PATHEMA: A CLADE SPECIFIC BIOINFORMATICS RESOURCE CENTER Lauren Brinkac The J. Craig Venter Institute
What is Pathema? <ul><li>Pathema ( http://pathema.jcvi.org ) </li></ul><ul><li>A NIAID Bioinformatics Resource Center desi...
What is Pathema? <ul><li>A customized suite of sophisticated bioinformatics software </li></ul><ul><li>An extensive librar...
All  Bacillus  (24) B. anthracis   (17) B. cereus   (3) B. thuringiensis   (2) B. subtilis B. pumilus All  Clostridium  (2...
 
Pathema  Header
Pathema  Header A quick link to locus and annotation search is available at the top of all Pathema pages
Pathema  Header An organism menu allows you to see all genomes available on Pathema
Pathema  Header The Header Menu
Pathema  Menus The Header Menu offers an efficient tool based way to navigate through Pathema
Pathema  Menus Clicking on “Searches” takes you to a detailed list of the tools available
Gene Search: Annotation The information “i”  gives you details about the tool Breadcrumbs to orient you
Gene Search: Annotation
Gene Search: Evidence
Gene Search
Gene Search: Evidence
Carts
Gene Cart
Carts
Genome Cart
Pathema  Home Page
Community Registration <ul><li>Participation and access to community curation tool. </li></ul><ul><li>Submission of experi...
Available  Pathema  Genomes
 
 
 
Detailed Strain Information <ul><li>52-year old male rice farmer </li></ul><ul><li>1710a </li></ul><ul><ul><li>Isolated fr...
 
 
 
 
 
 
 
 
 
All vs. Protein Alignment <ul><li>All of the proteins in Pathema are routinely blasted against one another and the blast r...
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Pathema  Blast
Protein Motif Search
Pathogenicity
Therapeutics
MUMmer: Align Genomes
Genome Homology Graph
Genome Homology Graph
Protein Scatter Plot
Color by Identity
Change the Settings
GC Comparison Graph
Pseudo-2D Gel
Downloads
Batch Download
Batch Download
Downloads
Gene Attribute Download
Gene Attribute Download
What is the future of Pathema? <ul><li>We are relying on your feedback! </li></ul><ul><ul><li>Data exchange & Integration ...
JCVI’s Annotation Service  <ul><li>A  free service  which provides automated annotation and tools for analysis of another ...
Acknowledgements <ul><li>P.I.:  Granger Sutton </li></ul><ul><li>Funding:  NIAID </li></ul><ul><li>Subcontract: University...
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Pathema: A Clade Specific Bioinformatics Resource Center

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Conference: Meeting at NIH, Sep. 22, 2008
Presenter: Lauren Brinkac

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  • Pathema: A Clade Specific Bioinformatics Resource Center

