LOGIC PROGRAMING-BASED QUERY SYSTEM CHROMOSOMAL INFORMATION

由计算机科学家和计算机科学家组成的计算生物学“协作室” 生物学家，每隔5个月在NIH或ANL聚集3-5天 致力于开发一套新的综合工具 基因组信息的操纵已经被组织起来。发展中的 这些信息学工具，整合了数据的汇编和分析 在两次会议之间通过互联网继续。最初的目标是 这项研究是为了建立必要的最低标准来描述 可能被逻辑操纵的基因组图谱数据。其结果是 协同努力已发展为三个原型演绎 数据库系统：第一，大肠杆菌染色体查询系统，包含 Ken Rudd在NCBI提供的DNA序列比对信息， 分辨率物理图谱、已鉴定的结构基因和比对的噬菌体 MAP；第二，在LBL为 收集了30多种不同类型的基因和 人类21号染色体的物理图谱数据；第三，关系 丹·哈特尔为果蝇提供的信息的表述 细胞遗传学图谱和酵母人工染色体(YAC)杂交数据。 这些原型中的每一个的对齐染色体信息可能是 使用在ANL开发的通用图形显示程序查看 “合作实验室” 这些原型数据表示系统中的每一个的共同特征 是每个系统都使用逻辑编程语言PROLOG。我们可以的 快速开发对集成数据的复杂查询，以利用 所推断出的复杂的相互关系。例如，在E. Coli系统中，找到在 任何基因中DNA螺旋的相同面都是简单的Prolog查询。我们是 现在使用这些系统来关联不同类型的 每种染色体类型所代表的遗传信息。

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.