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OntologyVis (version 0.0.2)

Ontology file (.obo):

(Optional) Ontology observations file (TSV):

Maximum depth:

Maximum depth for the level of detail to show in the visualization

(Optional) Ontology subsets:

Specify the comma-separated list of ontology subsets to use. If set, only the ontology entries that are generic (not belonging to any subset) and ontology entries that are marked as being part of one of the allowed subsets are added to the result list of entries.

Sizing:

How to size the ontology terms. See details in documentation below.

Display individual observation items:

Whether to render the individual observation items in the visualization. Disable this if you expect many (thousands) of individual observation items per ontology entry.

Try to use only one term per observation items:

If checked, the algorithm will try to reduce the number of terms to which an observation item is associated. The observation item can still appear in more than one term circle, but the algorithm will try to reduce this by preferring the bigger circles.

Allow ontology terms to be nested under more than one super class:

Some ontology classes can have multiple super classes. Check this to allow nesting the classes under each of its super classes. Even when NOT checking this option, the ontology classes can still appear in more than one term circle/superclass, but the algorithm will try to reduce this by preferring the bigger circles.

Output

This method will generate different visualizations to allow exploring 'ontology annotated' results. It generates ontology circles and ontology pie chart visualizations.

Circles: The inner circles (white circles) are the most specific (or at depth=maximum depth) level of detail containing the individual observation items.

Sizing: * Simple sizing: Each observation item is given the same size. The more observation items found for a certain ontology circle, the bigger it will be. * Quantification based sizing: Each observation item is sized according to the given quantification column.

Colors: * Red borders show the items that have more than one parent in the given ontology scheme. The current visualization avoids redundancy by placing each circle inside the parent circle where it has more siblings with observations (not yet an iterative process, so nr of siblings is calculated only at start).