ProvCaRe: Characterizing scientific reproducibility of biomedical research studies using semantic provenance metadata
ProvCaRe: Characterizing scientific reproducibility of biomedical research studies using semantic provenance metadata
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DOI：
10.1016/j.ijmedinf.2018.10.009
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发表时间：
2019-01-01
影响因子：
4.9
通讯作者：
Redline, Susan
中科院分区：
文献类型：
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作者：
Sahoo, Satya S.;Valdez, Joshua;Redline, Susan
目的：研究的可重复性是推进生物医学科学的关键，它建立在可靠的结果基础上，减少已发表结果与研究数据之间的不一致。我们建议，来自研究的可用数据与来源元数据相结合，为评估科学可重复性提供一个框架。我们开发了ProvCaRe平台，对435,248篇已发表的文章进行建模、提取和查询语义来源信息。方法：ProvCaRe平台包括：(1)S3模型和形式化本体；(2)以出处为中心的文本处理工作流，利用从文章中提取的元数据生成由主语、谓语和宾语组成的出处三元组；(3)支持“来源感知”假设驱动搜索查询的ProvCaRe知识库。采用一种新的基于来源的排序算法对搜索查询结果中的文章进行排序。结果：ProvCaRe知识库包含4890万个来源三元组。七个研究假设被用作评估的搜索查询，并使用五类来源术语分析了所得的来源三元组。描述与人群队列相关的来源的术语最多（34%），其次是描述统计数据分析方法的术语29%，只有5%的术语描述了研究中使用的测量工具。此外，分析表明，一些文章在多个种源类别中包含了更多的种源术语，这表明这些研究具有更高的可重复性。结论：ProvCaRe知识库（https://provcare.case.edu/）是最大的生物医学研究来源资源之一，它结合了直观的搜索功能和新的基于来源的排名功能，列出与搜索查询相关的文章。
Objective: Reproducibility of research studies is key to advancing biomedical science by building on sound results and reducing inconsistencies between published results and study data. We propose that the available data from research studies combined with provenance metadata provide a framework for evaluating scientific reproducibility. We developed the ProvCaRe platform to model, extract, and query semantic provenance information from 435, 248 published articles.Methods: The ProvCaRe platform consists of: (1) the S3 model and a formal ontology; (2) a provenance-focused text processing workflow to generate provenance triples consisting of subject, predicate, and object using metadata extracted from articles; and (3) the ProvCaRe knowledge repository that supports "provenance-aware" hypothesis-driven search queries. A new provenance-based ranking algorithm is used to rank the articles in the search query results.Results: The ProvCaRe knowledge repository contains 48.9 million provenance triples. Seven research hypotheses were used as search queries for evaluation and the resulting provenance triples were analyzed using five categories of provenance terms. The highest number of terms (34%) described provenance related to population cohort followed by 29% of terms describing statistical data analysis methods, and only 5% of the terms described the measurement instruments used in a study. In addition, the analysis showed that some articles included a higher number of provenance terms across multiple provenance categories suggesting a higher potential for reproducibility of these research studies.Conclusion: The ProvCaRe knowledge repository (https://provcare.case.edu/) is one of the largest provenance resources for biomedical research studies that combines intuitive search functionality with a new provenance-based ranking feature to list articles related to a search query.