Specifying updates in biomedical databases

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 the 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 optimizations that can substantially improve the performance of complex updates