CSIRO Data61, Sydney, Australia.
Australian National University, Canberra, Australia.
BMC Bioinformatics. 2020 Dec 21;21(Suppl 19):572. doi: 10.1186/s12859-020-03894-8.
Finding relevant literature is crucial for many biomedical research activities and in the practice of evidence-based medicine. Search engines such as PubMed provide a means to search and retrieve published literature, given a query. However, they are limited in how users can control the processing of queries and articles-or as we call them documents-by the search engine. To give this control to both biomedical researchers and computer scientists working in biomedical information retrieval, we introduce a public online tool for searching over biomedical literature. Our setup is guided by the NIST setup of the relevant TREC evaluation tasks in genomics, clinical decision support, and precision medicine.
To provide benchmark results for some of the most common biomedical information retrieval strategies, such as querying MeSH subject headings with a specific weight or querying over the title of the articles only, we present our evaluations on public datasets. Our experiments report well-known information retrieval metrics such as precision at a cutoff of ranked documents.
We introduce the A2A search and benchmarking tool which is publicly available for the researchers who want to explore different search strategies over published biomedical literature. We outline several query formulation strategies and present their evaluations with known human judgements for a large pool of topics, from genomics to precision medicine.
对于许多生物医学研究活动和循证医学实践来说，查找相关文献是至关重要的。 搜索引擎（如 PubMed）提供了一种方法，可以根据查询搜索和检索已发表的文献。 但是，用户对查询和文章（我们称之为文档）的处理方式受到搜索引擎的限制。 为了将这种控制能力赋予从事生物医学研究的研究人员和从事生物医学信息检索的计算机科学家，我们引入了一个公共在线工具，用于在生物医学文献中进行搜索。 我们的设置以 NIST 在基因组学、临床决策支持和精准医学方面的相关 TREC 评估任务的设置为指导。
为了为一些最常见的生物医学信息检索策略（例如使用特定权重查询 MeSH 主题词或仅查询文章标题）提供基准结果，我们在公共数据集上进行了评估。 我们的实验报告了众所周知的信息检索指标，例如在排名文档的截止点处的精度。
我们介绍了 A2A 搜索和基准测试工具，该工具可供希望探索在已发表的生物医学文献上使用不同搜索策略的研究人员使用。 我们概述了几种查询制定策略，并针对来自基因组学到精准医学的大量主题展示了它们的评估结果以及已知的人工判断。
