Information extraction for enhanced access to disease outbreak reports

Ralph Grishman, Silja Huttunen, Roman Yangarber

Research output: Contribution to journalArticlepeer-review


Document search is generally based on individual terms in the document. However, for collections within limited domains it is possible to provide more powerful access tools. This paper describes a system designed for collections of reports of infectious disease outbreaks. The system, Proteus-BIO, automatically creates a table of outbreaks, with each table entry linked to the document describing that outbreak; this makes it possible to use database operations such as selection and sorting to find relevant documents. Proteus-BIO consists of a Web crawler which gathers relevant documents; an information extraction engine which converts the individual outbreak events to a tabular database; and a database browser which provides access to the events and, through them, to the documents. The information extraction engine uses sets of patterns and word classes to extract the information about each event. Preparing these patterns and word classes has been a time-consuming manual operation in the past, but automated discovery tools now make this task significantly easier. A small study comparing the effectiveness of the tabular index with conventional Web search tools demonstrated that users can find substantially more documents in a given time period with Proteus-BIO.

Original languageEnglish (US)
Pages (from-to)236-246
Number of pages11
JournalJournal of Biomedical Informatics
Issue number4
StatePublished - Aug 2002

ASJC Scopus subject areas

  • Computer Science Applications
  • Health Informatics


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