: a community-drivencustomizable gene annotation portal                Chunlei Wu, Ph.D.           The Scripps Research In...
: a community-drivencustomizable gene annotation portal                Chunlei Wu, Ph.D.           The Scripps Research In...
3High-throughput molecular profiling is powerful                                    Testable                              ...
4Gene databases are numerous and overlapping                            … and hundreds                               more …
5Why is there so much redundancy?                         Users                  Requests                                 ...
6Why do developers define the gene report view?           BioGPS emphasizes user customizability
7BioGPS: User customizability           Websites display content for a “typical” user      Solution: Users should individu...
8Community extensibility and user customizability                 http://biogps.org
9The plugin interface is simple and universalPubmed   http://www.ncbi.nlm.nih.gov/sites/entrez?...&Term={{Symbol}}STRING  ...
10The plugin interface is simple and universal
11The plugin interface is simple and universal
12The plugin interface is simple and universal
13The plugin interface is simple and universal
14The plugin interface is simple and universal
15“Expression Chart” plugin                                NCBI GEO:                            Loaded >2000 GEO datasets
16Success depends on a positive feedback loop                  Resource-sharing utility                              1   1...
17Evaluating the BioGPS positive feedback loop                          Utility                                    Users  ...
18BioGPS has a critical mass of users           Utility                     Users    Contributors                         ...
19Explicit and implicit community contributions      Utility                UsersContributors       478 plugins registered...
20Community participation scales with      community usage                  Users           Requests                      ...
21Summary          • Easy access to resources            you already know about          • Discover resources you         ...
Gene annotation web services           http://MyGene.Info            Two principles:              – Simplicity            ...
Gene Query Service   user query  matching gene IDs/symbols/names               (JSON output)  http://mygene.info/query?q=...
Gene Annotation Service    gene id  full or filtered gene annotation object             (JSON output)  http://mygene.info...
Targeted use case:   Quickly build a gene-centric online resource without   the need of maintaining a local gene annotatio...
26A use case: gene query autocomplete widget: <html> <body> <label for="gene_query">Enter a gene here: </label> <input sty...
27Group memberAndrew Su (Head)Ian MacleodBenjamin GoodEric ClarkeSalvatore LoguercioPast contributors     BioGPS Users    ...
28
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20120717 ismb2012

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

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20120717 ismb2012

  1. 1. : a community-drivencustomizable gene annotation portal Chunlei Wu, Ph.D. The Scripps Research Institute La Jolla, CA ISMB2012 July 17, 2012
  2. 2. : a community-drivencustomizable gene annotation portal Chunlei Wu, Ph.D. The Scripps Research Institute La Jolla, CA ISMB2012 July 17, 2012
  3. 3. 3High-throughput molecular profiling is powerful Testable hypothesis
  4. 4. 4Gene databases are numerous and overlapping … and hundreds more …
  5. 5. 5Why is there so much redundancy? Users Requests Community development Resources Time BioGPS emphasizes community extensibility
  6. 6. 6Why do developers define the gene report view? BioGPS emphasizes user customizability
  7. 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. 8. 8Community extensibility and user customizability http://biogps.org
  9. 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. 10. 10The plugin interface is simple and universal
  11. 11. 11The plugin interface is simple and universal
  12. 12. 12The plugin interface is simple and universal
  13. 13. 13The plugin interface is simple and universal
  14. 14. 14The plugin interface is simple and universal
  15. 15. 15“Expression Chart” plugin NCBI GEO: Loaded >2000 GEO datasets
  16. 16. 16Success depends on a positive feedback loop Resource-sharing utility 1 100 2 200 Number of Number of contributors users
  17. 17. 17Evaluating the BioGPS positive feedback loop Utility Users Contributors Utility defined by user customizability and simple visualization of Gene Expression data
  18. 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. 19. 19Explicit and implicit community contributions Utility UsersContributors 478 plugins registered (~300 publicly shared) by over 100 users spanning 150+ domains
  20. 20. 20Community participation scales with community usage Users Requests Community participation Resources Time
  21. 21. 21Summary • Easy access to resources you already know about • Discover resources you don’t know about
  22. 22. Gene annotation web services http://MyGene.Info Two principles: – Simplicity – Performance
  23. 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. 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. 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. 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. 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
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