Abstract
AbstractBioPAX is a pathway data exchange language that is widely used by pathway database resources. Here we describe a mechanism that allows users to curate pathway data in diagrams using CellDesigner, a pathway graphical editing tool, and save the pathway data in BioPAX format. We used this mechanism to create BioPAX files for all 165 pathways from the PANTHER database. In addition, we are also working on graphically visualizing BioPAX data by importing them into CellDesigner.
Highlights
BioPAX Pathway Physical entity Interaction CellularLocationVocabularyCellDesigner Protein RNA and AntiSenseRNA Gene Simple molecule Ion Unknown, Degraded, Drug Phenotype Heterodimer Modification Binding region.
CellDesigner State transition, truncation, transcription, translation Association or dissociation Transport Degradation Catalysis physical stimulation, modulation, trigger, inhibition, unknown inhibition
Mapping ExampleReaction ID: r1 r1 is a State_transition reactant is s71_a1 product is s71_a2 modifier is s61 modifier is s65 modification type is Stimulation logical_operator is Or.
Summary
CellDesigner Protein RNA and AntiSenseRNA Gene Simple molecule Ion Unknown, Degraded, Drug Phenotype Heterodimer Modification Binding region. CellDesigner State transition, truncation, transcription, translation Association or dissociation Transport Degradation Catalysis physical stimulation, modulation, trigger, inhibition, unknown inhibition
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