pathema-clostridium a niaid bioinformatics resource center (brc)
DESCRIPTION
Conference: IBRCC2008 meeting, Sept 14-18, 2008 in Philadelphia, PA Presenter: Susmita ShrivastavaTRANSCRIPT
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
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
GENE SEARCHGENE SEARCH
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
GENE SEARCHGENE SEARCH
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
GENOME SEARCHGENOME SEARCH
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
GENOME SEARCHGENOME SEARCH
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
CHARACTERIZED GENECHARACTERIZED GENE
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
MOTIF SEARCH TOOLMOTIF SEARCH TOOL
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NEW FEATURE
PRIMER DETECTIONPRIMER DETECTION
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
EPITOPESEPITOPES
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
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
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
PATHWAY COMPARISONPATHWAY COMPARISON
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
PATHWAY COMPARISONPATHWAY COMPARISON
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW FEATURE
PATHWAY COMPARISONPATHWAY COMPARISON
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
TRANSPORTERTRANSPORTER
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
INTERGENIC REGIONINTERGENIC REGION
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
CLOSTOX-TOXIN DBCLOSTOX-TOXIN DB
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
CLOSTOX- TOXIN DBCLOSTOX- TOXIN DB
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
CLOSTOX- TOXIN DBCLOSTOX- TOXIN DB
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
CLOSTOX- TOXIN DBCLOSTOX- TOXIN DB
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
CLOSTOX PHYLOGENYCLOSTOX PHYLOGENY
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
NEW
FEATURE
CLOSTOX PHYLOGENYCLOSTOX PHYLOGENY
h ttp://path e m a.jcv i .orgh ttp://path e m a.jcv i .org
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 : [email protected]@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)