Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, United States of America.
Xornet Inc., Rochester, New York, United States of America.
PLoS One. 2021 Mar 8;16(3):e0248335. doi: 10.1371/journal.pone.0248335. eCollection 2021.
Over a decade ago, we introduced Anne O'Tate, a free, public web-based tool http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi to support user-driven summarization, drill-down and mining of search results from PubMed, the leading search engine for biomedical literature. A set of hotlinked buttons allows the user to sort and rank retrieved articles according to important words in titles and abstracts; topics; author names; affiliations; journal names; publication year; and clustered by topic. Any result can be further mined by choosing any other button, and small search results can be expanded to include related articles. It has been deployed continuously, serving a wide range of biomedical users and needs, and over time has also served as a platform to support the creation of new tools that address additional needs. Here we describe the current, greatly expanded implementation of Anne O'Tate, which has added additional buttons to provide new functionalities: We now allow users to sort and rank search results by important phrases contained in titles and abstracts; the number of authors listed on the article; and pairs of topics that co-occur significantly more than chance. We also display articles according to NLM-indexed publication types, as well as according to 50 different publication types and study designs as predicted by a novel machine learning-based model. Furthermore, users can import search results into two new tools: e) Mine the Gap!, which identifies pairs of topics that are under-represented within set of the search results, and f) Citation Cloud, which for any given article, allows users to visualize the set of articles that cite it; that are cited by it; that are co-cited with it; and that are bibliographically coupled to it. We invite the scientific community to explore how Anne O'Tate can assist in analyzing biomedical literature, in a variety of use cases.
十多年前，我们引入了 Anne O'Tate，这是一个免费的、基于网络的工具，网址是 http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi，用于支持用户驱动的 PubMed 搜索结果的摘要、深入挖掘和挖掘，PubMed 是生物医学文献的主要搜索引擎。一组热链接按钮允许用户根据标题和摘要中的重要单词、主题、作者姓名、隶属关系、期刊名称、出版年份以及按主题聚类对检索到的文章进行排序和排名。任何结果都可以通过选择其他按钮进一步挖掘，并且可以将小的搜索结果扩展到包括相关文章。它一直在不断部署，为广泛的生物医学用户和需求提供服务，并且随着时间的推移，它也一直作为一个平台来支持创建满足其他需求的新工具。在这里，我们描述了 Anne O'Tate 的当前、大大扩展的实现，它增加了其他按钮来提供新的功能：我们现在允许用户根据标题和摘要中包含的重要短语、文章中列出的作者数量以及共同出现的主题对搜索结果进行排序和排名。我们还根据 NLM 索引的出版物类型以及根据一种新的基于机器学习的模型预测的 50 种不同的出版物类型和研究设计来显示文章。此外，用户可以将搜索结果导入两个新工具：e）挖掘差距！，它识别出在一组搜索结果中代表性不足的主题对，以及 f）引文云，它允许用户为任何给定的文章可视化引用它的文章集；被它引用的文章；与它共同引用的文章；以及与它有书目联系的文章。我们邀请科学界探索 Anne O'Tate 如何在各种用例中协助分析生物医学文献。
