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FABLE v2.0: customized gene lists from MEDLINE

Pete White white at
Fri Nov 17 15:07:44 PST 2006

FABLE (Fast Automated Biomedical Literature Extraction) version 2.0 is now
available for general viewing at:
New features in v2.0:

* New "Gene Lister" application allows users to create lists of relevant
human genes from the biomedical literature by entering arbitrary boolean
keyword searches. Users can find human genes associated with drugs,
diseases, people, places, institutions, genes, proteins‹any text that occurs
in the biomedical literature. Examples:

    Identify genes associated with a disease:
        Schizophrenia AND bipolar NOT depression
    Identify genes associated with a disease attribute:
        Metastasis AND "colon cancer"
    Identify genes associated with a person:
        Asthma AND "Doe JA"
    Identify genes associated with a place:
        "University of Pennsylvania" AND "heart disease"
    Identify genes associated with genes:
        Myoglobin NOT hemoglobin
    Identify genes associated with techniques:

* Data is now refreshed weekly from MEDLINE®/PubMed®.

* For all search results, the user can click next to the listed gene
symbol(s) to see all synonyms for the symbols.

* Links to the Help and Overview pages now produce context-sensitive
highlighting to make it easier for users to find what they're looking for.

* Users can now download single page results, no longer being restricted to
downloading the entire search results.

About FABLE: FABLE performs document retrieval and gene list extractions 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. A query interface allows users to search for articles mentioning
particular genes or proteins of interest, or to generate lists of genes
mentioned in articles associated with any keyword(s). Identified articles
and gene lists can be sorted in various ways, depending upon users'
preference. FABLE also allows users to download articles and gene sets using
a variety of formats. Feedback regarding FABLE is both welcomed and

FABLE 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 grants from the National Science Foundation and the National
Institutes of Health.
The BioIE website is at:

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