A method for the development of disease-specific reference standards vocabularies from textual biomedical literature resources.
A method for the development of disease-specific reference standards vocabularies from textual biomedical literature resources.
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DOI：
10.1016/j.artmed.2016.02.003
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发表时间：
2016-03
影响因子：
7.5
通讯作者：
Haug PJ
中科院分区：
文献类型：
--
作者：
Wang L;Bray BE;Shi J;Del Fiol G;Haug PJ
疾病特定词汇表是许多基于知识的智能系统和应用程序的基础，如文本注释、队列选择、疾病诊断建模和治疗建议。参考标准在疾病特定词汇表的自动化方法的开发和验证中至关重要。本研究的目标是设计和测试一种通用的方法，用于从专家精选的、特定于疾病的生物医学文献资源中开发词汇参考标准。我们从教科书、基于证据的综合在线资源、临床实践指南和期刊文章等文献资源中形成了特定疾病的语料库。医学专家将疾病专用术语分为四类(即原因或风险因素、体征或症状、诊断测试或结果以及治疗)进行注释和判定。注释被映射到UMLS概念。我们评估了来源的变化，每个来源对建立疾病特定词汇表的贡献，词汇相对于使用的来源数量的饱和度，以及该方法对不同疾病的普适性。这项研究在四个类别中产生了2588个心力衰竭的独特字符串注释，在治疗类别中分别产生了193个和425个关于肺血栓和类风湿性关节炎的字符串注释。大约80%的注释被映射到UMLS概念。心力衰竭来源之间的一致性范围在0.28到0.46之间。这些来源对最终词汇量的贡献在18%到49%之间。随着来源的探索，心力衰竭词汇在所有四个类别中都接近饱和，包括最少的六个来源(或者如果只有两个或更多的来源出现计数术语，则在四到七个来源之间)。就治疗类别而言，其他两种疾病达到接近饱和所需的来源较少。我们开发了一种开发特定疾病参考词汇表的方法。专家精选的生物医学文献资源对于获取特定疾病的医学知识是非常重要的。使用相对较少的文献来源，在疾病特定词汇表中达到接近饱和是可行的。
Disease-specific vocabularies are fundamental to many knowledge-based intelligent systems and applications like text annotation, cohort selection, disease diagnostic modeling, and therapy recommendation. Reference standards are critical in the development and validation of automated methods for disease-specific vocabularies. The goal of the present study is to design and test a generalizable method for the development of vocabulary reference standards from expert-curated, disease-specific biomedical literature resources. We formed disease-specific corpora from literature resources like textbooks, evidence-based synthesized online sources, clinical practice guidelines, and journal articles. Medical experts annotated and adjudicated disease-specific terms in four classes (i.e., causes or risk factors, signs or symptoms, diagnostic tests or results, and treatment). Annotations were mapped to UMLS concepts. We assessed source variation, the contribution of each source to build disease-specific vocabularies, the saturation of the vocabularies with respect to the number of used sources, and the generalizability of the method with different diseases. The study resulted in 2588 string-unique annotations for heart failure in four classes, and 193 and 425 respectively for pulmonary embolism and rheumatoid arthritis in treatment class. Approximately 80% of the annotations were mapped to UMLS concepts. The agreement among heart failure sources ranged between 0.28 and 0.46. The contribution of these sources to the final vocabulary ranged between 18% and 49%. With the sources explored, the heart failure vocabulary reached near saturation in all four classes with the inclusion of minimal six sources (or between four to seven sources if only counting terms occurred in two or more sources). It took fewer sources to reach near saturation for the other two diseases in terms of the treatment class. We developed a method for the development of disease-specific reference vocabularies. Expert-curated biomedical literature resources are substantial for acquiring disease-specific medical knowledge. It is feasible to reach near saturation in a disease-specific vocabulary using a relatively small number of literature sources.
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影响因子：
14.9
作者：
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通讯作者：
Musen MA
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通讯作者：
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