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