Natural language processing (NLP) tools in extracting biomedical concepts from research articles: a case study on autism spectrum disorder.
Natural language processing (NLP) tools in extracting biomedical concepts from research articles: a case study on autism spectrum disorder.
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DOI：
10.1186/s12911-020-01352-2
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发表时间：
2020-12-30
影响因子：
3.5
通讯作者：
Zhou Y
中科院分区：
文献类型：
--
作者：
Peng J;Zhao M;Havrilla J;Liu C;Weng C;Guthrie W;Schultz R;Wang K;Zhou Y
自然语言处理（NLP）工具可以促进从非结构化的自由文本（如研究文章或临床笔记）中提取生物医学概念。NLP软件工具CLAMP、cTAKES和MetaMap是提取生物医学概念实体的最广泛使用的工具之一。然而，它们在从文献中提取疾病特异性术语方面的表现尚未进行广泛比较，特别是对于具有多种表型和临床表现的复杂神经精神疾病。我们使用自闭症谱系障碍（ASD）作为案例研究，比较评估这些NLP工具。我们收集了827个ASD相关的术语，作为绩效评估的基准列表。然后，我们应用CLAMP、cTAKES和MetaMap对PubMed的544篇全文文章和20,408篇摘要进行分析，以提取ASD相关术语。我们使用精确度，召回率和F1评分来评估预测性能。我们发现CLAMP在F1评分方面的表现最好，其次是cTAKES，然后是MetaMap。实验结果表明，CLAMP的查准率远高于cTAKES和MetaMap，而cTAKES和MetaMap的查全率高于CLAMP。本研究中使用的分析方案可以应用于其他神经精神或神经发育障碍，缺乏明确定义的术语集来描述其表型表现。
Natural language processing (NLP) tools can facilitate the extraction of biomedical concepts from unstructured free texts, such as research articles or clinical notes. The NLP software tools CLAMP, cTAKES, and MetaMap are among the most widely used tools to extract biomedical concept entities. However, their performance in extracting disease-specific terminology from literature has not been compared extensively, especially for complex neuropsychiatric disorders with a diverse set of phenotypic and clinical manifestations. We comparatively evaluated these NLP tools using autism spectrum disorder (ASD) as a case study. We collected 827 ASD-related terms based on previous literature as the benchmark list for performance evaluation. Then, we applied CLAMP, cTAKES, and MetaMap on 544 full-text articles and 20,408 abstracts from PubMed to extract ASD-related terms. We evaluated the predictive performance using precision, recall, and F1 score. We found that CLAMP has the best performance in terms of F1 score followed by cTAKES and then MetaMap. Our results show that CLAMP has much higher precision than cTAKES and MetaMap, while cTAKES and MetaMap have higher recall than CLAMP. The analysis protocols used in this study can be applied to other neuropsychiatric or neurodevelopmental disorders that lack well-defined terminology sets to describe their phenotypic presentations.
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