Pathema-Clostridium A NIAID Bioinformatics Resource Center (BRC)
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Pathema-Clostridium A NIAID Bioinformatics Resource Center (BRC)

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Conference: IBRCC2008 meeting, Sept 14-18, 2008 in Philadelphia, PA ...

Conference: IBRCC2008 meeting, Sept 14-18, 2008 in Philadelphia, PA
Presenter: Susmita Shrivastava

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  • 1. PATHEMA-CLOSTRIDIUM A N IAID B io in fo rm a tic s Re s o u rc e Ce n te r (B RC) Susmita Shrivastava J. Craig Venter Institute
  • 2. The NIAID BRC Mandate  Provide high quality sequence, annotation and tool development for all NIAID category A-C pathogens  All 8 BRC’s have their separate organism and website  PATHEMA hosts 6 organisms from 4 clades. Entamoeba histolytica  Bacillus anthracis  Burkholderia mallei & Burkholderia pseudomallei  Clostridium botulinum & Clostridium perfringens 
  • 3. PATHEMA (pathema.jcvi.org) Each clade has its own website Allows us to tailor the tools/resources available for individual clade Indepth curatorial analysis of target genome and tools to help analyze and visualize the results Provide services to the community Offer workshops and classes on the resource Organize annotation jamboree for each clade Designed to meet the needs of the clostridium research community focussing on community feedback
  • 4. PATHEMA PORTAL PAGE h ttp ://p a th e m a .jc v i.o rg
  • 5. PATHEMA-CLOSTRIDIUM http://pathema.jcvi.org
  • 6. PATHEMA-CLOSTRIDIUM http://pathema.jcvi.org
  • 7. THE HEADER MENU h ttp ://p a th e m a .jc v i.o rg
  • 8. GENE SEARCH h ttp ://p a th e m a .jc v i.o rg
  • 9. GENE SEARCH h ttp ://p a th e m a .jc v i.o rg
  • 10. GENOME SEARCH h ttp ://p a th e m a .jc v i.o rg
  • 11. GENOME SEARCH h ttp ://p a th e m a .jc v i.o rg
  • 12. NE TUR FE WE A CHARACTERIZED GENE h ttp ://p a th e m a .jc v i.o rg
  • 13. NE TUR FE WE A MOTIF SEARCH TOOL h ttp ://p a th e m a .jc v i.o rg
  • 14. NE UR FE WE AT PRIMER DETECTION h ttp ://p a th e m a .jc v i.o rg
  • 15. NE TU FE W RE A EPITOPES h ttp ://p a th e m a .jc v i.o rg
  • 16. NE TUR FE WE A COMPARATIVE TOOLS h ttp ://p a th e m a .jc v i.o rg
  • 17. NE TUR FE WE A GENOME REGION DISPLAY h ttp ://p a th e m a .jc v i.o rg
  • 18. NE TUR FE WE A GENOME REGION DISPLAY h ttp ://p a th e m a .jc v i.o rg
  • 19. NE TUR FE WE A PATHWAY COMPARISON h ttp ://p a th e m a .jc v i.o rg
  • 20. NE W PATHWAY COMPARISON FE AT UR E h ttp ://p a th e m a .jc v i.o rg
  • 21. NE TUR FE WE A PATHWAY COMPARISON h ttp ://p a th e m a .jc v i.o rg
  • 22. NE TUR FE WE A TRANSPORTER h ttp ://p a th e m a .jc v i.o rg
  • 23. NE UR FE WE AT INTERGENIC REGION h ttp ://p a th e m a .jc v i.o rg
  • 24. NE TUR FE WE CLOSTOX-TOXIN DB A h ttp ://p a th e m a .jc v i.o rg
  • 25. NE TUR FE WE A CLOSTOX- TOXIN DB h ttp ://p a th e m a .jc v i.o rg
  • 26. NE TUR FE WE CLOSTOX- TOXIN DB A h ttp ://p a th e m a .jc v i.o rg
  • 27. NE TUR FE WE A CLOSTOX- TOXIN DB h ttp ://p a th e m a .jc v i.o rg
  • 28. NE TUR FE WE A CLOSTOX PHYLOGENY h ttp ://p a th e m a .jc v i.o rg
  • 29. NE TU FE W RE A CLOSTOX PHYLOGENY h ttp ://p a th e m a .jc v i.o rg
  • 30. FUTURE GOALS Help users in developing customized tools for  their research, based on their feedback Expand community annotation especially for  toxins and epitopes
  • 31. WHAT’S COMING NEXT? h ttp ://p a th e m a .jc v i.o rg
  • 32. CO SOO MI N Comprehensive Data Mining NG  Collaborated with the Cognitive Science Branch of the National Library Medicine to provide scientific content on Pathema organisms  SemMed* manages the results of PubMed searches by summarizing and visualizing semantic predications extracted from MEDLINE citations via natural language processing.  For the first deployment, Pathema will provide a view of precomputed SemMed searches for Clostridium toxin, rather than access to the full functionality of SemMed Kilicoglu et. al; (2008) Proceedings of the Third International Symposium for the Symantic Mining in Biomedicine, 69-76
  • 33. CO SOO Proposed Interface for Structured MI N NG SemMed Data Causes Effects Clostridium Stimulates Location of Toxin Inhibits Interacts with To p -le v e l in te rfa c e w ill p ro v id e qu ic k n a v ig a tio n to a re a s o f p a rtic u la r in te re s t to
  • 34. CO SOO Subject-specific Data MI N NG Return: “Causes”
  • 35. “Clostridium Toxin Causes CO SOO MI N NG Necrotic Enteritis” It should be possible to quickly yet thoroughly explore the full corpus of knowledge on Pathema organisms using this interface, or to drill down on a subject of particular interest.
  • 36. PATHEMA-CLOSTRIDIUM TEAM  Coordinator : Lauren Brinkac  Analyst : Susmita Shrivastava  Engineers : Tanja Davidson  Seth Schobel  Erin Beck   PI : Granger Sutton, Owen White  Contact us : clostridium@jcvi.org This project is funded by The National Institute Of Allergy and Infectious Diseases (NIH-NIAID-DMID-04-34)