cidgoh / ontotrek Goto Github PK

Hi!
There is a common practice that a big ontology family uses <owl:imports> to group things thematically. There can be an ontology consisting only of imports, like, e.g. this one created to keep all the parts of Digital Construction ontologies.
Is it possible to visualize such ontology in OntoTrek?

I am restructuring code to work directly off of OWL rdf/xml files, courtesy of rdflib.js . This will make it MUCH easier to render any given ontology in 3d. No more need for ontofetch.py.

Allow more than one ontology to be displayed within same graph, by successively selecting them. Perhaps delete ontology from graph by selecting root node and hitting delete.

IAO:definition is used within OBOFoundry ontologies. Others may use dc:description so allow that to be read in. More of an ontofetch.py capability.

The rendering may appear to place it on its own in empty space, at some depth Example: Ecocore "behavioural quality" has a deprecated parent, and in sidebar that parent is listed by ID only.

Is the PATO ontology .owl file misformed? The following error is obtained when trying to render it:

Uncaught TypeError: Cannot read property 'prefix' of undefined
    at development.js:154
    at updateObj (3d-force-graph.min.js:5)
    at 3d-force-graph.min.js:2
    at Array.forEach (<anonymous>)
    at 3d-force-graph.min.js:2
    at eu (3d-force-graph.min.js:2)
    at Au (3d-force-graph.min.js:5)
    at Function.update (3d-force-graph.min.js:5)
    at 3d-force-graph.min.js:2
    at c (3d-force-graph.min.js:2)

Drawing links from some "other_parents" items to a given node, where the other parent in question hasn't been created yet I guess, creates an odd branch depth jump, ultimately resulting in much more spread out graph. It may arise when parent node has been deprecated and so hasn't been created in graph if switch to show deprecated items is off.

Code is in line 604 of common.js, around "// 3rd pass does secondary parent LINKS which could be to shallower nodes"

Create a cached xyx version of a graph that can be saved after it is rendered. Then we can add that as the default to display, and just have an option to clear a cache and regenerate from source owl file.

Enable highlight / hiding of branches of ontology temporarily - e.g. select node and have all sub-notes hidden/emphasized.

Protege and Robot (https://github.com/ontodev/robot) have the capability of generating one or more explanations for errors. Feed these into OntoTrek to enable visualization of the conflicting inheritance classes.

E.g. if it is reported that "populated place, Alaska" is unsatisfiable, then run robot:

robot explain --input genepio-edit.owl --reasoner HermiT --axiom "'populated place, Alaska' EquivalentTo owl:Nothing" --explanation output.md

This yields:

populated place, Alaska EquivalentTo Nothing

• populated place, Alaska SubClassOf Municipality
  • Municipality SubClassOf geopolitical region
    • geopolitical region SubClassOf designated area on Earth
      • designated area on Earth SubClassOf site
        • site SubClassOf immaterial entity
• populated place, Alaska SubClassOf material entity
• material entity DisjointWith immaterial entity

Enable OntoTrek to receive this markdown and display contradiction.

It seems when fetching a branch of ontology via ontofetch.py that the label of the initial term fetched may not be retrieved or stored in the output json in all cases.

Improve navigation animation by checking out new https://github.com/vasturiano/3d-force-graph controlType parameter. “Eliminate pitch and roll in flight experience”

It seems like a hidden data structure left over from previous render is slowing an algorithm down. Currently the workaround is to reload the app, apply settings, then select an ontology.