    1. 1. PATHEMA: A CLADE SPECIFIC BIOINFORMATICS RESOURCE CENTER Lauren Brinkac The J. Craig Venter Institute
    2. 2. What is Pathema? <ul><li>Pathema ( http://pathema.jcvi.org ) </li></ul><ul><li>A NIAID Bioinformatics Resource Center designed to support bio-defense and infectious disease research. </li></ul><ul><li>Pathema provides detailed curation of six target pathogens: </li></ul><ul><ul><li>Category A priority pathogens: </li></ul></ul><ul><ul><li>Bacillus anthracis, Clostridium botulinum </li></ul></ul><ul><ul><li>Category B priority pathogens: </li></ul></ul><ul><ul><li>Burkholderia mallei, Burkholderia pseudomallei, </li></ul></ul><ul><ul><li>Clostridium perfringens, Entamoeba histolytica </li></ul></ul>
    3. 3. What is Pathema? <ul><li>A customized suite of sophisticated bioinformatics software </li></ul><ul><li>An extensive library of literature and manually curated data </li></ul><ul><li>Comparative analysis tools customized to retrieve, display, and compute results relevant to ongoing bio-defense research </li></ul><ul><li>Overarching Goal: to provide core resources that will accelerate scientific progress on understanding, detecting, diagnosing and treating Category A-C pathogens and other pathogens involved in new and re-emerging infectious diseases. </li></ul>
    4. 4. All Bacillus (24) B. anthracis (17) B. cereus (3) B. thuringiensis (2) B. subtilis B. pumilus All Clostridium (25) C. perfringens (9) C. botulinum (9) C. difficile C. thermocellum C. acetobutylicum C. tetani C. butyricum C. novyi C. phytofermentans All Burkholderia (28) B. mallei (11) B. pseudomallei (10) B. thailandensis B. cenocepacia B. sp. B. phages (4) P. aeruginosa R. solanacearum All Entamoeba (3) E. histolytica E. dispar E. invadens
    5. 6. Pathema Header
    6. 7. Pathema Header A quick link to locus and annotation search is available at the top of all Pathema pages
    7. 8. Pathema Header An organism menu allows you to see all genomes available on Pathema
    8. 9. Pathema Header The Header Menu
    9. 10. Pathema Menus The Header Menu offers an efficient tool based way to navigate through Pathema
    10. 11. Pathema Menus Clicking on “Searches” takes you to a detailed list of the tools available
    11. 12. Gene Search: Annotation The information “i” gives you details about the tool Breadcrumbs to orient you
    12. 13. Gene Search: Annotation
    13. 14. Gene Search: Evidence
    14. 15. Gene Search
    15. 16. Gene Search: Evidence
    16. 17. Carts
    17. 18. Gene Cart
    18. 19. Carts
    19. 20. Genome Cart
    20. 21. Pathema Home Page
    21. 22. Community Registration <ul><li>Participation and access to community curation tool. </li></ul><ul><li>Submission of experimentally characterized proteins. </li></ul><ul><li>Participation in future usability studies. </li></ul><ul><li>Community recognition. </li></ul>
    22. 23. Available Pathema Genomes
    23. 27. Detailed Strain Information <ul><li>52-year old male rice farmer </li></ul><ul><li>1710a </li></ul><ul><ul><li>Isolated from blood culture 1996 </li></ul></ul><ul><ul><li>Disseminated disease </li></ul></ul><ul><ul><li>Survived to discharge </li></ul></ul><ul><ul><li>Relapsed in 1999 </li></ul></ul><ul><li>1710b </li></ul><ul><ul><li>Isolated from blood culture 1999 </li></ul></ul><ul><ul><li>Died on day of admission </li></ul></ul><ul><li>23-year old female rice farmer </li></ul><ul><li>1106a </li></ul><ul><ul><li>Isolated from pus aspirated from liver abcess 1993 </li></ul></ul><ul><ul><li>Survived to discharge </li></ul></ul><ul><ul><li>Relapsed in 1996 </li></ul></ul><ul><li>1106b </li></ul><ul><ul><li>Isolated from pus aspirated from liver abcess 1999 </li></ul></ul><ul><ul><li>Survived to discharge </li></ul></ul>
    24. 37. All vs. Protein Alignment <ul><li>All of the proteins in Pathema are routinely blasted against one another and the blast results are stored in the database. </li></ul><ul><li>When a new genome is added to the database the all vs. all searches are re-run. </li></ul><ul><li>The information from the All vs. All blast searches is displayed throughout Pathema for cross genome analyses. </li></ul>
    25. 62. Pathema Blast
    26. 63. Protein Motif Search
    27. 64. Pathogenicity
    28. 65. Therapeutics
    29. 66. MUMmer: Align Genomes
    30. 67. Genome Homology Graph
    31. 68. Genome Homology Graph
    32. 69. Protein Scatter Plot
    33. 70. Color by Identity
    34. 71. Change the Settings
    35. 72. GC Comparison Graph
    36. 73. Pseudo-2D Gel
    37. 74. Downloads
    38. 75. Batch Download
    39. 76. Batch Download
    40. 77. Downloads
    41. 78. Gene Attribute Download
    42. 79. Gene Attribute Download
    43. 80. What is the future of Pathema? <ul><li>We are relying on your feedback! </li></ul><ul><ul><li>Data exchange & Integration </li></ul></ul><ul><ul><li>Genome sequence analysis </li></ul></ul><ul><ul><li>Custom data analysis </li></ul></ul><ul><ul><li>Custom tool development </li></ul></ul><ul><li>Clade-specific Annotation Jamborees: </li></ul><ul><ul><li>Incorporate Expert Annotation </li></ul></ul><ul><ul><li>Free JCVI clade-specific workshops </li></ul></ul><ul><li>New Genome Sequences & Annotation Data </li></ul>
    44. 81. JCVI’s Annotation Service <ul><li>A free service which provides automated annotation and tools for analysis of another center's prokaryotic sequence. </li></ul><ul><li>Two components: </li></ul><ul><ul><li>Production of output from JCVI's automated annotation pipeline - includes search results and automatically generated annotation in a MySQL database and associated files. </li></ul></ul><ul><ul><li>The manual annotation tool Manatee - an open source web based interface for interacting with and editing annotation data. </li></ul></ul><ul><li>JCVI Annotation Training Course </li></ul>
    45. 82. Acknowledgements <ul><li>P.I.: Granger Sutton </li></ul><ul><li>Funding: NIAID </li></ul><ul><li>Subcontract: University of Maryland, Baltimore, IGS </li></ul><ul><li>Informatics Engineers Informatics Analysts </li></ul><ul><li>Tanja Davidsen (manager) Scott Durkin (manager) </li></ul><ul><li>Erin Beck Ramana Madupu </li></ul><ul><li>Alex Richter Susmita Shrivastava </li></ul><ul><li>Kevin Galinsky Bob Dodson </li></ul><ul><li>Jay Sundarm Derek Harkins </li></ul><ul><li>Seth Schobel Lis Caler </li></ul><ul><li>Owen White (University of Maryland, Baltimore) </li></ul><ul><li>Anu Ganapathy YongMei Zhao </li></ul><ul><li>Josh Orvis Aaron Gussman </li></ul><ul><li>Kevin Galens Jonathon Crabtree </li></ul>

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