Entity Composition/Refinement

 

Sometimes, the terms contained in the ontologies are just not specific enough for your needs.  In those cases, you might need to 'post-compose' or refine a term. 

For this exercise, I will demonstrate with two example phrases to capture

Step 1:  Bring up the refinement window

Click the "Comp" button next to the field that you wish to create a composed term.  It will open the refinement window:

Step 2:  Select a term to refine.

Statement (a) can be translated into two terms: 

the axon of the projection neuron

however, we need to have a relationship betwen the two terms:

the axon which is part of the projection neuron

In the Phenote world, the shorthand for this new term will look like:

Axon^part_of(Projection neuron)

So, begin typing the terms into the fields within the window.  This interface will act similarly to the main Data Entry panel; as you begin typing a list of partial matches will display below the field, and any terms you mouseover will be displayed in the Term Info panel.  You can navigate through the Term Info panel and use terms just as you would in the main window.

The refinement window would look like:

Step 3:  Add additional refinements, if necessary

Statement (b) needs to be broken down into three terms:

the projection neurons which are part_of the mesocortex which is part_of the temporal part of the head

In order to create a 3-term refinement, additional fields will need to be added.  After entering the first two terms, click the add (+) button to increase the number of fields for entry.  The resulting window will look like:

Then, fill in the additional relationship(s) and terms...

You can continue to add additional refinements in this same way, if necessary.

The Phenote shorthand for this will read:

Projection neuron^part_of(Mesocortex)^part_of(Temporal part of head)

Step 4:  Select OK for your new term

Once you select "OK", your newly composed term will be copied back to the Data Entry field in the main window, and to the Annotation Spreadsheet.  These terms will be presented in the Phenote shorthand, and will look like: