tmVar 3.0: an improved variant concept recognition and normalization tool.
tmVar 3.0: an improved variant concept recognition and normalization tool.
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DOI：
10.1093/bioinformatics/btac537
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发表时间：
2022-09-15
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先前的研究表明，自动文本挖掘工具对于成功大规模解锁科学文献中的变异信息变得越来越重要。尽管过去进行了多次尝试，但现有工具的识别范围和精度仍然有限。我们提出tmVar 3.0：一个改进的变体识别和规范化系统。与之前的版本相比，tmVar 3.0可以识别更广泛的变异相关实体（例如等位基因和拷贝数变异），并将同一篇文章中属于同一基因组序列位置的不同变体组合在一起，以提高准确性。此外，tmVar 3.0还提供了高级的变体规范化选项，例如来自ClinGen Allele Registry的特定于等位基因的标识符。当在三个独立的基准数据集上进行评估时，tmVar 3.0表现出最先进的性能，在变体识别和规范化方面的F-measure超过90%。tmVar 3.0以及整个PubMed和PMC数据集的注释都可以免费下载。https://github.com/ncbi/tmVar3
Previous studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision. We propose tmVar 3.0: an improved variant recognition and normalization system. Compared to its predecessors, tmVar 3.0 recognizes a wider spectrum of variant-related entities (e.g. allele and copy number variants), and groups together different variant mentions belonging to the same genomic sequence position in an article for improved accuracy. Moreover, tmVar 3.0 provides advanced variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar 3.0 exhibits state-of-the-art performance with over 90% in F-measure for variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar 3.0 as well as annotations for the entire PubMed and PMC datasets are freely available for download. https://github.com/ncbi/tmVar3
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