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

  • Dieter Van de Craen
  • Frank Neven
  • Kerstin Koch
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4075)

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.

Keywords

Directed Acyclic Graph Disjunctive Normal Form True Propagation Sequence Record Containment Test 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Dieter Van de Craen
    • 1
  • Frank Neven
    • 1
  • Kerstin Koch
    • 1
  1. 1.Hasselt University and Transnational University of Limburg, School for Information Technology 

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