Ismb2012_poster_cwu

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BIoGPS poster at ISMB2012

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Ismb2012_poster_cwu

  1. 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. Its 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

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