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http://hdl.handle.net/1942/1419
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. | Keywords: | PUBCRAWLER; GENBANK | Document URI: | http://hdl.handle.net/1942/1419 | ISBN: | 0302-9743 | DOI: | 10.1007/11799511_25 | ISI #: | 000239622300023 | Category: | A1 | Type: | Journal Contribution |
Appears in Collections: | Research publications |
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dils2006-neven.pdf | Peer-reviewed author version | 299.67 kB | Adobe PDF | View/Open |
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