pathways database system: an integrated system for biological pathways l. krishnamurthy, j. nadeau,...
TRANSCRIPT
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Pathways Database System: An Integrated System For Biological Pathways
L. Krishnamurthy, J. Nadeau, G. Ozsoyoglu, M. Ozsoyoglu, G. Schaeffer, M. Tasan and W. XuBioinformatics Vol. 19 no. 8 2003. Pages 930-937
Presented by
Mohamed Uduman
Bioinformatics Computing II
Spring 043
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Outline
Background Pathways Database System Architecture of the system Data model Tools of the Pathways Database System Other pathway tools Future Developments Conclusion Questions
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Background
Genome sequencing – what to do with data? DNA sequence good for analyzing
Organization Evolution Mutation
Biological Pathways “Pathways are the sequential and cumulative action
of genetically distinct but functionally related molecules.”
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Background
Biological Pathways Metabolic & biochemical
Transcription & protein synthesis
Signal Transduction
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Pathways Database System
Genomic pathway information: Store / manage Analyze Visualize Query
Features GUI tools Multiple abstraction levels for viewing information XML output
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Architecture
Pathways Browser
Browser Tool Visualization Tool
Querying Tool
Services
Data Extraction
Querying Services
Relational Database
Pathways DB
HTTP SOAP
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Pathways Data Model
Molecular entityBasic molecules (protein, enzyme, gene, amino acid, substrate, co-factors etc...)
ProcessReaction between molecular entities
PathwaysInterconnection of processes
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Pathways Browser
Tree pane
Query result pane
Visualization pane
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Browser Tool
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Visualization Tool
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Querying Tool
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Querying Service (QRS)
Query functions submit predefined queries Results passed as XML Supports SOAP / HTTP protocols
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Query Functions
Basic query
Statistical query
Neighborhood query
Path-finding query
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Other Pathway Tools
Biocarta
ExPASy Biochemical pathways
Signaling Pathway database
PathDB
Gene Ontology
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Future Developments
Ability to add new pathways
Ability to modify views
Incorporating GO
Enhance the visualization tool
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Conclusion
Pathways Database System is an integrated system
for storing, analyzing and visualizing biology
pathways.
Biological pathways show the “bigger picture”
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Questions or Comments ?
Presented by
Mohamed Uduman
Bioinformatics Computing II
Spring 043