SNPedia
Encyclopedia
SNPedia is a wiki-based bioinformatics
web site that serves as a database of single nucleotide polymorphism
s (SNPs). Each article on a SNP provides a short description, links to scientific articles and personal genomics
web sites, as well as microarray information about that SNP. Thus SNPedia may support the interpretation of results of personal genotyping from, e.g., 23andMe
, Navigenics
, deCODEme or Knome
.
SNPedia is a semantic wiki
, powered by MediaWiki
and the Semantic MediaWiki
extension.
SNPedia was created, and is run by, geneticist Greg Lennon
and programmer Mike Cariaso, who at the time of the site's founding were both located in Bethesda, Maryland
.
In May 2011, the website claimed to have over 22,000 SNPs in their database.
computer program called Promethease, also developed by the SNPedia team, allows users to compare personal genetics results against the SNPedia database, generating a report with information about a person's attributes, such as propensity to diseases, based on the presence of specific SNP's within their genome.
In May 2008 Cariaso, using Promethease, won an online contest sponsored by 23andMe to determine as much information as possible about an anonymous woman based only on her genome. Cariaso won in all three categories of "accuracy, creativity and cleverness". In 2009, the anonymous woman ("Lilly Mendel") was revealed to be 23andMe co-founder Linda Avey
, allowing a direct comparison between her actual traits and those predicted by Promethease a year earlier.
said:
In January 2011, technology journalist Ronald Bailey
posted the full result of his Promethease report online. Writing about his decision in Reason
magazine, he stated:
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
web site that serves as a database of single nucleotide polymorphism
Single nucleotide polymorphism
A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes in an individual...
s (SNPs). Each article on a SNP provides a short description, links to scientific articles and personal genomics
Personal genomics
Personal genomics is the branch of genomics concerned with the sequencing and analysis of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism analysis chips , or partial or full genome sequencing...
web sites, as well as microarray information about that SNP. Thus SNPedia may support the interpretation of results of personal genotyping from, e.g., 23andMe
23andMe
23andMe is a privately held personal genomics and biotechnology company based in Mountain View, California that is developing new methods and technologies that will enable consumers to understand their own genetic information...
, Navigenics
Navigenics
Navigenics, Inc. is a privately held personal genomics company, based in Foster City, California, that uses genetic testing to help people determine their individual risk for dozens of health conditions....
, deCODEme or Knome
Knome
Knome is an American personal genomics company that sells human whole genome and exome analysis and sequencing services to researchers and consumers...
.
SNPedia is a semantic wiki
Semantic Wiki
A semantic wiki is a wiki that has an underlying model of the knowledge described in its pages. Regular, or syntactic, wikis have structured text and untyped hyperlinks...
, powered by MediaWiki
MediaWiki
MediaWiki is a popular free web-based wiki software application. Developed by the Wikimedia Foundation, it is used to run all of its projects, including Wikipedia, Wiktionary and Wikinews. Numerous other wikis around the world also use it to power their websites...
and the Semantic MediaWiki
Semantic MediaWiki
Semantic MediaWiki is an extension to MediaWiki that allows for annotating semantic data within wiki pages, thus turning a wiki that incorporates the extension into a semantic wiki...
extension.
SNPedia was created, and is run by, geneticist Greg Lennon
and programmer Mike Cariaso, who at the time of the site's founding were both located in Bethesda, Maryland
Bethesda, Maryland
Bethesda is a census designated place in southern Montgomery County, Maryland, United States, just northwest of Washington, D.C. It takes its name from a local church, the Bethesda Meeting House , which in turn took its name from Jerusalem's Pool of Bethesda...
.
In May 2011, the website claimed to have over 22,000 SNPs in their database.
Promethease
An associated freewareFreeware
Freeware is computer software that is available for use at no cost or for an optional fee, but usually with one or more restricted usage rights. Freeware is in contrast to commercial software, which is typically sold for profit, but might be distributed for a business or commercial purpose in the...
computer program called Promethease, also developed by the SNPedia team, allows users to compare personal genetics results against the SNPedia database, generating a report with information about a person's attributes, such as propensity to diseases, based on the presence of specific SNP's within their genome.
In May 2008 Cariaso, using Promethease, won an online contest sponsored by 23andMe to determine as much information as possible about an anonymous woman based only on her genome. Cariaso won in all three categories of "accuracy, creativity and cleverness". In 2009, the anonymous woman ("Lilly Mendel") was revealed to be 23andMe co-founder Linda Avey
Linda Avey
Linda Avey is an American biotech analyst, biologist, and the co-founder of 23andMe.Avey spent 20 years in sales and business development in biopharmaceuticals. Avey helped develop research programs for Affymetrix and Perlegen Sciences....
, allowing a direct comparison between her actual traits and those predicted by Promethease a year earlier.
Reception
In a June 2008 article on personal genomics, a doctor from the Southern Illinois University School of MedicineSouthern Illinois University School of Medicine
Southern Illinois University School of Medicine is an allopathic medical school located in Springfield, Illinois, the state capital. It is part of the Southern Illinois University system, which includes a campus in Edwardsville as well as the flagship in Carbondale. The medical school was founded...
said:
In January 2011, technology journalist Ronald Bailey
Ronald Bailey
Ronald Bailey is the science editor for Reason magazine. He was born in San Antonio, Texas and raised in Washington County, Virginia, and attended the University of Virginia, where he earned a B.A...
posted the full result of his Promethease report online. Writing about his decision in Reason
Reason (magazine)
Reason is a libertarian monthly magazine published by the Reason Foundation. The magazine has a circulation of around 60,000 and was named one of the 50 best magazines in 2003 and 2004 by the Chicago Tribune.- History :...
magazine, he stated:
See also
- dbSNPDbSNPThe Single Nucleotide Polymorphism Database is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information in collaboration with the National Human Genome Research Institute...
- Online Mendelian Inheritance in Man
- Full Genome SequencingFull genome sequencingFull genome sequencing , also known as whole genome sequencing , complete genome sequencing, or entire genome sequencing, is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time...
- Predictive MedicinePredictive medicinePredictive medicine is a rapidly emerging field of medicine that entails predicting disease and instituting preventive measures in order to either prevent the disease altogether or significantly decrease its impact upon the patient...
External links
- SNPedia
- http://www.genome.gov/GWAStudies
- Michael Cariaso - Next-Gen Sequencing, Wikis and SNPedia, WebcastWebcastA webcast is a media presentation distributed over the Internet using streaming media technology to distribute a single content source to many simultaneous listeners/viewers. A webcast may either be distributed live or on demand...
from Bio-ITWorld.com.