Automatically generating gene summaries from biomedical literature

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution


Biologists often need to find information about genes whose function is not described in the genome databases. Currently they must try to search disparate biomedical literature to locate relevant articles, and spend considerable efforts reading the retrieved articles in order to locate the most relevant knowledge about the gene. We describe our software, the first that automatically generates gene summaries from biomedical literature. We present a two-stage summarization method, which involves first retrieving relevant articles and then extracting the most informative sentences from the retrieved articles to generate a structured gene summary. The generated summary explicitly covers multiple aspects of a gene, such as the sequence information, mutant phenotypes, and molecular interaction with other genes. We propose several heuristic approaches to improve the accuracy in both stages. The proposed methods are evaluated using 10 randomly chosen genes from FlyBase and a subset of Medline abstracts about Drosophila. The results show that the precision of the top selected sentences in the 6 aspects is typically about 50-70%, and the generated summaries are quite informative, indicating that our approaches are effective in automatically summarizing literature information about genes. The generated summaries not only are directly useful to biologists but also serve as useful entry points to enable them to quickly digest the retrieved literature articles.

Original languageEnglish (US)
Title of host publicationProceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006
Number of pages12
StatePublished - 2006
Event11th Pacific Symposium on Biocomputing 2006, PSB 2006 - Maui, HI, United States
Duration: Jan 3 2006Jan 7 2006

Publication series

NameProceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006


Other11th Pacific Symposium on Biocomputing 2006, PSB 2006
Country/TerritoryUnited States
CityMaui, HI

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • General Medicine


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