ismb2012_poster_cwu
TRANSCRIPT
: 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. [email protected], [email protected], [email protected]
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