1. Pathways Database System: An Integrated System For Biological Pathways L. Krishnamurthy, J. Nadeau, G. Ozsoyoglu, M. Ozsoyoglu, G. Schaeffer, M. Tasan and W. Xu Bioinformatics Vol. 19 no. 8 2003. Pages 930-937 Presented by Mohamed Uduman Bioinformatics Computing II Spring 043

2. Outline Background Pathways Database System Architecture of the system Data model Tools of the Pathways Database System Other pathway tools Future Developments Conclusion Questions

3. 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.”

4. Background Biological Pathways  Metabolic & biochemical  Transcription & protein synthesis  Signal Transduction

5. Pathways Database System Genomic pathway information:  Store / manage  Analyze  Visualize  Query Features  GUI tools  Multiple abstraction levels for viewing information  XML output

6. Architecture Pathways Browser Browser Tool Visualization Tool Querying Tool Services Data Extraction Querying Services Relational Database Pathways DB HTTPSOAP

7. Pathways Data Model Molecular entity Basic molecules (protein, enzyme, gene, amino acid, substrate, co-factors etc...) Process Reaction between molecular entities Pathways Interconnection of processes

8. Pathways Browser Tree pane Query result pane Visualization pane

9. Browser Tool

10. Visualization Tool

11. Querying Tool

13. Querying Service (QRS) Query functions submit predefined queries Results passed as XML Supports SOAP / HTTP protocols

14. Query Functions Basic query Statistical query Neighborhood query Path-finding query

15. Other Pathway Tools Biocarta ExPASy Biochemical pathways Signaling Pathway database PathDB Gene Ontology

16. Future Developments Ability to add new pathways Ability to modify views Incorporating GO Enhance the visualization tool

17. Conclusion Pathways Database System is an integrated system for storing, analyzing and visualizing biology pathways. Biological pathways show the “bigger picture”

18. Questions or Comments ? Presented by Mohamed Uduman Bioinformatics Computing II Spring 043