BioPAX Tutorial; Examples from the Paxtools User's Guide. (PubMed ID: 24068901 Link: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003194)

basicTraversal_3.groovy

//BASIC TRAVERSAL
// Get names for all elements in a BioPAX OWL file and then for just Proteins
import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.level3.Protein;

// Load a sample test BioPAX File via Simple IO Handler
InputStream f = new FileInputStream(new File("data/biopax3-short-metabolic-pathway.owl"));
BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(f);

// Iterate through all BioPAX Elements and print basic info
println "ALL ELEMENTS:\n"; 

Set<BioPAXElement> elementSet = model.getObjects();
for (BioPAXElement currentElement : elementSet) {
	String rdfId = currentElement.getRDFId();
	String className =	currentElement.getClass().getName();
	println("Element: " + rdfId + ": " + className);
}

// Get Proteins Only
println "\nPROTEINS ONLY:\n"; 

Set<Protein> proteinSet = model.getObjects(Protein.class);
for (Protein currentProtein : proteinSet) {
	println(currentProtein.getName() + ": " + currentProtein.getDisplayName());
}

combinedExample_10.groovy

//COMBINED EXAMPLE
// Combined example
import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.level3.Interaction; 
import org.biopax.paxtools.model.level3.Xref; 
import org.biopax.paxtools.query.QueryExecuter;
import org.biopax.paxtools.query.algorithm.Direction;
import org.biopax.paxtools.query.algorithm.LimitType;
import org.biopax.paxtools.controller.EditorMap;
import org.biopax.paxtools.controller.SimpleEditorMap;
import org.biopax.paxtools.controller.Completer; 
import org.biopax.paxtools.controller.Cloner;
import org.biopax.paxtools.pattern.miner.SIFSearcher; 
import org.biopax.paxtools.pattern.miner.SIFEnum; 
import org.biopax.paxtools.model.BioPAXLevel;

Set<BioPAXElement> findElements(Model model, String[] ids) {
  Set<BioPAXElement> set = new HashSet<BioPAXElement>();
	for (String id : ids) {
    	BioPAXElement bpe = model.getByID(id);
		if (bpe != null) {
			set.add(bpe);
		}
	}
	return set;
}

// READ FILE
InputStream f = new FileInputStream(new File("data/raf_map_kinase_cascade_reactome.owl"));

BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(f);

// RUN GRAPH QUERY
source = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1630_1_9606"); //phospho-Cdc2
target = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1624_1_9606"); //MEK1

result = QueryExecuter.runPathsFromTo(source, target, model, LimitType.NORMAL, 3);

// COMPLETE MODEL 
Completer c = new Completer(SimpleEditorMap.L3);
result = c.complete(result, model);
Cloner cln = new Cloner(SimpleEditorMap.L3, BioPAXLevel.L3.getDefaultFactory());
Model excisedModel = cln.clone(model, result)

// EXTRACT PUBMED XREFS FOR REMAINING INTERACTIONS
for (Interaction interaction : excisedModel.getObjects(Interaction.class)) {
	// Print the name of the interaction
	System.out.println("* " + interaction.getDisplayName());
	// Get all external references
	for (Xref xref : interaction.getXref()) {
		String db = xref.getDb();
    String id = xref.getId(); 
    String url = "";
		
    // Convert PubMed ids to URLs for easy access
    if (db.equalsIgnoreCase("PubMed")) {
			url = " (http://www.ncbi.nlm.nih.gov/pubmed/" + id + ")";
			// Print the external reference information
			System.out.println("\t" + xref.getDb() + ":" + xref.getId() + url);
    }
	}
}

// SIF CONVERSION
ByteArrayOutputStream os = new ByteArrayOutputStream();

// null in first pattern forces return HGNC IDs 
SIFSearcher searcher = new SIFSearcher(null, SIFEnum.values());
searcher.searchSIF(excisedModel, os, false);

