Challenges in integrating biological data sources

Abstract

Scientific data of importance to biologists reside in a number of different data sources, such as GenBank, GSDB, SWISS-PROT, EMBL, and OMIM, among many others. Some of these data sources are conventional databases implemented using database management systems (DBMSs) and others are structured files maintained in a number of different formats (e.g., ASN.1 and ACE). In addition, software packages such as sequence analysis packages (e.g., BLAST and FASTA) produce data and can therefore be viewed as data sources. To counter the increasing dispersion and heterogeneity of data, different approaches to integrating these data sources are appearing throughout the bioinformatics community. This paper surveys the technical challenges to integration, classifies the approaches, and critiques the available tools and methodologies.