (1995) Internet-based support for bioscience research: a collaborative genome center for human chromosome 12. J Am Med Inform Assoc 2:351-64
Nadkarni, P M; Cheung, K H (1995) SQLGEN: a framework for rapid client-server database application development. Comput Biomed Res 28:479-99
Miller, P L; Nadkarni, P M; Kucherlapati, R et al. (1995) Network-based informatics support of research collaborations in the Human Genome Project and the Human Brain Project. Medinfo 8 Pt 2:1541-4
Nadkarni, P M (1994) GDBDICT: a program to extract GDB schema information into a relational database. Genomics 19:185-6
Wright, L W; Lichter, J B; Reinitz, J et al. (1994) Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty. Comput Appl Biosci 10:435-42
Nadkarni, P M; Reeders, S T; Zhou, J (1993) CECIL: a database for storing and retrieving clinical and molecular information on patients with Alport syndrome. Proc Annu Symp Comput Appl Med Care :649-53

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