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  FABLE v2.0: customized gene lists from MEDLINE

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Author Topic:   FABLE v2.0: customized gene lists from MEDLINE
posted 11-18-2006 12:08 AM     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 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 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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