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Title: An extensible light-weight XML-based monitoring system for sequence databases
Authors: VAN DE CRAEN, Dieter 
NEVEN, Frank 
KOCH, Kerstin 
Issue Date: 2006
Publisher: Springer-Verlag Berlin
Source: Data Integration in the Life Sciences, Proceedings. p. 280-296
Series/Report: Lecture Notes in Computer Science
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 certain data by means of queries/constraints, they are then notified when new data arrives satisfying these queries/constraints. We describe a sequence 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 constraints 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 sequences to a general untrusted system, but that they can run XSeqM locally. To keep the system light-weight, we therefore introduce an optimization 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.
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ISBN: 0302-9743
DOI: 10.1007/11799511_25
ISI #: 000239622300023
Category: A1
Type: Journal Contribution
Appears in Collections:Research publications

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