BioFast

Bleiholder, Jens; Naumann, Felix; Lacroix, Zoé; Raschid, Louiqa; Murthy, Hyma; Vidal, María-Esther

doi:10.1145/1024694.1024706

Cited by 10 publications

References 5 publications

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

Craen

Neven

Koch

2006

Lecture Notes in Computer Science

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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 lightweight , 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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