This tutorial will give a brief overview of how to modify a Protégé-Frames dictionary using Java.

Download Protege:

protege.stanford.edu/

Reference the API:

protege.stanford.edu/protege/3.4/docs/api/core/

The Following examples will require these imports:

import edu.stanford.smi.protege.model.Cls;
import edu.stanford.smi.protege.model.Instance;
import edu.stanford.smi.protege.model.KnowledgeBase;
import edu.stanford.smi.protege.model.Project;
import edu.stanford.smi.protege.model.Slot;

Assuming you’ve successfully associated the appropriate Protege libraries with your Eclipse, lets get started with some simple HOW-TOs in programmatical Protege ontology manipulation;

For this tutorial I will be using the RadLex Lexicon/Dictionary.

The first thing you will need is the actual project files.
Mine are called : RadLex.pins, RadLex.pont, and RadLex.pprj
These files are created when you save a Lexicon/Dictionary in Frames format using Protege.

Create a pointer to them in your java code. I have mine in in C:\smelo\RadLex.pprj
You only have to point to the *.pprj file.

//Get the project file of the lexicon you want to manipulate
private static final String PROJECT_FILE_Pointer = "C:\\smelo\\RadLex.pprj";

Next, you will need to get the KnowledgeBase object.

//errors object is required in getting the project
Collection errors = new ArrayList();
//Get Project project
Project project = new Project(PROJECT_FILE_Pointer, errors);
//Get Knowledgebase kb
KnowledgeBase kb = project.getKnowledgeBase();

In Protege Frames, each Term/Concept/Lexicon Entity/Thingy is considered a “class”(Cls). The entire RadLex dictionary is nothing more then a bunch of terms(classes) with attributes(slots), and the relationships amongst them.

So lets iterate through all the classes in the KnowledgeBase.

To do this we need to get a class iterator:

//RadLex Class iterator
Iterator radClsIter = kb.getClses().iterator();

Loop through every class

In RadLex, the “name” of every class is its Radlex Id number, or “RID###..”
such as “RID1099” “RID35707” “RID3874” ….

Every RadLex class contains a number of “slots” or attributes that you can populate:

Using the method .getOwnSlots() on a Cls Object will show you a list of all the slots and their names

These are all different attributes(slots) of a single concept(Cls) in RadLex:

Slot(Related_Condition), Slot(Anatomical_Site), Slot(Related_modality), Slot(ACR_ID), Slot(UMLS_Term), Slot(Is_A), Slot(UMLS_ID), Slot(Misspelling of term), Slot(Has_Subtype), Slot(Non-English_name), Slot(Member_Of), Slot(Preferred_name), Slot(Source), Slot(Non-Sanctioned Synonym), Slot(Synonym), Slot(Version_Number), Slot(Term_Status), Slot(SNOMED_ID), Slot(Acronym), Slot(SNOMED_Term), Slot(ACR_Term), Slot(Comment), Slot(Image_URL), Slot(Definition), Slot(:ROLE), Slot(:DOCUMENTATION), Slot(:SLOT-CONSTRAINTS), Slot(:DIRECT-INSTANCES), Slot(:DIRECT-SUPERCLASSES), Slot(:DIRECT-SUBCLASSES), Slot(:DIRECT-TEMPLATE-SLOTS), Slot(:NAME), Slot(:DIRECT-TYPE)

Some slot types are simple strings, while others are more complex Instances.

while( radClsIter.hasNext() )
{
	Cls currentClass = radClsIter.next();
}

So now that we have a brief scattered overview of the RadLex Lexicon/Dictionary,
and we know how to iterate through each Concept/Term/Class within it. Lets do some practical HOW-TOs.

HOW TO get the value of “Preferred_name” slot from a class object(currentClass)?

One way of retrieving of the content of a slot of a class would be by the slot’s name.
So all you have to do is, get another slot iterator this time for the class(term/concept), and compare its name with the one you want.
Then, iterate through the content of the slot and display its value.(You might not have to do this last step; it depends of the type of slot)

In RadLex the Preferred_name slot of a class is populated with an Instance type.
So we have to get the instance of a slot then get the name of the Instance.

String slotName = "Preferred_name"; 
 
Iterator slotIter = currentClass.getOwnSlots().iterator();
 
//Iterate through the slots
while( slotIter.hasNext() )
{
	Slot currentSlot = slotIter.next();
 
	//Compare the slot name with your slotName String
	if( slotName.equals( currentSlot.getName() ) )
    	{
		Object slotContentObject = null;
 
		//Create another iterator for the content of the slot
    		Iterator iterSlotContent = currentClass.getOwnSlotValues(currentSlot).iterator();
 
    		if( iterSlotContent.hasNext() )
    		{
    			slotContentObject = iterSlotContent.next(); 
 
			//if the content of a slot is of type Instance
    			if(slotContentObject instanceof Instance)
  			{
				//cast to Instance
    				Instance instSlotValue = (Instance) slotContentObject;
 
				//use the method getBrowserText() on the Instance to get its String content
    				System.out.println(instSlotValue.getBrowserText());
    			}
    		}
    	}
}

HOW TO change the Definition slot of a Class/Concept/Term by specific “name” (RID) and save to project file?

Say we want to change the content of the “Definition” slot in Cls “RID35712”:

String slotName = "Definition"; 
 
//get the Cls object of the Term/Concept/Class
Cls myConcept = kb.getCls( "RID35712" );
 
Iterator myConceptClsIter = myConcept.getOwnSlots().iterator();
while( myConceptClsIter.hasNext() )
{
	Slot currentSlot = myConceptClsIter.next();
	if(slotName.equals(currentSlot.getName()) )
	{
		//set new Definition
		myConcept.setOwnSlotValue(currentSlot, "This is my new Definition for Term RID35712");
	}
}
 
//save changes
project.save(errors);

HOW TO display ALL synonyms of the entire project?

What if we want to list the names of ALL synonyms throughout the entire dictionary

Iterator radClsIter = kb.getClses().iterator();
 
while( radClsIter.hasNext() ){
        Cls currentClass = radClsIter.next();
        String prefName = findPreferredName(currentClass);
 
        String slotName = "Synonym";
        Iterator slotIter = currentClass.getOwnSlots().iterator();
 
        while( slotIter.hasNext() )
        {
    		Slot currentSlot = slotIter.next();
    		if(slotName.equals(currentSlot.getName()) )
    		{
    			Object slotContentObject = null;
    			Iterator iterSlotContent = currentClass.getOwnSlotValues(currentSlot).iterator();
    			if( iterSlotContent.hasNext() )
    			{
    				slotContentObject = iterSlotContent.next();
    				if(slotContentObject instanceof Instance)
    				{
    					Instance instSlotValue = (Instance) slotContentObject;
    					System.out.println(instSlotValue.getBrowserText());
    				}
    			}
    		}
    	}
}

HOW TO create a new Class/Concept/Term and Add it as a child of RID35712?

We will be assigning the “name” as new unique “RID12345” and adding it as child of the term “RID35712”

Collection myCol =   kb.getClsNameMatches("RID35712",1);
kb.createCls("RID12345", myCol);

That covers a few basics, if you would like an example of something I havent covered, feel free to leave a comment.

GL & HF :D