Valx: A System for Extracting and Structuring Numeric Lab Test Comparison Statements from Text.
Valx: A System for Extracting and Structuring Numeric Lab Test Comparison Statements from Text.
复制标题
Valx：用于从文本中提取和构建数字实验室测试比较语句的系统。
DOI：
10.3414/me15-01-0112
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发表时间：
2016-05-17
影响因子：
1.7
通讯作者：
Weng C
中科院分区：
文献类型：
--
作者：
Hao T;Liu H;Weng C
开发一种自动化方法，用于从文本中提取和构建数字实验室检查比较声明，并使用临床试验合格性标准文本评价该方法。利用来自统一医学语言系统（UMLS）的语义知识和从互联网获取的领域知识，Valx采取7个步骤来提取和规范化数字实验室测试表达式：1）文本预处理，2）数字、单位和比较运算符提取，3）使用混合知识的变量识别，4）变量-数字关联，5）基于上下文的关联过滤，6）度量单位规范化; 7）基于启发式规则的比较语句验证。我们的参考标准是三位评分员对两个变量的所有比较声明的基于共识的注释，即，从ClinicalTrials.gov中的所有1型和2型糖尿病试验中确定的HbA1c和葡萄糖。构建HbA1c比较声明的精确度、召回率和F-测量值对于1型糖尿病试验分别为99.6%、98.1%、98.8%，对于2型糖尿病试验分别为98.8%、96.9%、97.8%。对于1型糖尿病试验和2型糖尿病试验，构建葡萄糖比较语句的精确度、召回率和F-测量分别为97.3%、94.8%、96.1%和92.3%、92.3%、92.3%。Valx在临床试验总结中有效地提取和构建自由文本实验室测试比较声明。未来的研究是必要的，以测试其普遍性超出资格标准文本。开源的Valx使其能够在协作科学界中进一步评估和持续改进。
To develop an automated method for extracting and structuring numeric lab test comparison statements from text and evaluate the method using clinical trial eligibility criteria text. Leveraging semantic knowledge from the Unified Medical Language System (UMLS) and domain knowledge acquired from the Internet, Valx takes 7 steps to extract and normalize numeric lab test expressions: 1) text preprocessing, 2) numeric, unit, and comparison operator extraction, 3) variable identification using hybrid knowledge, 4) variable - numeric association, 5) context-based association filtering, 6) measurement unit normalization, and 7) heuristic rule-based comparison statements verification. Our reference standard was the consensus-based annotation among three raters for all comparison statements for two variables, i.e., HbA1c and glucose, identified from all of Type 1 and Type 2 diabetes trials in ClinicalTrials.gov. The precision, recall, and F-measure for structuring HbA1c comparison statements were 99.6%, 98.1%, 98.8% for Type 1 diabetes trials, and 98.8%, 96.9%, 97.8% for Type 2 Diabetes trials, respectively. The precision, recall, and F-measure for structuring glucose comparison statements were 97.3%, 94.8%, 96.1% for Type 1 diabetes trials, and 92.3%, 92.3%, 92.3% for Type 2 diabetes trials, respectively. Valx is effective at extracting and structuring free-text lab test comparison statements in clinical trial summaries. Future studies are warranted to test its generalizability beyond eligibility criteria text. The open-source Valx enables its further evaluation and continued improvement among the collaborative scientific community.