pathema-clostridium a niaid bioinformatics resource center (brc)

PATHEMA-CLOSTRIDIUMPATHEMA-CLOSTRIDIUMA NIAID Bio in formatics Re sou rce Ce n te r A NIAID Bioin form atics Re sou rce Ce n te r

(BRC)(BRC)

Susmita ShrivastavaJ. Craig Venter Institute

The NIAID BRC MandateThe NIAID BRC Mandate Provide high quality sequence, annotation and tool Provide high quality sequence, annotation and tool

development for all NIAID category A-C development for all NIAID category A-C pathogenspathogens

All 8 BRC’s have their separate organism and All 8 BRC’s have their separate organism and websitewebsite

PATHEMA hosts 6 organisms from 4 clades.PATHEMA hosts 6 organisms from 4 clades. Entamoeba histolyticaEntamoeba histolytica

Bacillus anthracisBacillus anthracis

Burkholderia mallei & Burkholderia pseudomallei Burkholderia mallei & Burkholderia pseudomallei

Clostridium botulinumClostridium botulinum & Clostridium perfringens & Clostridium perfringens

PATHEMA (pathema.jcvi.org)PATHEMA (pathema.jcvi.org)Each clade has its own websiteEach clade has its own website

Allows us to tailor the tools/resources available for individual clade Allows us to tailor the tools/resources available for individual clade

Indepth curatorial analysis of target genome and Indepth curatorial analysis of target genome and tools to help analyze and visualize the resultstools to help analyze and visualize the results

Provide services to the communityProvide services to the communityOffer workshops and classes on the resourceOffer workshops and classes on the resource

Organize annotation jamboree for each cladeOrganize annotation jamboree for each clade

Designed to meet the needs of the clostridium Designed to meet the needs of the clostridium research community focussing on community research community focussing on community feedbackfeedback

PATHEMA PORTAL PAGEPATHEMA PORTAL PAGE

h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org

PATHEMA-CLOSTRIDIUMPATHEMA-CLOSTRIDIUM

http://pathema.jcvi.orghttp://pathema.jcvi.org

PATHEMA-CLOSTRIDIUMPATHEMA-CLOSTRIDIUM

http://pathema.jcvi.orghttp://pathema.jcvi.org

THE HEADER MENUTHE HEADER MENU

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GENE SEARCHGENE SEARCH

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GENE SEARCHGENE SEARCH

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GENOME SEARCHGENOME SEARCH

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GENOME SEARCHGENOME SEARCH

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CHARACTERIZED GENECHARACTERIZED GENE

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NEW

FEATURE

MOTIF SEARCH TOOLMOTIF SEARCH TOOL

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NEW FEATURE

PRIMER DETECTIONPRIMER DETECTION

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NEW

FEATURE

EPITOPESEPITOPES

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NEW

FEATURE

COMPARATIVE TOOLSCOMPARATIVE TOOLS

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NEW

FEATURE

GENOME REGION DISPLAYGENOME REGION DISPLAY

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NEW

FEATURE

GENOME REGION DISPLAYGENOME REGION DISPLAY

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NEW

FEATURE

PATHWAY COMPARISONPATHWAY COMPARISON

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NEW

FEATURE

PATHWAY COMPARISONPATHWAY COMPARISON

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NEW FEATURE

PATHWAY COMPARISONPATHWAY COMPARISON

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NEW

FEATURE

TRANSPORTERTRANSPORTER

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NEW

FEATURE

INTERGENIC REGIONINTERGENIC REGION

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NEW

FEATURE

CLOSTOX-TOXIN DBCLOSTOX-TOXIN DB

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NEW

FEATURE

CLOSTOX- TOXIN DBCLOSTOX- TOXIN DB

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NEW

FEATURE

CLOSTOX- TOXIN DBCLOSTOX- TOXIN DB

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NEW

FEATURE

CLOSTOX- TOXIN DBCLOSTOX- TOXIN DB

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NEW

FEATURE

CLOSTOX PHYLOGENYCLOSTOX PHYLOGENY

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NEW

FEATURE

CLOSTOX PHYLOGENYCLOSTOX PHYLOGENY

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NEW

FEATURE

FUTURE GOALS FUTURE GOALS

Help users in developing customized tools for Help users in developing customized tools for their research, based on their feedbacktheir research, based on their feedback

Expand community annotation especially for Expand community annotation especially for toxins and epitopestoxins and epitopes

WHAT’S COMING NEXT?WHAT’S COMING NEXT?

h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org

Comprehensive Data MiningComprehensive Data MiningCOMING

SOON

Collaborated with the Cognitive Science Branch of the Collaborated with the Cognitive Science Branch of the National Library Medicine to provide scientific content on National Library Medicine to provide scientific content on Pathema organismsPathema organisms

SemMed* manages the results of PubMed searches by SemMed* manages the results of PubMed searches by summarizing and visualizing semantic predications extracted summarizing and visualizing semantic predications extracted from MEDLINE citations via natural language processing.from MEDLINE citations via natural language processing.

For the first deployment, Pathema will provide a view of For the first deployment, Pathema will provide a view of precomputed SemMed searches for Clostridium toxin, rather precomputed SemMed searches for Clostridium toxin, rather than access to the full functionality of SemMedthan access to the full functionality of SemMed

Kilicoglu et. al; (2008) Proceedings of the Third International Symposium for the Kilicoglu et. al; (2008) Proceedings of the Third International Symposium for the Symantic Mining in Biomedicine, 69-76Symantic Mining in Biomedicine, 69-76

Proposed Interface for Structured Proposed Interface for Structured SemMed DataSemMed Data

COMING

SOON

ClostridiumToxin

Causes

Stimulates

Inhibits Interacts with

Location of

Effects

Top-le ve l in te rface w ill provide qu ick n avigation to are as of particu lar in te re st to

u se rs .

Subject-specific Data Subject-specific Data Return: “Causes”Return: “Causes”

COMING

SOON

““Clostridium Toxin Causes Clostridium Toxin Causes Necrotic Enteritis”Necrotic Enteritis”

COMING

SOON

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.

PATHEMA-CLOSTRIDIUM TEAMPATHEMA-CLOSTRIDIUM TEAM

Coordinator : Lauren BrinkacCoordinator : Lauren Brinkac

Analyst : Susmita ShrivastavaAnalyst : Susmita Shrivastava

Engineers : Engineers : Tanja DavidsonTanja Davidson

Seth SchobelSeth Schobel

Erin BeckErin Beck

PI : Granger Sutton, Owen WhitePI : Granger Sutton, Owen White

Contact us : Contact us : clostridium@jcvi.orgclostridium@jcvi.org

This project is funded by The National Institute Of Allergy and Infectious This project is funded by The National Institute Of Allergy and Infectious Diseases (NIH-NIAID-DMID-04-34)Diseases (NIH-NIAID-DMID-04-34)