ismb2012_poster_cwu

: a community-driven customizable gene annotation portal

Testablehypothesis

Candidate genes

http://www.ncbi.nlm.nih.gov/pubmed?term={{Symbol}}

MyGene.Info: gene annotation web services(Powers BioGPS gene query, now for public use)

Gene databases are numerous and overlapping

Chunlei Wu, Ian MacLeod, Andrew I. Sucwu@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

Users

Requests

Resources

Time

Communitydevelopment

… and hundreds more …

Structural biologist

Geneticist

PDB

PFAM

NCBI

BioGPS

eQTL

MGI

dbSNP

BioGPS

Genome Browser

System BiologistExpression

GeneCards

BioGPS

KEGG

BioGPS users “like” a resource

by adding it into a custom layout, so

that other users can discover popular

resources they might miss.

Why another portal? User customizability

User customizability Community Extensibility

Users can customize their gene-report ”layout”

Users can add new resources to BioGPS as “plugins”

BioGPS users contributed > 400 resources in plugin library

Simply need a URL template:

http://string-db.org/newstring_cgi?...&identifier={{EnsemblGene}}

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}}… …

~ 30 types of gene-specific identifiers

Community Extensibility

Discover resources by what’s popular among other users

Top 10 organizations:

HarvardNIHScrippsUCSDMIT

StanfordUCSFU PennWash UUNC

Development resources do not scale with increased users and

feature-requests

Developers typically define the gene-report view

Why? Why?

BioGPS users: (up to Jul 8, 2012)

Queried 680k genes in last year

Viewed 800k gene-reports in last year

Signed up 5600 user accounts

Saved 2200 layouts (>1300 users)

Added 400 plugins (>100 users)

http://biogps.org

BioGPS has critical mass

BioGPS iPhone Apphttp://sulab.org/category/biogps

http://twitter.com/biogps

Gene query service:http://mygene.info/query?q=<query>“user query” “gene id”

MyGene.Info provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized.

Gene annotation servicehttp://mygene.info/gene/<geneid>“gene id” “a specific annotation/identifiers”

Full query documentation at:

http://mygene.info