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20120717 ismb2012

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BioGPS is presented at ISMB2012 (07/17/2012)

BioGPS is presented at ISMB2012 (07/17/2012)

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  • next gen sequencing identifies candidate genesAlso Microarray data, proteomics, GWAS, methylation, post-translational modifications, translocation detection, etc.What do these genes do?
  • Developer resources do not scale with usagePractical effects:Core developers’ time is always the rate-limiting step Addition of new features and data always feels slowEventually, new databases are created to fill the gap80% duplication for 20% innovation
  • The second design principle is “user customizability”. Websites display content for a “typical” user Users have different needs BioGPS allows users to personalize their own gene annotation report. We call each resources as a pluginThe second design principle is “user customizability”. Typically, websites defines what they think user should know about a gene. But users should individually decide what content is relevant, because researchers from different areas need to know the different aspect of the gene annotation,….. BioGPS allows users to personalize a gene annotation report based what they think is the most relevant.
  • MODs and portals
  • Genetics resources
  • Literature resources
  • Protein resources
  • Pathway and expression databases
  • Transcript

    • 1. : a community-drivencustomizable gene annotation portal Chunlei Wu, Ph.D. The Scripps Research Institute La Jolla, CA ISMB2012 July 17, 2012
    • 2. : a community-drivencustomizable gene annotation portal Chunlei Wu, Ph.D. The Scripps Research Institute La Jolla, CA ISMB2012 July 17, 2012
    • 3. 3High-throughput molecular profiling is powerful Testable hypothesis
    • 4. 4Gene databases are numerous and overlapping … and hundreds more …
    • 5. 5Why is there so much redundancy? Users Requests Community development Resources Time BioGPS emphasizes community extensibility
    • 6. 6Why do developers define the gene report view? BioGPS emphasizes user customizability
    • 7. 7BioGPS: User customizability Websites display content for a “typical” user Solution: Users should individually decide relevant contentStructural biologist Geneticist System Biologist BioGPS BioGPS BioGPS NCBI eQTL dbSNP Expression KEGG PDB Genome PFAM Browser MGI GeneCards
    • 8. 8Community extensibility and user customizability http://biogps.org
    • 9. 9The plugin interface is simple and universalPubmed http://www.ncbi.nlm.nih.gov/sites/entrez?...&Term={{Symbol}}STRING http://string-db.org/newstring_cgi?...&identifier={{EnsemblGene}} KEGG http://www.genome.jp/dbget-bin/www_bget?hsa:{{EntrezGene}} URL template Rendered URL Gene entity
    • 10. 10The plugin interface is simple and universal
    • 11. 11The plugin interface is simple and universal
    • 12. 12The plugin interface is simple and universal
    • 13. 13The plugin interface is simple and universal
    • 14. 14The plugin interface is simple and universal
    • 15. 15“Expression Chart” plugin NCBI GEO: Loaded >2000 GEO datasets
    • 16. 16Success depends on a positive feedback loop Resource-sharing utility 1 100 2 200 Number of Number of contributors users
    • 17. 17Evaluating the BioGPS positive feedback loop Utility Users Contributors Utility defined by user customizability and simple visualization of Gene Expression data
    • 18. 18BioGPS has a critical mass of users Utility Users Contributors Top 10 organizations 1. Harvard 6. Stanford 2. NIH 7. UCSF 3. Scripps 8. U Penn 4. UCSD 9. Wash U 5. MIT 10. UNC
    • 19. 19Explicit and implicit community contributions Utility UsersContributors 478 plugins registered (~300 publicly shared) by over 100 users spanning 150+ domains
    • 20. 20Community participation scales with community usage Users Requests Community participation Resources Time
    • 21. 21Summary • Easy access to resources you already know about • Discover resources you don’t know about
    • 22. Gene annotation web services http://MyGene.Info Two principles: – Simplicity – Performance
    • 23. Gene Query Service user query  matching gene IDs/symbols/names (JSON output) http://mygene.info/query?q=<query>Examples: http://mygene.info/query?q=cdk2 http://mygene.info/query?q=cdk2+AND+species:human http://mygene.info/query?q=cdk? http://mygene.info/query?q=p* http://mygene.info/query?q=entrezgene:1017 http://mygene.info/query?q=ensemblgene:ENSG00000123374
    • 24. Gene Annotation Service gene id  full or filtered gene annotation object (JSON output) http://mygene.info/gene/<geneid> Examples: http://mygene.info/gene/1017 http://mygene.info/gene/ENSG00000123374 http://mygene.info/gene/1017?filter=name,symbol,summary http://mygene.info/gene/1017?filter=name,symbol,refseq.rna Nice species supported: human, mouse, rat, fruitfly, nematode, zebrafish, thale cress, frog.
    • 25. Targeted use case: Quickly build a gene-centric online resource without the need of maintaining a local gene annotation database Use it in a web application: Server side - Making direct HTTP calls Client side - Setup a server-side proxy - JSONP calls - Cross-domain AJAX calls via CORS (Cross-Origin Resource Sharing) Demo and full documentation at http://mygene.info Source code: https://bitbucket.org/newgene/genedoc/src
    • 26. 26A use case: gene query autocomplete widget: <html> <body> <label for="gene_query">Enter a gene here: </label> <input style="width:250px" class="mygene_query_target"> <script src="http://mygene.info/widget/autocomplete/js/mygene_query_min.js" type="text/javascript"></script> </body> </html> http://mygene.info/doc/widget/autocomplete
    • 27. 27Group memberAndrew Su (Head)Ian MacleodBenjamin GoodEric ClarkeSalvatore LoguercioPast contributors BioGPS Users ISMB travel supportMarc LegliseJon HussCamilo OrozcoJeff JanesSerge Batalov Funding and Support BioGPS: GM083924
    • 28. 28