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Pathema-Clostridium A NIAID Bioinformatics Resource Center (BRC)
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
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CHARACTERIZED GENE
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MOTIF SEARCH TOOL
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PRIMER DETECTION
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EPITOPES
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COMPARATIVE TOOLS
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GENOME REGION DISPLAY
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GENOME REGION DISPLAY
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PATHWAY COMPARISON
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PATHWAY COMPARISON
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TRANSPORTER
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INTERGENIC REGION
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CLOSTOX-TOXIN DB
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CLOSTOX- TOXIN DB
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CLOSTOX- TOXIN DB
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CLOSTOX- TOXIN DB
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CLOSTOX PHYLOGENY
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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
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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
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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
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)