System.out.println("\nCONTENTS:\n\n" + os);

excisor_6.groovy

// EXCISOR
// Excise a ProteinReference from the model
import org.biopax.paxtools.controller.EditorMap;
import org.biopax.paxtools.controller.SimpleEditorMap;
import org.biopax.paxtools.controller.Completer; 
import org.biopax.paxtools.controller.Cloner;

import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;

import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.BioPAXElement; 
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.ProteinReference;
import org.biopax.paxtools.model.level3.UnificationXref;

Model excise(Model model, Set<BioPAXElement> result) {
  Completer c = new Completer(SimpleEditorMap.L3);
  result = c.complete(result, model);
  Cloner cln = new Cloner(SimpleEditorMap.L3, BioPAXLevel.L3.getDefaultFactory());
  return cln.clone(model, result);
}

Set<BioPAXElement> findElements(Model model, String[] ids) {
  Set<BioPAXElement> set = new HashSet<BioPAXElement>();
	for (String id : ids) {
    	BioPAXElement bpe = model.getByID(id);
		if (bpe != null) {
			set.add(bpe);
		}
	}
	return set;
}

InputStream f = new FileInputStream(new File("data/intrinsic_apoptosis_reactome.owl"))

BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(f);

//MEK1
String[] ids = ["http://www.reactome.org/biopax/52/109606#ProteinReference1"];

Set<BioPAXElement> result = findElements(model, ids);

Model clonedModel = excise(model, result);

System.out.println("UnificationXref COUNT:"); 
System.out.println("ORIGINAL MODEL: " + model.getObjects(UnificationXref.class).size()); 
System.out.println("EXTRACTED MODEL: " + clonedModel.getObjects(UnificationXref.class).size());

ByteArrayOutputStream os = new ByteArrayOutputStream();
handler.convertToOWL(clonedModel, os);
String output = new String(os.toByteArray());
System.out.println("\nCONTENTS:\n\n" + output);

exportSif_8.groovy

// EXPORT SIF
// Export model to SIF
import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.pattern.miner.SIFSearcher; 
import org.biopax.paxtools.pattern.miner.SIFEnum; 

InputStream f = new FileInputStream(new File("data/raf_map_kinase_cascade_reactome.owl"));
ByteArrayOutputStream os = new ByteArrayOutputStream();

BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(f);

// null in first pattern forces return HGNC IDs 
SIFSearcher searcher = new SIFSearcher(null, SIFEnum.values());
searcher.searchSIF(model, os, false);
System.out.println("CONTENTS:\n\n" + os);

firstModel_1.groovy

// First Model
// Create a simple model with one protein and one reaction where the protein as a reaction participant
import org.biopax.paxtools.model.BioPAXFactory;
import org.biopax.paxtools.model.Model; 
import org.biopax.paxtools.model.BioPAXLevel; 
import org.biopax.paxtools.model.level3.Protein; 
import org.biopax.paxtools.model.level3.BiochemicalReaction; 
import org.biopax.paxtools.model.level3.PhysicalEntity; 

BioPAXFactory factory = BioPAXLevel.L3.getDefaultFactory();
Model model = factory.createModel();
model.setXmlBase("http://biopax.org/tutorial/");

Protein protein1 = model.addNew(Protein.class, "http://biopax.org/tutorial/test1");
protein1.addName("Tutorial Example Some Transporter 1");
protein1.setDisplayName("TEST1");

Protein retrievedProtein = model.getByID("http://biopax.org/tutorial/test1");
println("DISPLAY NAME: " + retrievedProtein.getDisplayName()); 

BiochemicalReaction rxn1 = model.addNew(BiochemicalReaction.class, "http://biopax.org/tutorial/rxn1");
rxn1.addLeft(protein1);

Set<PhysicalEntity> reactants = rxn1.getLeft();
for(reactant in reactants) {
	println("LEFT REACTANT: " + reactant.getDisplayName()); 
}

graphQuery_9.groovy

//GRAPH QUERY
// Run graph queries: "Paths From To" and "Neighborhood"
import org.biopax.paxtools.controller.Cloner;
import org.biopax.paxtools.controller.Completer;
import org.biopax.paxtools.controller.SimpleEditorMap;
import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.BioPAXLevel;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.query.QueryExecuter;
import org.biopax.paxtools.query.algorithm.Direction;
import org.biopax.paxtools.query.algorithm.LimitType;
import org.biopax.paxtools.io.sif.SimpleInteractionConverter;

