Specifying necessary and sufficient definitions using the text-editor cross-product tab
To define a new term entirely using a neccessary and sufficient (cross-product) definition, right click in the ontology tree editor and choose: add new root term. Then add the appropriate definition to the new term in the cross-product tab of the text editor:
Render to highlight terms defined as intersections
The following render was used in figures 2 and 3 of the poster. It is extremely useful as a way of keeping track of which terms have intersection definitions when using the ontology tree editor or the graph editor.
Filter to import all paths to root for a specific term
Loading multiple ontologies into OBO-Edit for reasoning purposes is not viable unless the ontologies are small. It is much easier to simply load in the smallest subset of the ontology necessary for reasoning: all is_a paths to root for each foreign term used. This can be done with the following filter:
Only two terms are shown, but the filter can be extended to cover as many terms as necessary.
This filter can be built a term at a time as foreign terms are used in XP definitions, using the load/save filter option in the search panel and then loaded for filtered save by choosing the "filter terms" option at save time. Note, the 'allow dangling parents' option should NOT be checked.
If the source ontology doesn't assert all is_a links, but instead relies on a reasoner, you should check the 'save implied links [save for presentation]' option.
Alternatively, here is a simple perl script for rolling these filters.
It takes a return delimited list of IDs as input and makes an XML file that can be loaded as a filter and then used to save out all paths to root.
Other useful renders
When aiming at is_a completeness but also at reducing multiple inheritance, the following renders are useful.
This render highlights unclassified terms:
A stricter version highlights all terms without complete is_a paths to root:
This render highlights terms with more than one asserted is_a parent: