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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Update out-of date-information in a pathway data set, or create a personalized pathway relevant to a specialized research topic.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.