BioGPS is a community-driven, customizable gene annotation portal that allows users to query genes and view gene reports. It aggregates information from over 400 gene databases and resources contributed by users. Users can customize the layout and content of gene reports. The portal has had over 680,000 gene queries, 800,000 gene reports viewed, and 400 resources added by users in the last year. An associated MyGene.Info service provides programmatic access to gene annotation data.

1. : a community-driven customizable gene annotation portal
Chunlei Wu, Ian MacLeod, Andrew I. Su
cwu@scripps.edu, imacleod@scripps.edu, asu@scripps.edu
Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA
Candidate genes Testable
hypothesis
Gene databases are numerous and overlapping
http://www.ncbi.nlm.nih.gov/pubmed?term={{Symbol}}
Users can add new resources to BioGPS as “plugins”
Simply need a URL template:
http://string-db.org/newstring_cgi?...&identifier={{EnsemblGene}}
… and hundreds more …
http://www.genome.jp/dbget-bin/www_bget?hsa:{{EntrezGene}}
http://smart.embl-heidelberg.de/smart/show_motifs.pl?ID={{Uniprot}}
http://flybase.org/reports/{{FLYBASE}}.html
http://omim.org/entry/{{MIM}}
Users can customize their gene-report ”layout” ……
~ 30 types of gene-specific identifiers
BioGPS
 BioGPS users contributed > 400 resources in plugin library
NCBI
Structural biologist PDB
PFAM
BioGPS
eQTL dbSNP
Why? Why?
Geneticist  Discover resources by what’s popular among other users
Genome
Users MGI
Browser
Requests
BioGPS BioGPS users “like” a resource
Community
development
Expression KEGG by adding it into a custom layout, so
Resources
System Biologist that other users can discover popular
Time GeneCards resources they might miss.
Developers typically define the Development resources do not
gene-report view scale with increased users and
feature-requests
MyGene.Info: gene annotation web services
(Powers BioGPS gene query, now for public use)
BioGPS users: (up to Jul 8, 2012)
MyGene.Info provides simple-to-use REST web services to query/retrieve gene annotation
Queried 680k genes in last year data. It's designed with simplicity and performance emphasized.
Viewed 800k gene-reports in last year Gene query service: Gene annotation service
http://mygene.info/query?q=<query> http://mygene.info/gene/<geneid>
Signed up 5600 user accounts “user query”  “gene id” “gene id”  “a specific annotation/identifiers”
Saved 2200 layouts (>1300 users) Full query documentation at:
Added 400 plugins (>100 users)
http://mygene.info
Top 10 organizations:
Harvard Stanford http://biogps.org BioGPS iPhone App
NIH UCSF http://sulab.org/category/biogps
Scripps U Penn http://twitter.com/biogps
UCSD Wash U
MIT UNC