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  Announcing FABLE v3.0: aligning literature with human genomic sequence

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Author Topic:   Announcing FABLE v3.0: aligning literature with human genomic sequence
posted 05-25-2007 04:01 PM     Click Here to See the Profile for pswhite   Click Here to Email pswhite     Edit/Delete Message Reply w/Quote
FABLE (Fast Automated Biomedical Literature Extraction) version 3.0 is now available for general viewing at:

New features in v3.0:

* Literature-enabled local mirror of the UCSC Genome Browser — just like the standard UCSC Genome Browser, but with a literature track ("LitTrack") that connects journal articles with the genome locations of the genes referenced in the articles. Currently, human assemblies are supported.
* New "Did you mean" feature for Gene Lister searches: when a query returns no results, alternate spellings are suggested.
* Faster searches courtesy of updated hardware.

About FABLE: FABLE performs gene-based extraction of information from MEDLINE abstracts, including

* Identification of abstracts mentioning a human gene
* Generation of lists of human genes associated with any set of keywords
* Viewing of abstracts as an annotation track aligned to the human genome sequence assembly

FABLE combines a high-performance named entity recognition extractor and a comprehensive human gene normalizer that have each 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, and to view and browse literature records aligned to genomic sequence using an imbedded instance of the popular UCSC Genome Browser.

Feedback regarding FABLE is both welcomed and encouraged.

FABLE was developed by the BioIE group at the University of Pennsylvania and The Children’s 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: http://bioie.ldc.upenn.edu.


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