ArticlePloS one2013
A multistage gene normalization system integrating multiple effective methods.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains.BioMed research international · 2015Article
- Finding sequences for over 270 orphan enzymes.PloS one · 2014Article
- BioCreative-IV virtual issue.Database : the journal of biological databases and curation · 2014Article
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6 authors.
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Abstract
Gene/protein recognition and normalization is an important preliminary step for many biological text mining tasks. In this paper, we present a multistage gene normalization system which consists of four major subtasks: pre-processing, dictionary matching, ambiguity resolution and filtering. For the first subtask, we apply the gene mention tagger developed in our earlier work, which achieves an F-score of 88.42% on the BioCreative II GM testing set. In the stage of dictionary matching, the exact matching and approximate matching between gene names and the EntrezGene lexicon have been combined. For the ambiguity resolution subtask, we propose a semantic similarity disambiguation method based on Munkres' Assignment Algorithm. At the last step, a filter based on Wikipedia has been built to remove the false positives. Experimental results show that the presented system can achieve an F-score of 90.1%, outperforming most of the state-of-the-art systems.
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