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LitSense: making sense of biomedical literature at sentence level

机译:LitSense:从句子层面理解生物医学文献

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摘要

Literature search is a routine practice for scientific studies as new discoveries build on knowledge from the past. Current tools (e.g. PubMed, PubMed Central), however, generally require significant effort in query formulation and optimization (especially in searching the full-length articles) and do not allow direct retrieval of specific statements, which is key for tasks such as comparing/validating new findings with previous knowledge and performing evidence attribution in biocuration. Thus, we introduce LitSense, which is the first web-based system that specializes in sentence retrieval for biomedical literature. LitSense provides unified access to PubMed and PMC content with over a half-billion sentences in total. Given a query, LitSense returns best-matching sentences using both a traditional term-weighting approach that up-weights sentences that contain more of the rare terms in the user query as well as a novel neural embedding approach that enables the retrieval of semantically relevant results without explicit keyword match. LitSense provides a user-friendly interface that assists its users to quickly browse the returned sentences in context and/or further filter search results by section or publication date. LitSense also employs PubTator to highlight biomedical entities (e.g. gene/proteins) in the sentences for better result visualization. LitSense is freely available at .
机译:文献检索是科学研究的常规做法,因为新发现是建立在过去知识基础之上的。但是,当前的工具(例如PubMed,PubMed Central)通常在查询表述和优化(特别是在搜索全文文章)方面需要大量的工作,并且不允许直接检索特定的语句,这对于诸如比较/利用以前的知识验证新发现并在生物治疗中进行证据归因。因此,我们引入了LitSense,这是第一个基于Web的系统,专门研究生物医学文献的句子检索。 LitSense提供对PubMed和PMC内容的统一访问,总共超过50亿个句子。给定查询后,LitSense会使用传统的术语加权方法(可对用户查询中包含更多稀有术语的句子进行加权)以及可检索语义相关结果的新型神经嵌入方法,返回最匹配的句子没有明确的关键字匹配。 LitSense提供了用户友好的界面,可帮助其用户快速浏览上下文中返回的句子和/或进一步按章节或发布日期过滤搜索结果。 LitSense还使用PubTator突出句子中的生物医学实体(例如基因/蛋白质),以便更好地可视化结果。 LitSense可从以下网站免费获得。

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