Is OBO-Edit2 running slowly?

Several of the components in OBO-Edit2 can cause slow performance. The easiest solution is to turn off components that you are not using. The biggest culprits are:

To turn off the Graph Editor or the Parent Editor, simply remove them from your layout.

You can tell if the Reasoner is on because the OBO-Edit titlebar will say "REASONER ON". To turn the Reasoner off, bring up the Reasoner Manager ([Reasoner] -> [Reasoner Manager]) and select "OFF" from the pulldown list. Unless you specifically need the Reasoner, it's best to leave it off, because it uses a lot of memory and slows down OBO-Edit a lot.

The Verification Manager

When is the application running slowly? Is it when you are loading the file, commiting a term edit, or making the edit itself? If the slowness occurs at specific times then it may be because you are running verification checks that you are not aware of. To find this out, open the Verification Manager component ([Tools] -> [Verification Manager]). The verification manager controls look like this:

Figure 1
whole_panel

If you are experiencing slowness in one area of your editing, it is likely that you are running a lot of verification checks at just one stage of editing, and if you wish, you may turn off these checks and just run them manually on demand. In Figure 2 below, the different points when checks can be run are labeled A through G.

Figure 2
slow

Types of slowness:


1) Application slow to load the ontology file.

This may be because you are running a lot of checks on loading your ontology file. To solve this problem uncheck the boxes above labeled 'E'. You may want to run the verification checks manually at a more appropriate time by checking the relevant boxes labeled 'F' and clicking the 'Run Manual Check' button (see Figure 1).

2) Application slow to select a new term in the ontology editor panel after a text change has been made in the Text Editor Panel.

It is likely that you have several checks enabled 'On text commit'. To solve this problem uncheck the boxes above labeled 'A'. You may want to run the verification checks manually at a more appropriate time by checking the relevant boxes labeled 'F' and clicking the 'Run Manual Check' button.

3) Application slow to apply text edits.

It is likely that you have several checks enabled 'On text edit'. To solve this problem uncheck the boxes above labeled 'B'. You may want to run the verification checks manually at a more appropriate time by checking the relevant boxes labeled 'F' and clicking the 'Run Manual Check' button.

You may wish to keep the 'Definition check' enabled so that the application will underline spelling errors and typos as you work.

4) Application is slow to save the ontology file.

It is likely that you have several checks enabled 'On save'. To solve this problem uncheck the boxes above labeled 'D'. You may want to run the verification checks manually at a more appropriate time by checking the relevant boxes labeled 'F' and clicking the 'Run Manual Check' button.

5) Application is slow to run the reasoner.

The reasoner is slow on any large or complex ontology--we are working on improving this. However, it is also possible that verification checks are making the reasoner slower. It is likely that you have several checks enabled 'On reasoner'. To solve this problem uncheck the boxes above labeled 'C'. You may want to run the verification checks manually at a more appropriate time by checking the relevant boxes labeled 'F' and clicking the 'Run Manual Check' button.