Automatic summarization of mouse gene information by clustering and sentence extraction from MEDLINE abstracts.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Tools to automatically summarize gene information from the literature have the potential to help genomics researchers better interpret gene expression data and investigate biological pathways. The task of finding information on sets of genes is common for genomic researchers, and PubMed is still the first choice because the most recent and original information can only be found in the unstructured, free text biomedical literature. However, finding information on a set of genes by manually searching and scanning the literature is a time-consuming and daunting task for scientists. We built and evaluated a query-based automatic summarizer of information on mouse genes studied in microarray experiments. The system clusters a set of genes by MeSH, GO and free text features and presents summaries for each gene by ranked sentences extracted from MEDLINE abstracts. Evaluation showed that the system seems to provide meaningful clusters and informative sentences are ranked higher by the algorithm.

Original languageEnglish (US)
Pages (from-to)831-835
Number of pages5
JournalAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium
StatePublished - 2007

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MEDLINE
Cluster Analysis
Genes
Research Personnel
Genomics
PubMed
Gene Expression

ASJC Scopus subject areas

  • Medicine(all)

Cite this

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title = "Automatic summarization of mouse gene information by clustering and sentence extraction from MEDLINE abstracts.",
abstract = "Tools to automatically summarize gene information from the literature have the potential to help genomics researchers better interpret gene expression data and investigate biological pathways. The task of finding information on sets of genes is common for genomic researchers, and PubMed is still the first choice because the most recent and original information can only be found in the unstructured, free text biomedical literature. However, finding information on a set of genes by manually searching and scanning the literature is a time-consuming and daunting task for scientists. We built and evaluated a query-based automatic summarizer of information on mouse genes studied in microarray experiments. The system clusters a set of genes by MeSH, GO and free text features and presents summaries for each gene by ranked sentences extracted from MEDLINE abstracts. Evaluation showed that the system seems to provide meaningful clusters and informative sentences are ranked higher by the algorithm.",
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