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

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
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8. GENE SEARCH
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9. GENE SEARCH
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10. GENOME SEARCH
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11. GENOME SEARCH
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12. NE TUR
FE
WE
A
CHARACTERIZED GENE
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13. NE TUR
FE
WE
A
MOTIF SEARCH TOOL
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14. NE UR
FE
WE
AT
PRIMER DETECTION
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15. NE TU
FE
W RE
A
EPITOPES
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16. NE TUR
FE
WE
A
COMPARATIVE TOOLS
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17. NE TUR
FE
WE
A
GENOME REGION DISPLAY
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18. NE TUR
FE
WE
A
GENOME REGION DISPLAY
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19. NE TUR
FE
WE
A
PATHWAY COMPARISON
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20. NE
W
PATHWAY COMPARISON
FE
AT
UR
E
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21. NE TUR
FE
WE
A
PATHWAY COMPARISON
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22. NE TUR
FE
WE
A
TRANSPORTER
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23. NE UR
FE
WE
AT
INTERGENIC REGION
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24. NE TUR
FE
WE
CLOSTOX-TOXIN DB
A
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25. NE TUR
FE
WE
A
CLOSTOX- TOXIN DB
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26. NE TUR
FE
WE
CLOSTOX- TOXIN DB
A
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27. NE TUR
FE
WE
A
CLOSTOX- TOXIN DB
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28. NE TUR
FE
WE
A
CLOSTOX PHYLOGENY
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29. NE TU
FE
W RE
A
CLOSTOX PHYLOGENY
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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?
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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)