一种用于分子生物学数据库间查询互操作的元数据方法。

A metadata approach to query interoperation between molecular biology databases.

作者信息

Cheung K H, Nadkarni P M, Shin D G

机构信息

Center for Medical Informatics, Yale University School of Medicine, 333 Cedar Street, TMP-3, New Haven, CT 06510, USA.

出版信息

Bioinformatics. 1998;14(6):486-97. doi: 10.1093/bioinformatics/14.6.486.

DOI:10.1093/bioinformatics/14.6.486

PMID:9694987

Abstract

MOTIVATION

Molecular biology databases have been proliferating rapidly. Their heterogeneity and complexity pose a great challenge to efforts in database interoperation. To minimize the efforts of interoperating heterogeneous databases, it is useful to develop a system that lets a user of a particular genomic database access another related database as if the latter is structurally similar to the former.

RESULTS

We extend a structurally simple model-the entity-attribute-value (EAV) model-to describe uniformly metadata relating to individual databases. Such metadata, which are necessary for performing database comparisons, include descriptions of primitive database objects (including entities, attributes, domain values and entity relationships) and specification of correspondences among the database objects. We show how to decompose SQL queries and map them from one database to another based on the EAV representation of the basic database objects. A prototype system is implemented to demonstrate query interoperation between two chromosome map databases.

AVAILABILITY

Freely available (Cold Fusion source code and an Access database containing the mapping knowledge) upon request from the author.

CONTACT

kei.cheung@yale.edu

摘要

动机

分子生物学数据库一直在迅速增长。它们的异构性和复杂性给数据库互操作带来了巨大挑战。为了尽量减少异构数据库互操作的工作量，开发一个系统是很有用的，该系统能让特定基因组数据库的用户访问另一个相关数据库，就好像后者在结构上与前者相似。

结果

我们扩展了一个结构简单的模型——实体-属性-值（EAV）模型——来统一描述与各个数据库相关的元数据。这种元数据对于进行数据库比较是必要的，包括对原始数据库对象（包括实体、属性、域值和实体关系）的描述以及数据库对象之间对应关系的规范。我们展示了如何基于基本数据库对象的EAV表示来分解SQL查询并将其从一个数据库映射到另一个数据库。实现了一个原型系统来演示两个染色体图谱数据库之间的查询互操作。