OntoTrek 3D Viewer

OntoTrek is an OBOFoundry.org ontology terminology viewer that takes advantage of WebGL 3d graph rendering software. We have a few ontologies to choose from during this beta phase, some easy to load like AGRO and ECOCORE, and some big ones like CLO which can only be rendered by applying filters like "wireframe", no "labels", and limiting node depth. Some ontologies demonstrate nice organization under the Basic Formal Ontology (BFO, whose 34 nodes are big, sunny, and always in the same position), and others show an independent streak which may illustrate the difference between reference and application ontologies.

OntoTrek displays all class-subclass relations starting from the first top-level entity it finds (usually owl:Thing or BFO:0000001 entity). OntoTrek doesn't draw other object relations.

To begin, select an ontology, or enter an ontology URL in upper right "Search" tab and it will be displayed above. Alternately, enter a .owl file URL directly (it must be in rdf/xml format, and can't be a URL that redirects, so for github-hosted ontologies use the "raw.githubusercontent.com/..." link, e.g. https://raw.githubusercontent.com/obi-ontology/obi/master/obi.owl).

Note a current subtle bug is that settings applied to a graph yield successively slower redraws. To play with settings, reload the app in the browser, select settings, and then select an ontology.

This software is being developed at the Hsiao Lab which is associated with the University of British Columbia Department of Pathology and Laboratory Medicine, and with the PHSA Public Health Laboratory at the British Columbia Centre For Disease Control. The project's GitHub is here. Contact Damion Dooley for more information.

   







Select an ontology to view it; a legend of node and edge colors will be displayed here

Experimental tool: Enter Markdown formatted links of form [link label](URL) [relation type] [link label](URL) here to see them highlighted in current ontology:

To visualize a disjoint axiom-related unsatisfiability error about a particular term in a given ontology that you have encountered, install the command line robot tool and run the following robot command directly on that ontology to get the error explanation report.

> robot explain --input [YOUR ONTOLOGY FILE] --reasoner HermiT --axiom "'[PUT PROBLEM TERM'S rdfs:label HERE]' EquivalentTo owl:Nothing" --explanation output.md

Select the pertinent ontology, wait for it to be fully rendered, then enter the resulting explanation report text above, press Trace, and the conflicting relations will be highlighted.

Note that it can take a while to render an ontology, and until rendering is complete, changing settings or attempting to navigate to terms may not work.

Viewport navigation:

While your cursor is positioned over the display viewport, both mouse and trackpad take on the following functions:

Click on a node to focus on it; view will rotate and move towards that item. Clicking on a link will take you to its child (lower depth) node.

Trackpad:
Zoom: 2 finger motion up and down (no motion sideways).
Pan: 2 finger + click and hold mouse. Rotate: 3 finger motion.

Mouse:
Zoom: move + click/hold right button or D key.
Rotate: move + click/hold left button or A key.
Rotate: move + click/hold middle button or S key.