2009 HighPerfGeneNameNormWithGENO

• (Wermter et al., 2009) ⇒ Joachim Wermter, Katrin Tomanek, Udo Hahn. (2009). “High-Performance Gene Name Normalization with GENO.” In: Bioinformatics, 25(6). doi:10.1093/bioinformatics/btp071

Subject Headings: Gene Normalization Task, BioCreAtIvE Task.

Quotes

• Motivation: The recognition and normalization of textual mentions of gene and protein names is both particularly important and challenging. Its importance lies in the fact that they constitute the crucial conceptual entities in biomedicine. Their recognition and normalization remains a challenging task because of widespread gene name ambiguities within species, across species, with common English words and with medical sublanguage terms.
• Results: We present GENO, a highly competitive system for gene name normalization, which obtains an F-measure performance of 86.4% (precision: 87.8%, recall: 85.0%) on the BIOCREATIVE-II test set, thus being on a par with the best system on that task. Our system tackles the complex gene normalization problem by employing a carefully crafted suite of symbolic and statistical methods, and by fully relying on publicly available software and data resources, including extensive background knowledge based on semantic profiling. A major goal of our work is to present GENO's architecture in a lucid and perspicuous way to pave the way to full reproducibility of our results.

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	Author	volume	Date Value	title	type	journal	titleUrl	doi	note	year
2009 HighPerfGeneNameNormWithGENO	Katrin Tomanek Udo Hahn Joachim Wermter			High-Performance Gene Name Normalization with GENO			http://bioinformatics.oxfordjournals.org/cgi/reprint/25/6/815.pdf	10.1093/bioinformatics/btp071