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Table 2 A summary of the biological pathway visualization task taxonomy

From: A taxonomy of visualization tasks for the analysis of biological pathway data

Category Example task
Attribute tasks  
(A1) Multivariate Find all up-regulated genes in a biological pathway. Integrate results of a laboratory experiment into existing protein-protein interaction networks.
(A2) Comparison Compare a biological pathway to a pathway with the same functionality in a reference species.
(A3) Provenance Determine which studies provides the evidence for a link between two genes.
(A4) Uncertainty Understand which pathway components have the strongest empirical evidence relationships.
Relationship tasks  
(R1) Attributes Find all translocations of entities in a given biological pathway.
(R2) Direction Find the products or output of a biochemical reaction.
(R3) Grouping Expand a module entity to include all child-entities in the visualization.
(R4) Causality Find all genes downstream of the currently selected entity, which may be affected by a change in regulation.
(R5) Feedback Identify potential feedback loops in gene regulation.
Modification tasks  
(M1) Annotate Update out-of date-information in a pathway data set, or create a personalized pathway relevant to a specialized research topic.
(M2) Curate Identify errors and update historical data.