A computational biology """"""""collaboratory"""""""" of computer scientists and biologists, that gathers every 5 months for 3-5 days at the NIH or ANL to work on the development of a new set of integrated tools for the manipulation of genomic information has been organized. Development of these informatics tools, assembly and analysis of the integrated data continues over the Internet between meetings. The initial objective of this research was to establish the minimal criteria necessary to describe genomic map data that may be logically manipulated. The result of this collaborative effort has been the development of three prototype deductive database systems: First, the E. coli chromosome query system that contains information provided by Ken Rudd at NCBI for aligned DNA sequences, a high resolution physical map, identified structural genes, and an aligned phage map; second, at LBL an object oriented deductive database for the collective information of over thirty different types of genetic and physical map data for Human Chromosome 21; third, a relational representation of the information provided by Dan Hartl for the Drosophila cytogenetic map and Yeast Artificial chromosome (YAC) hybridization data. The aligned chromosome information for each of these prototypes may be viewed using a common graphical display program developed at the ANL for the """"""""Collaboratory."""""""" The common feature of each of these prototype data representation systems is that each system uses the logic programming language Prolog. We can rapidly develop complex queries of the integrated data that take advantage of the complicated inter-relationships inferred. For example, in the E. coli system, finding the longest repeated sequences that are found on the same face of the DNA helix within any gene is simple Prolog query. We are now using these systems to correlate the arrangement of different types of genetic information represented in each chromosome type.