Set<BioPAXElement> findElements(Model model, String[] ids) {
  Set<BioPAXElement> set = new HashSet<BioPAXElement>();
	for (String id : ids) {
    	BioPAXElement bpe = model.getByID(id);
		if (bpe != null) {
			set.add(bpe);
		}
	}
	return set;
}
 
InputStream f = new FileInputStream(new File("data/raf_map_kinase_cascade_reactome.owl"))

BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(f);

source = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1630_1_9606"); //phospho-Cdc2
target = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1624_1_9606"); //MEK1

result1 = QueryExecuter.runPathsFromTo(source, target, model, LimitType.NORMAL, 3);
System.out.println("RS: " + result1.size()); 

for (BioPAXElement currentElement : result1) {
	String rdfId = currentElement.getRDFId();
	String className =	currentElement.getClass().getName();
	println("Element: " + rdfId + ": " + className);
}

Set<BioPAXElement> source = findElements(model, "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN2360_1_9606"); //MEK2
Set<BioPAXElement> result2 = QueryExecuter.runNeighborhood(source, model, 1, Direction.BOTHSTREAM);
System.out.println("RS2: " + result2.size()); 

for (BioPAXElement currentElement : result2) {
	String rdfId = currentElement.getRDFId();
	String className =	currentElement.getClass().getName();
	println("Element: " + rdfId + ": " + className);
}

Completer c = new Completer(SimpleEditorMap.get(BioPAXLevel.L3));
result2 = c.complete(result2, model);

ByteArrayOutputStream os = new ByteArrayOutputStream();
SimpleInteractionConverter sifConverter = new SimpleInteractionConverter();

sifConverter.writeInteractionsInSIF(result, os);
System.out.println("CONTENTS:\n\n" + os);

listFiles_0.groovy

// List files in directory 
File folder = new File("data");
File[] files = folder.listFiles();

for(File file in files) {
	System.out.println(file.getName())
}

// Get file contents 
String fileContents = new File('data/biopax3-short-metabolic-pathway.owl').text
System.out.println("Contents:\n\n" + fileContents)

// Load file as InputStream
InputStream f = new FileInputStream(new File("data/biopax3-short-metabolic-pathway.owl"));

listProperties_5.groovy

//LIST PROPERTIES
// Display all properties for model objects
import org.biopax.paxtools.controller.EditorMap;
import org.biopax.paxtools.controller.SimpleEditorMap;
import org.biopax.paxtools.controller.PropertyEditor;
import org.biopax.paxtools.model.BioPAXElement; 
import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;

String[][] listProperties(BioPAXElement bpe) {
  // In order to use properties we first need an EditorMap
  EditorMap editorMap = SimpleEditorMap.L3;
  // And then get all the editors for our biopax element
  Set<PropertyEditor> editors = editorMap.getEditorsOf(bpe);
  
  // For each property
  for (PropertyEditor editor : editors) {
    // First column is the name of the property, e.g. "Name"
    // Second column is the value e.g. "p53"
    println("Property: " + editor.getProperty() + 
            " Value: " + editor.getValueFromBean(bpe).toString());
  }
}

// Load a sample test BioPAX File via Simple IO Handler
InputStream f = new FileInputStream(new File("data/biopax3-short-metabolic-pathway.owl"));
BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(f);

Set<BioPAXElement> elementSet = model.getObjects();
for (BioPAXElement currentElement : elementSet) {
  listProperties(currentElement);
  println("\n")
}

merging_7.groovy

// MERGER
// Merge to BioPAX OWL files 
import org.biopax.paxtools.controller.EditorMap;
import org.biopax.paxtools.controller.SimpleEditorMap;
import org.biopax.paxtools.controller.Merger;
import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.BioPAXElement; 

EditorMap editorMap = SimpleEditorMap.L3;

