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

Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, Bruce Schatz

Research output: Contribution to journalArticlepeer-review


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 and then extracting sentences for each specified semantic aspect. We address the issue of gene name variation in the first stage and propose several different methods for sentence extraction in the second stage. We evaluate the proposed methods using a test set with 20 genes. Experiment results show that the proposed methods can generate useful semi-structured gene summaries automatically from biomedical literature, and our proposed methods outperform general purpose summarization methods. Among all the proposed methods for sentence extraction, a probabilistic language modeling approach that models gene context performs the best.

Original languageEnglish (US)
Pages (from-to)1777-1791
Number of pages15
JournalInformation Processing and Management
Issue number6
StatePublished - Nov 2007


  • Genomics
  • Probabilistic language model
  • Summarization

ASJC Scopus subject areas

  • Information Systems
  • Media Technology
  • Computer Science Applications
  • Management Science and Operations Research
  • Library and Information Sciences


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