What is FABLE?
What's unique compared to PubMed©?
What terms can be used as search terms?
Is there a workaround for Article Finder's inability to search for arbitrary search terms?
How can I sort the articles by their relevance to my search?
What does "impact factor" mean?
How can I download search results?
What literature records does FABLE use?
How can I get a list of genes, and articles mentioning those genes, that are relevant to a specific disease, organ, biological process, author, institution, etc.?
What character encoding do you use?
I searched for "Jorgensen"; why didn't FABLE find "Jørgensen"?
How can I see a list of synonyms/aliases for a gene?
Why can't I search for cytogenetic positions in Gene Lister?
- What is FABLE?
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.
- What's unique compared to PubMed®?
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
FABLE also has some unique sorting options. More...
- What terms can be used as search terms?
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...
- Is there a workaround for Article Finder's inability to search for arbitrary search terms?
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
This limitation of the Article Finder will be addressed in FABLE v3 or v4.
- How can I sort the articles by their relevance to my search?
Choose the "relevance" option before your search (this is the
- What does "impact factor" mean?
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
- How can I download search results?
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...
- What literature records does FABLE use?
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.
- How can I get a list of genes, and articles mentioning those genes, that are relevant to a
specific disease, organ, biological process, author, institution, etc.?
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...
- What character encoding do you use?
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.
- I searched for "Jorgensen"; why didn't FABLE find "Jørgensen"?
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
- How can I see a list of synonyms/aliases for a gene?
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.