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FABLE: a search engine for identifying gene mentions in MEDLINE

Pete White white at
Wed Jul 19 14:31:39 PDT 2006

Announcing the release of FABLE v1.0, an online search engine for
identifying and normalizing names of genes and proteins in MEDLINE.
FABLE (Fast Automated Biomedical Literature Extraction) version 1.0 is now
available for general viewing (unrestricted access) at
<> .
FABLE v1.0 performs document retrieval of MEDLINE abstracts for queries of
genes, transcripts, and proteins by annotating text in a completely
automated process. The system is currently optimized for human genes. FABLE
combines a named entity recognition extractor and a human gene normalizer
that have been applied to all MEDLINE records. The system tracks a wide
range of commonly used synonyms and aliases for each human gene and maps
them to their official symbols. A query interface allows users to search for
articles mentioning particular genes or proteins of interest. Identified
articles can be sorted in various ways, depending upon users' preference,
including by relevance to the query and by journal impact factor. FABLE also
allows users to download their articles using a variety of formats. Feedback
regarding FABLE is both welcomed and encouraged.

FABLE v1.0 was developed by the BioIE group at the University of
Pennsylvania and the Children¹s Hospital of Philadelphia. FABLE and BioIE
are supported in part through a grant from the National Science Foundation.
FABLE is available at: <> .
Comments and suggestions regarding FABLE are appreciated and welcomed.
The BioIE website is at:

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