Updated api paramater description for /biopax-url-to-json as disscuss…

…ed in #14. Updated some comments. Added pc2.owl file to gitignore.

.gitignore

@@ -10,3 +10,4 @@ build
 out
 *.log
 *.out
+src/test/resources/pc2.owl

src/main/java/factoid/converter/BiopaxToFactoid.java

@@ -209,7 +209,7 @@ private JsonObject makeEntityJson(Entity entity) {
 		}
 
 		// if the entity has no grounding return null
-		// which will signal that the related document must be skipped as well
+		// which will signal that the related interaction must be skipped as well
 		if ( xref == null || org == null ) {
 			return null;
 		}
@@ -232,7 +232,7 @@ else if ( originalDb.equals("hgnc symbol") || originalDb.equals("refseq") ) {
 		else {
 			logger.warning("Unhandled xref database: " + originalDb);
 			// if the entity db is not handled return null
-			// which will signal that the related document must be skipped as well
+			// which will signal that the related interaction must be skipped as well
 			return null;
 		}
 

src/main/java/factoid/web/Controller.java

@@ -122,7 +122,7 @@ public String biopaxToFactoid(
     produces = "application/json"
   )
   public String biopaxUrlToFactoid(
-		  @ApiParam("URL of a BioPAX RDF/XML file") @RequestBody String url) {
+		  @ApiParam("URL of a TAR-GZ compressed BioPAX RDF/XML file") @RequestBody String url) {
 	  BiopaxToFactoid converter = new BiopaxToFactoid();
 	  try {
 		  String body = getContentFromUrl(url);