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Greene Bosc2008

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BOSC 2008 Lightning Talk: The E nteropathogen R esource I ntegration C enter (ERIC), A NIAID Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Disease http://www.ericbrc.org D. Pot 1 , J. Whitmore 1 , M. Shaker 1 , J. Fedorko 1 , K. Joshi 1 , S. Nanan 1 , P. Shetty 1 , J. Thangiah 1 , S. Zaremba 1 , G. Plunkett, III 2 , J. Glasner 2 , B. Anderson 2 , D. Baumler 2 , B. Biehl 2 , V. Burland 2 , E. Cabot 2 , E. Neeno-Eckwall 2 , B. Mau 2 , P. Liss 2 , M. Rusch 2 , F. R. Blattner 2 , N. T. Perna 2 , J. M. Greene 1 1 SRA International, Inc., Rockville MD and 2 University of Wisconsin, Madison WI
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
ERIC-Overview Genomes Annotations (ASAP) Genome Views and Comparisons (Mauve, GBrowse) Microarray Analysis (mAdb) ERIC is a portal based system using the JBoss portal . ASAP ( A Systematic Annotation Package for community annotation) from UW-Madison is being used to allow the scientific community to annotate genes for the five enteropathogens and related reference organism useful for comparative genomics.
ERIC Portal Home Page
[object Object],Mauve – whole genome comparison
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Mauve
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Text Mining
[object Object],Text Mining – Current Awareness
[object Object],[object Object],Text Mining - Search
[object Object],[object Object],[object Object],[object Object],Text Mining – Search Results
Extracted Terms and Relationships (requirements from Biologists) Frequency of Terms and Coloration Control (requirements from IT Types) Extracted Text from PubMed
What is different? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Before Now
Other ERIC Notes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],http://www.ericbrc.org
 
 
NetOwl Extractor Optimizing Manual Literature Annotation *Software licensed for use on ERIC bounded in red. Ontologies and patterns developed to mine text Pattern Writers

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Greene Bosc2008

  • 1. BOSC 2008 Lightning Talk: The E nteropathogen R esource I ntegration C enter (ERIC), A NIAID Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Disease http://www.ericbrc.org D. Pot 1 , J. Whitmore 1 , M. Shaker 1 , J. Fedorko 1 , K. Joshi 1 , S. Nanan 1 , P. Shetty 1 , J. Thangiah 1 , S. Zaremba 1 , G. Plunkett, III 2 , J. Glasner 2 , B. Anderson 2 , D. Baumler 2 , B. Biehl 2 , V. Burland 2 , E. Cabot 2 , E. Neeno-Eckwall 2 , B. Mau 2 , P. Liss 2 , M. Rusch 2 , F. R. Blattner 2 , N. T. Perna 2 , J. M. Greene 1 1 SRA International, Inc., Rockville MD and 2 University of Wisconsin, Madison WI
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  • 3. ERIC-Overview Genomes Annotations (ASAP) Genome Views and Comparisons (Mauve, GBrowse) Microarray Analysis (mAdb) ERIC is a portal based system using the JBoss portal . ASAP ( A Systematic Annotation Package for community annotation) from UW-Madison is being used to allow the scientific community to annotate genes for the five enteropathogens and related reference organism useful for comparative genomics.
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  • 11. Extracted Terms and Relationships (requirements from Biologists) Frequency of Terms and Coloration Control (requirements from IT Types) Extracted Text from PubMed
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  • 16. NetOwl Extractor Optimizing Manual Literature Annotation *Software licensed for use on ERIC bounded in red. Ontologies and patterns developed to mine text Pattern Writers