自动从科学文献中提取药代动力学参数,提升数据获取效率。
Automated Extraction of Pharmacokinetic Parameters from Structured XML Scientific Articles: Enhancing Data Accessibility at Scale
- 基于结构化XML文档的自动化表格信息抽取方法
- 可精准识别行列标题关联的细胞内容,适应复杂排版
- 适合医药研发、数据集成团队快速获取高质量药代数据
在药理学领域,缺乏集中、全面且及时更新的药代动力学(PK)数据存储库,导致研发团队需耗费大量时间从不同出版物中搜集所需定量参数。这些定量信息主要以表格形式存在,常见于XML、HTML或PDF格式的在线资源及补充材料中,是科学与监管文件中的关键信息单元。然而,从表格中提取数据通常依赖人工,耗时费力,现有自动化机器学习模型因表格布局多样、结构复杂而难以准确识别和提取。信息提取与阅读顺序判断的难度高度依赖表格结构复杂度。为实现高效准确的数据获取,亟需开发能依据行列标题正确解析单元格内容的AI算法,以替代长期依赖的人工方式。该研究旨在通过人工智能技术实现大规模、高精度的药代动力学参数自动化提取。
原文摘要 · Abstract (English)
In the field of pharmacology, there is a notable absence of centralized, comprehensive, and up-to-date repositories of PK data. This poses a significant challenge for R&D as it can be a time-consuming and challenging task to collect all the required quantitative PK parameters from diverse scientific publications. This quantitative PK information is predominantly organized in tabular format, mostly available as XML, HTML, or PDF files within various online repositories and scientific publications, including supplementary materials. This makes tables one of the crucial components and information elements of scientific or regulatory documents as they are commonly utilized to present quantitative information. Extracting data from tables is typically a labor-intensive process, and alternative automated machine learning models may struggle to accurately detect and extract the relevant data due to the complex nature and diverse layouts of tabular data. The difficulty of information extraction and reading order detection is largely dependent on the structural complexity of the tables. Efforts to understand tables should prioritize capturing the content of table cells in a manner that aligns with how a human reader naturally comprehends the information. FARAD has been manually extracting tabular data and other information from literature and regulatory agencies for over 40 years. However, there is now an urgent need to automate this process due to the large volume of publications released daily. The accuracy of this task has become increasingly challenging, as manual extraction is tedious and prone to errors, especially given the staffing shortages we are currently facing. This necessitates the development of AI algorithms for table detection and extraction that are able to precisely handle cells organized according to the table structure, as indicated by column and/or row header information.
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