A GeneRIF or Gene Reference Into Function is a short (255 characters or fewer) statement about the function of a gene. GeneRIFs provide a simple

mechanism Mechanism may refer to: *Mechanism (economics), a set of rules for a game designed to achieve a certain outcome **Mechanism design, the study of such mechanisms *Mechanism (engineering), rigid bodies connected by joints in order to accomplish a ...

for allowing

scientist A scientist is a person who Scientific method, researches to advance knowledge in an Branches of science, area of the natural sciences. In classical antiquity, there was no real ancient analog of a modern scientist. Instead, philosophers engag ...

s to add to the functional

annotation An annotation is extra information associated with a particular point in a document or other piece of information. It can be a note that includes a comment or explanation. Annotations are sometimes presented Marginalia, in the margin of book page ...

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

s described in the Entrez Gene database. In practice, ''function'' is constructed quite broadly. For example, there are GeneRIFs that discuss the role of a gene in a disease, GeneRIFs that point the viewer towards a review article about the gene, and GeneRIFs that discuss the structure of a gene. However, the stated intent is for GeneRIFs to be about gene function. Currently over half a million geneRIFs have been created for genes from almost 1000 different species. GeneRIFs are always associated with specific entries in the Entrez Gene database. Each GeneRIF has a pointer to the PubMed ID (a type of document identifier) of a scientific publication that provides evidence for the statement made by the GeneRIF. GeneRIFs are often extracted directly from the document that is identified by the PubMed ID, very frequently from its title or from its final sentence. GeneRIFs are usually produced by

NCBI The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is loca ...

indexers, but anyone may submit a GeneRIF. To be processed, a valid Gene ID must exist for the specific gene, or the Gene staff must have assigned an overall Gene ID to the

species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...

. The latter case is implemented via records in Gene with the symbol NEWENTRY. Once the Gene ID is identified, only three types of information are required to complete a

submission Deference (also called submission or passivity) is the condition of submitting to the espoused, legitimate influence of one's superior or superiors. Deference implies a yielding or submitting to the judgment of a recognized superior, out of re ...

: # a concise

phrase In grammar, a phrasecalled expression in some contextsis a group of words or singular word acting as a grammatical unit. For instance, the English language, English expression "the very happy squirrel" is a noun phrase which contains the adject ...

describing a function or functions (less than 255 characters in length, preferably more than a restatement of the title of the paper); # a published paper describing that function, implemented by supplying the PubMed ID of a citation in PubMed; # a valid

e-mail address An email address identifies an email box to which messages are delivered. While early messaging systems used a variety of formats for addressing, today, email addresses follow a set of specific rules originally standardized by the Internet Engineeri ...

(which will remain confidential).

Example

Here are some GeneRIFs taken from Entrez Gene for GeneID 7157, the human gene

TP53 p53, also known as tumor protein p53, cellular tumor antigen p53 (UniProt name), or transformation-related protein 53 (TRP53) is a regulatory transcription factor protein that is often mutated in human cancers. The p53 proteins (originally thou ...

. The

PubMed PubMed is an openly accessible, free database which includes primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institute ...

document identifiers have been omitted from the examples. Note the wide variability with respect to the presence or absence of punctuation and of sentence-initial capital letters. * p53 and c-erbB-2 may have independent role in carcinogenesis of gall bladder cancer * Degradation of endogenous HIPK2 depends on the presence of a functional p53 protein. * p53 codon 72 alleles influence the response to anticancer drugs in cells from aged people by regulating the cell cycle inhibitor p21WAF1 * Logistic regression analysis showed p53 and COX-2 as dependent predictors in pancreatic carcinogenesis, and a reciprocal relationship to neoplastic progression between p53 and COX-2. GeneRIFs are an unusual type of textual genre, and they have recently been the subject of a number of articles from the natural language processing community.

External links

NCBI's web page describing GeneRIFs
*

References

* Paper describing a

Text Retrieval Conference The Text REtrieval Conference (TREC) is an ongoing series of workshops focusing on a list of different information retrieval (IR) research areas, or ''tracks.'' It is co-sponsored by the National Institute of Standards and Technology (NIST) and ...

"shared task" involving automatic prediction of GeneRIFs. * {{Cite conference , url = http://helix-web.stanford.edu/psb06/lu.pdf , author1= Lu, Zhiyong , author2=K. Bretonnel Cohen , author3=Lawrence Hunter , title = Finding GeneRIFs via Gene Ontology annotations , year = 2006 , conference = Proc. Pacific Symposium on Biocomputing 2006 , pages = 52–63 , url-status = dead , archiveurl = https://web.archive.org/web/20060213042043/http://helix-web.stanford.edu/psb06/lu.pdf , archivedate = 2006-02-13 Lu et al.'s paper describing a system that automatically suggests GeneRIFs. Molecular biology Genomics Natural language processing Bioinformatics