Digital Symposium Collection 2000

Specifying Updates in Biomedical Databases H. Liefke and S. Davidson   View Paper (PDF)   Return to Paper Session 1: Scientific and Statistical Data Warehouses Abstract Many of the publicly available biomedical data sources -- such as Genbank and SwissProt -- are not stored in traditional databases but in a variety of file formats (e.g. ASN.1 and EMBL). The data is complex, involving deeply nested structures. While query languages for such data have been well-studied, the issue of updating such databases has not. The need for a concise update language is critical since the changes to the data are typically very small when compared to the entire value. Starting with a query language called Collection Programming Language (CPL), we describe an extension called CPL+ which provides an intuitive framework for updates on complex values. We illustrate the language using examples and present various optimization that can substantially improve the performance of complex updates. Keywords: updates, complex value databases, biological databases, optimization, object-oriented databases, rewriting Copyright(C) 2000 ACM