InputStream f1 = new FileInputStream(new File("data/biopax3-short-metabolic-pathway.owl"))
InputStream f2 = new FileInputStream(new File("data/raf_map_kinase_cascade_reactome.owl"))

BioPAXIOHandler handler = new SimpleIOHandler();
Model srcModel1 = handler.convertFromOWL(f1);
Model srcModel2 = handler.convertFromOWL(f2);

Model targetModel = editorMap.getLevel().getDefaultFactory().createModel();
Merger merger = new Merger(editorMap);

merger.merge(targetModel, srcModel1, srcModel2);

String id1 = "http://www.biopax.org/examples/myExampleProtein_54";
String id2 = "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1643_1_9606"; 
BioPAXElement bpe1 = targetModel.getByID(id1);
BioPAXElement bpe2 = targetModel.getByID(id2);

if (bpe1 != null && bpe2 != null) {
	System.out.println("BOTH FOUND\n"); 
} else {
	System.out.println("ERROR\n");   
}

ByteArrayOutputStream os = new ByteArrayOutputStream();
handler.convertToOWL(targetModel, os);
String output = new String(os.toByteArray());
System.out.println("CONTENTS:\n\n" + output);

pathAccessors_4.groovy

//PATHACCESSORS
// Extract UnificationXRefs for Proteins that pathwayComponents
import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.Pathway;
import org.biopax.paxtools.model.level3.Xref;
import org.biopax.paxtools.controller.PathAccessor; 

InputStream f = new FileInputStream(new File("data/akt_signaling_pathway.owl"))

BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(f);

// Set up the Path Accessor
PathAccessor pathAccessor = new PathAccessor("Pathway/pathwayComponent*:Protein/entityReference/xref:UnificationXref");

// Iterate through all proteins in the model
for(Pathway currentPathway : model.getObjects(Pathway.class)) {
	println("Pathway:" + currentPathway.getName());
	Set<Xref> unificationXrefs = pathAccessor.getValueFromBean(currentPathway);
	
  	for(Xref currentRef : unificationXrefs) {
		println("Unification XRef: " + currentRef.getDb() + ": " + currentRef.getId());
	}
}

pattern_11.groovy

//PATTERNS
// Print protein pairs that are in the same complex

import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level3.ProteinReference;
import org.biopax.paxtools.pattern.constraint.*;
import org.biopax.paxtools.pattern.*;
import org.biopax.paxtools.model.level3.Complex;

InputStream f = new FileInputStream(new File("data/akt_signaling_pathway.owl"))

BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(f);

// Set up the pattern
Pattern p = new Pattern(ProteinReference.class, "Protein 1");
	p.add(ConBox.erToPE(), "Protein 1", "SPE1");
	p.add(ConBox.linkToComplex(), "SPE1", "Complex");
	p.add(new Type(Complex.class), "Complex");
	p.add(ConBox.linkToSimple(), "Complex", "SPE2");
	p.add(ConBox.peToER(), "SPE2", "Protein 2");
	p.add(ConBox.equal(false), "Protein 1", "Protein 2");
	p.add(new Type(ProteinReference.class), "Protein 2");

List<Match> matches = Searcher.searchPlain(model, p);

for (Match match : matches)
{
	ProteinReference pr1 = (ProteinReference) match.get("Protein 1", p);
	ProteinReference pr2 = (ProteinReference) match.get("Protein 2", p);

	println(pr1.getDisplayName() + " is in same complex with " + pr2.getDisplayName());
}

simpleIO_2.groovy

// SIMPLEIO
// Read BioPAX OWL file and extract properties for a given protein 
import org.biopax.paxtools.io.BioPAXIOHandler;
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.Model;

InputStream f = new FileInputStream(new File("data/biopax3-short-metabolic-pathway.owl"))

BioPAXIOHandler handler = new SimpleIOHandler();
Model model = handler.convertFromOWL(f);

String id1 = "http://www.biopax.org/examples/myExampleProtein_54";

ByteArrayOutputStream os = new ByteArrayOutputStream();

handler.convertToOWL(model, os, id1);

String output = new String(os.toByteArray());

println("CONTENTS:\n\n" + output);