An Extensible Light-Weight XML-Based Monitoring System for Sequence Databases

Abstract. Life science researchers want biological information in their interest to become available to them as soon as possible. A monitoring system is a solution that relieves biologists from periodic exploration of databases. In particular, it allows them to express their interest in cer-tain data by means of queries/constraints; they are then notified when new data arrives satisfying these queries/constraints. We describe a se-quence monitoring system XSeqM where users can combine metadata queries on sequence records with constraints on an alignment against a given source sequence. The system is an XML-based solution where con-straints are specified through search fields in a user-friendly web interface and which are then translated to corresponding XPath-expressions. The system is easily extensible as addition of new databases to the system then only amounts to the specification of new mappings from search fields to XPath-expressions. To protect private source sequences obtained in labs, it is imperative that researchers do not have to upload their se-quences to a general untrusted system, but that they can run XSeqM locally. To keep the system light-weight, we therefore introduce an op-timization technique based on query containment to reduce the number of XPath-evaluations which constitutes the bottleneck of the system. We experimentally validate this technique and show that it can drastically improve the running time.