Generating gene summaries from biomedical literature: A study of semi-structured summarization

Most knowledge accumulated through scientific discoveries in genomics and related biomedical disciplines is buried in the vast amount of biomedical literature. Since understanding gene regulations is fundamental to biomedical research, summarizing all the existing knowledge about a gene based on literature is highly desirable to help biologists digest the literature. In this paper, we present a study of methods for automatically generating gene summaries from biomedical literature. Unlike most existing work on automatic text summarization, in which the generated summary is often a list of extracted sentences, we propose to generate a semi-structured summary which consists of sentences covering specific semantic aspects of a gene. Such a semi-structured summary is more appropriate for describing genes and poses special challenges for automatic text summarization. We propose a two-stage approach to generate such a summary for a given gene – first retrieving articles about a gene an...

• Type: Journal
• Year: 2007
• Where: IPM
• Authors: Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce R. Schatz
• Keywords: Automatic Text Summarization, Biomedical Literature, Gene, IPM 2007