title: Building a genome database using an object-oriented approach.
abstract: GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.
authors.affiliation: Université de Montréal, Département de Biochimie 2900 Blvd Edouard-Montpetit, Montreal, Québec Canada, H3C 3J7. ania@bch.umontreal.ca
authors.forename: Anna
authors.initials: A
authors.lastname: Barbasiewicz
authors.forename: Lin
authors.initials: L
authors.lastname: Liu
authors.forename: B Franz
authors.initials: BF
authors.lastname: Lang
authors.forename: Gertraud
authors.initials: G
authors.lastname: Burger
mesh_terms: D030541:Databases, Genetic; D016678:Genome; D011381:Programming Languages; D018511:Systems Integration; D017432:Unified Medical Language System