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Community-Driven Gene Annotation Portal
- 1. : a community-driven customizable gene annotation portal Chunlei Wu, Ph.D. The Scripps Research Institute La Jolla, CA ISMB2012 July 17, 2012
- 2. : a community-driven customizable gene annotation portal Chunlei Wu, Ph.D. The Scripps Research Institute La Jolla, CA ISMB2012 July 17, 2012
- 3. 3 High-throughput molecular profiling is powerful Testable hypothesis
- 4. 4 Gene databases are numerous and overlapping … and hundreds more …
- 5. 5 Why is there so much redundancy? Users Requests Community development Resources Time BioGPS emphasizes community extensibility
- 6. 6 Why do developers define the gene report view? BioGPS emphasizes user customizability
- 7. 7 BioGPS: User customizability Websites display content for a “typical” user Solution: Users should individually decide relevant content Structural biologist Geneticist System Biologist BioGPS BioGPS BioGPS NCBI eQTL dbSNP Expression KEGG PDB Genome PFAM Browser MGI GeneCards
- 8. 8 Community extensibility and user customizability http://biogps.org
- 9. 9 The plugin interface is simple and universal Pubmed 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. 10 The plugin interface is simple and universal
- 11. 11 The plugin interface is simple and universal
- 12. 12 The plugin interface is simple and universal
- 13. 13 The plugin interface is simple and universal
- 14. 14 The plugin interface is simple and universal
- 15. 15 “Expression Chart” plugin NCBI GEO: Loaded >2000 GEO datasets
- 16. 16 Success depends on a positive feedback loop Resource-sharing utility 1 100 2 200 Number of Number of contributors users
- 17. 17 Evaluating the BioGPS positive feedback loop Utility Users Contributors Utility defined by user customizability and simple visualization of Gene Expression data
- 18. 18 BioGPS 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. 19 Explicit and implicit community contributions Utility Users Contributors 478 plugins registered (~300 publicly shared) by over 100 users spanning 150+ domains
- 20. 20 Community participation scales with community usage Users Requests Community participation Resources Time
- 21. 21 Summary • 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. 26 A 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. 27 Group member Andrew Su (Head) Ian Macleod Benjamin Good Eric Clarke Salvatore Loguercio Past contributors BioGPS Users ISMB travel support Marc Leglise Jon Huss Camilo Orozco Jeff Janes Serge Batalov Funding and Support BioGPS: GM083924
- 28. 28
Hinweis der Redaktion
- 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