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Automated structure extraction and XML conversion of life science database flat files.

Stephan Philippi·Jacob Köhler
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Abstract

In the light of the increasing number of biological databases, their integration is a fundamental prerequisite for answering complex biological questions. Database integration, therefore, is an important area of research in bioinformatics. Since most of the publicly available life science databases are still exclusively exchanged by means of proprietary flat files, database integration requires parsers for very different flat file formats. Unfortunately, the development and maintenance of database specific flat file parsers is a nontrivial and time-consuming task, which takes considerable effort in large-scale integration scenarios. This paper introduces heuristically based concepts for automatic structure extraction from life science database flat files. On the basis of these concepts the FlatEx prototype is developed for the automatic conversion of flat files into XML representations.

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AlgorithmsArtificial IntelligenceBiological Science DisciplinesDatabase Management SystemsDatabases, FactualElectronic Data ProcessingHypermediaInformation Storage and RetrievalSoftwareJournal Article

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BibTeXRIS

Stephan Philippi, Jacob Köhler. 2006. Automated structure extraction and XML conversion of life science database flat files.. https://doi.org/10.1109/titb.2006.875653

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