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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
Outline
Background Pathways Database System Architecture of the system Data model Tools of the Pathways Database System Other pathway tools Future Developments Conclusion Questions
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.”
Background
Biological Pathways Metabolic & biochemical
Transcription & protein synthesis
Signal Transduction
Pathways Database System
Genomic pathway information: Store / manage Analyze Visualize Query
Features GUI tools Multiple abstraction levels for viewing information XML output
Architecture
Pathways Browser
Browser Tool Visualization Tool
Querying Tool
Services
Data Extraction
Querying Services
Relational Database
Pathways DB
HTTP SOAP
Pathways Data Model
Molecular entityBasic molecules (protein, enzyme, gene, amino acid, substrate, co-factors etc...)
ProcessReaction between molecular entities
PathwaysInterconnection of processes
Pathways Browser
Tree pane
Query result pane
Visualization pane
Browser Tool
Visualization Tool
Querying Tool
Querying Service (QRS)
Query functions submit predefined queries Results passed as XML Supports SOAP / HTTP protocols
Query Functions
Basic query
Statistical query
Neighborhood query
Path-finding query
Other Pathway Tools
Biocarta
ExPASy Biochemical pathways
Signaling Pathway database
PathDB
Gene Ontology
Future Developments
Ability to add new pathways
Ability to modify views
Incorporating GO
Enhance the visualization tool
Conclusion
Pathways Database System is an integrated system
for storing, analyzing and visualizing biology
pathways.
Biological pathways show the “bigger picture”
Questions or Comments ?
Presented by
Mohamed Uduman
Bioinformatics Computing II
Spring 043