FABLE stands for Fast Automated Biomedical Literature Extraction. FABLE is a completely automated way to identify objects of biological interest in biomedical literature. FABLE currently targets genes and proteins, and it uses MEDLINE®/PubMed® abstracts and associated annotations (such as MeSH terms). FABLE uses state-of-the art information extraction tools to perform this task.

In general, FABLE has much higher recall for (identifies more instances of) the objects of interest. For example, searching for either the official gene symbol "MYCN" or its commonly used alias "N-myc" in PubMed® will identify 653 and 1,431 articles in PubMed®, respectively, with only 31 articles in common between these searches. A search that includes synonyms with FABLE's Article Finder will identify 2,207 articles, as it will recognize that MYCN and N-myc are equivalent. The Article Finder will also often identify articles mentioning genes that PubMed® failed to recognize as being mentioned. FABLE's Gene Lister is a tool that can automatically generate lists of genes relevant to one or more specific, user-specified concepts from the literature. FABLE also has some unique sorting options. More...

For the Article Finder, search terms should be limited to names of unique genes and proteins, especially human genes. Moreover, search terms that are neither genes nor proteins will yield no results. More... For the Gene Lister , any word, phrase, or set of words/phrases can be used. More...

Yes. You can use the Gene Lister to see the list of genes matching an arbitrary query, then click on the "number of articles" link associated with a particular gene. The result will be an Article Finder search matching both your Gene Lister search terms and the gene indicated. This limitation of the Article Finder will be addressed in FABLE v3 or v4.

Choose the "relevance" option before your search (this is the default). More...

As defined by Wikipedia: "Impact Factor is a measure of importance of scientific journals. It is calculated each year by Thompson Scientific for those journals which it tracks, and the factors are published in the Journal Citation Report."

You can choose any of 3 formats (Excel, XML, CSV), and then click the "submit" button on the result page. What happens next depends on the software you are using. For CSV downloads, make sure your spreadsheet or other software interprets the file as Unicode UTF-8. More...

By using FABLE, you are agreeing to the Terms of Use for FABLE, CHOP, and any externally-derived datasets such as MEDLINE®/PubMed®. Please see the "Terms of Use" and "Acknowledgments" sections.

FABLE uses a combination of the latest publicly available abstracts from the National Library of Medicine's MEDLINE® set of biomedical abstracts, and all additional biomedical abstracts categorized as "Publisher Status" from the National Center for Biotechnology Information's PubMed® repository. The "Publisher Status" category includes many abstracts that have been electronically submitted ahead of print. FABLE's dataset is updated weekly; the most recent date of inclusion is shown on the home page.

Fable's Gene Lister application allows users to create lists of relevant genes from the biomedical literature by entering arbitrary boolean keyword searches. For example, to find genes/articles relevant to lung cancer and chromosomal deletions, enter the following query in the Gene Lister search box: "lung cancer" "chromosomal deletion". More...

FABLE uses Unicode UTF-8 for both input and output purposes. Author names will be correctly spelled with appropriate accents, etc. Any errors most likely originate in the source MEDLINE® data. Unicode input is really only an issue for the Gene Lister application, because the Article Finder only allows you to search for gene symbols and aliases, whereas Gene Lister allows you to search for anything.

As of FABLE v2.1, users can search for Unicode/UTF-8 search terms in the Gene Lister application, but an exact match is required. FABLE v3.1 will allow you to use "jorgensen" to match both "Jorgensen" and "Jørgensen".

For Article Finder searches using the default Synonyms option, the user can click on the matching gene symbol(s) (indicated by the blue triangle) at the top of the search results to see all synonyms for the symbols. Similarly, results of Gene Lister searches display a "Synonyms" column; for each entry in this column, the blue triangle to the left of the entry can be clicked on to display all recorded synonyms for the corresponding gene.

The cytogenetic positions shown on LitTrack links are taken from our mirror of the UCSC Genome Browser database. Gene Lister searches only for data that we extract from MEDLINE, not anything stored in other external databases.

The LitTrack form on the FABLE home page links to the search page of our customized UCSC Genome Browser mirror. LitTrack is our custom track for the UCSC Genome Browser, visible from the track display page. Literature hits are displayed as items on this track. More...