Posted here: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(New page: == Specifying necessary and sufficient definitions using the text-editor cross-product tab == Image:head_sensillum_XP.png == Render to highlight terms defined as intersections == Th...)
 
Line 11: Line 11:
== Filter to import all paths to root for a specific term ==
== 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 paths to root for each foreign term used.  This can be done with the following filter:
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:


[[Image:Paths_to_root_import_filter.png]]
[[Image:Paths_to_root_import_filter.png]]


Only the first two terms are shown.
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.
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.
Line 21: Line 21:
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.
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.


- a perl script for rolling these filters can be be found here:
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.
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.

Revision as of 05:39, 13 May 2009

Specifying necessary and sufficient definitions using the text-editor cross-product tab

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.

Render to color specific links

Render for namespace

When using imported terms, it is useful to render them differently

Other useful renders

When aiming at is_a completeness but also at reducing multiple inheritance, the following renders are useful