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.
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