Generating Gene Summaries from Biomedical Literature: A Study of Semi-Structured Summarization

Publication Type

Journal Article

Publication Date

11-2007

Abstract

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.

Discipline

Databases and Information Systems | Numerical Analysis and Scientific Computing

Publication

Information Processing and Management

Volume

43

Issue

6

First Page

1777

Last Page

1791

ISSN

0306-4573

Identifier

10.1016/j.ipm.2007.01.018

Publisher

Elsevier

Additional URL

http://dx.doi.org/10.1016/j.ipm.2007.01.018

Link to Full Text

Share

COinS