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Information Management of Genome Enabled Data Streams for Pseudomonas syringae on the Pseudomonas-Plant Interaction (PPI) Website.

Lindeberg M - Genes (Basel) (2011)

Bottom Line: Major P. syringae data streams include genome sequence data, newly identified type III effectors, biological characterization data for type III effectors, and regulatory feature characterization.To maximize data access, the Pseudomonas-Plant Interaction (PPI) website [1] is primarily focused on categorization of type III effectors and curation of effector functional data represented in the Hop database and Pseudomonas-Plant Interaction Resource, respectively.The PPI website further serves as a conduit for incorporation of new genome characterization data into the annotation records at NCBI and other data repositories, and clearinghouse for additional data sets and updates in response to the evolving needs of the research community.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology and Plant Microbe Biology, 302 Plant Science Building, Cornell University, Ithaca NY 14853, USA. ML16@cornell.edu.

ABSTRACT
Genome enabled research has led to a large and ever-growing body of data on Pseudomonas syringae genome variation and characteristics, though systematic capture of this information to maximize access by the research community remains a significant challenge. Major P. syringae data streams include genome sequence data, newly identified type III effectors, biological characterization data for type III effectors, and regulatory feature characterization. To maximize data access, the Pseudomonas-Plant Interaction (PPI) website [1] is primarily focused on categorization of type III effectors and curation of effector functional data represented in the Hop database and Pseudomonas-Plant Interaction Resource, respectively. The PPI website further serves as a conduit for incorporation of new genome characterization data into the annotation records at NCBI and other data repositories, and clearinghouse for additional data sets and updates in response to the evolving needs of the research community.

No MeSH data available.


Related in: MedlinePlus

Strategy for data management used at the Pseudomonas-Plant Interaction (PPI) genome resources website [1].
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f2-genes-02-00841: Strategy for data management used at the Pseudomonas-Plant Interaction (PPI) genome resources website [1].

Mentions: Although corrected hop gene nomenclature and mapping of HrpL binding sites were an early focus of annotation updates, proteome and transcriptome sequencing have more recently led to updated gene coordinates, addition of locus qualifiers describing the bioinformatic and experimental support for individual gene calls, and annotation of small RNAs. In light of the constant challenge presented by the large numbers of hypothetical and conserved hypothetical genes in bacterial genomes, incorporation of these qualifiers into the Pto DC3000 genome provides invaluable information for those using the Pto DC3000 annotation as a basis for annotation of related genomes. An outline of the overall data handling strategy employed for a variety of data types at the PPI website is shown in Figure 2.


Information Management of Genome Enabled Data Streams for Pseudomonas syringae on the Pseudomonas-Plant Interaction (PPI) Website.

Lindeberg M - Genes (Basel) (2011)

Strategy for data management used at the Pseudomonas-Plant Interaction (PPI) genome resources website [1].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3927588&req=5

f2-genes-02-00841: Strategy for data management used at the Pseudomonas-Plant Interaction (PPI) genome resources website [1].
Mentions: Although corrected hop gene nomenclature and mapping of HrpL binding sites were an early focus of annotation updates, proteome and transcriptome sequencing have more recently led to updated gene coordinates, addition of locus qualifiers describing the bioinformatic and experimental support for individual gene calls, and annotation of small RNAs. In light of the constant challenge presented by the large numbers of hypothetical and conserved hypothetical genes in bacterial genomes, incorporation of these qualifiers into the Pto DC3000 genome provides invaluable information for those using the Pto DC3000 annotation as a basis for annotation of related genomes. An outline of the overall data handling strategy employed for a variety of data types at the PPI website is shown in Figure 2.

Bottom Line: Major P. syringae data streams include genome sequence data, newly identified type III effectors, biological characterization data for type III effectors, and regulatory feature characterization.To maximize data access, the Pseudomonas-Plant Interaction (PPI) website [1] is primarily focused on categorization of type III effectors and curation of effector functional data represented in the Hop database and Pseudomonas-Plant Interaction Resource, respectively.The PPI website further serves as a conduit for incorporation of new genome characterization data into the annotation records at NCBI and other data repositories, and clearinghouse for additional data sets and updates in response to the evolving needs of the research community.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology and Plant Microbe Biology, 302 Plant Science Building, Cornell University, Ithaca NY 14853, USA. ML16@cornell.edu.

ABSTRACT
Genome enabled research has led to a large and ever-growing body of data on Pseudomonas syringae genome variation and characteristics, though systematic capture of this information to maximize access by the research community remains a significant challenge. Major P. syringae data streams include genome sequence data, newly identified type III effectors, biological characterization data for type III effectors, and regulatory feature characterization. To maximize data access, the Pseudomonas-Plant Interaction (PPI) website [1] is primarily focused on categorization of type III effectors and curation of effector functional data represented in the Hop database and Pseudomonas-Plant Interaction Resource, respectively. The PPI website further serves as a conduit for incorporation of new genome characterization data into the annotation records at NCBI and other data repositories, and clearinghouse for additional data sets and updates in response to the evolving needs of the research community.

No MeSH data available.


Related in: MedlinePlus