A Protocol for Maintaining Multidatabase Referential Integrity

Abstract

The bioinformatics community is becoming increasingly reliant on the creation of links among biological databases (DBs) as a foundation for DB interoperability. For example, a link might be created from a protein in one DB (such as PIR), to a gene in another DB (such as GDB), by storing the unique identifier (id) of the gene object within an attribute of the protein object. User interfaces can then support navigation from the protein to the gene, and multiDB queries can join the protein with the gene. The unique id of the gene is serving as a foreign key. However, a variety of factors, such as changes in the underlying biology, can cause object ids to become invalid, thus producing invalid links among DBs. Invalid links are a violation of multi-database referential integrity. We propose a network protocol whereby a database administrator can provide information about changes to the identifiers of objects in their database via Internet, to allow other databases to maintain referential integrity. We request comments from the bioinformatics community for the purpose of building a consensus on the proposed protocol.