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Open Access Commentary

Which gene did you mean?

Barend Mons

Author Affiliations

Biosemantics Group Rotterdam, Department of Medical Informatics, Erasmus MC – University Medical Center Rotterdam, P.O. Box 1738, NL-3000 DR Rotterdam, the Netherlands

MGC – Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333AL LEIDEN, the Netherlands

BMC Bioinformatics 2005, 6:142  doi:10.1186/1471-2105-6-142

Published: 7 June 2005


Computational Biology needs computer-readable information records. Increasingly, meta-analysed and pre-digested information is being used in the follow up of high throughput experiments and other investigations that yield massive data sets. Semantic enrichment of plain text is crucial for computer aided analysis. In general people will think about semantic tagging as just another form of text mining, and that term has quite a negative connotation in the minds of some biologists who have been disappointed by classical approaches of text mining. Efforts so far have tried to develop tools and technologies that retrospectively extract the correct information from text, which is usually full of ambiguities. Although remarkable results have been obtained in experimental circumstances, the wide spread use of information mining tools is lagging behind earlier expectations. This commentary proposes to make semantic tagging an integral process to electronic publishing.