Converting as data properties

Author: alopezo

README.md

@@ -16,13 +16,16 @@ Binaries are also available in the releases section of the [github repository](h
 
 Run the executable from the command line, for example:
 
-`java -jar owl-test-x.x.x-SNAPSHOT-jar-with-dependencies.jar /folder/sct2_Concept_Snapshot_INT_20150131.txt /folder/sct2_StatedRelationship_Snapshot_INT_20150131.txt /folder/outputFile.owl http://snomed.org/`
+`java -jar owl-test-x.x.x-SNAPSHOT-jar-with-dependencies.jar /folder/sct2_Concept_Snapshot_INT_20150131.txt /folder/sct2_StatedRelationship_Snapshot_INT_20150131.txt /folder/sct2_Description_Snapshot_INT_20150131.txt /folder/der2_cRefset_LanguageSnapshot-en_INT_20150131 /folder/outputFile.owl http://snomed.org/ TRUE`
 
 Parameters (in this order):
  * Path to RF2 Concepts Snapshot file
  * Path to RF2 Stated Relationships Snapshot file
+ * Path to RF2 Stated Descriptons Snapshot file
+ * Path to RF2 Stated Language Refset Snapshot file
  * Path to output file (it will be created or replaced by this process)
  * IRI for the resulting ontology
+ * Boolean value to enable transformation of to concrete domains (Data Properties) ("TRUE"/"FALSE")
 
 ## About the conversion
 
@@ -36,4 +39,23 @@ Parameters (in this order):
    * *Has active ingredient*
    * *Laterality*
    * *Has dose form*
- * A sub-property chain is created between *Direct substance* and *Has active ingredient*
+ * A sub-property chain is created between *Direct substance* and *Has active ingredient*
+ 
+## Concrete domains conversion
+ 
+ Since the July 2017 release of the international edition, some relationships that specify numerical values are 
+ represented using concepts for the example:
+
+ * Source: 318420003 | Product containing atenolol 50 mg/1 each oral tablet (virtual clinical drug) |
+ * Attribute: 732947008 | Has presentation strength denominator unit (attribute) |
+ * Destination: 732774003 | 50 (qualifier value) |
+
+ If the "Concrete domains conversion" parameter is sent as "TRUE", those relationships are converted into OWL Data 
+ Properties, instead of the normal OWL Object Properties. Classification results should be identical, but having 
+ actual values instead of concept references may allow for more detailed queries and computations.
+ 
+ Attributes that are currently converted as data properties:
+ 
+ * 732944001 | Has presentation strength numerator value (attribute) | - DataType: float
+ * 732947008 | Has presentation strength denominator unit (attribute) | - DataType: float
+

pom.xml

@@ -2,8 +2,8 @@
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>com.termmed</groupId>
-	<artifactId>owl-test</artifactId>
-	<version>0.0.2-SNAPSHOT</version>
+	<artifactId>rf2-to-owl</artifactId>
+	<version>0.0.3-SNAPSHOT</version>
 	<dependencies>
 		<dependency>
 			<groupId>net.sourceforge.owlapi</groupId>

src/com/termmed/owl/DirectRunner.java

@@ -0,0 +1,51 @@
+/*
+ *
+ *  * Copyright (C) 2014 termMed IT
+ *  * www.termmed.com
+ *  *
+ *  * Licensed under the Apache License, Version 2.0 (the "License");
+ *  * you may not use this file except in compliance with the License.
+ *  * You may obtain a copy of the License at
+ *  *
+ *  *      http://www.apache.org/licenses/LICENSE-2.0
+ *  *
+ *  * Unless required by applicable law or agreed to in writing, software
+ *  * distributed under the License is distributed on an "AS IS" BASIS,
+ *  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  * See the License for the specific language governing permissions and
+ *  * limitations under the License.
+ *
+ */
+
+package com.termmed.owl;
+
+/**
+ * Created by alo on 4/6/16.
+ *
+ * @author Alejandro Rodriguez
+ */
+public class DirectRunner {
+    /**
+     * The main method.
+     *
+     * @param args the arguments
+     * @throws Exception the exception
+     */
+    public static void main(String[] args) throws Exception {
+        String conceptFile = "/Users/alo/Downloads/SnomedCT_RF2Release_INT_20170731/Snapshot/Terminology/sct2_Concept_Snapshot_INT_20170731.txt";
+        String relationshipFile = "/Users/alo/Downloads/SnomedCT_RF2Release_INT_20170731/Snapshot/Terminology/sct2_Relationship_Snapshot_INT_20170731.txt";
+        String outputFile = "/Users/alo/Downloads/conceptsOwlComplete-cd-alo.xml";
+        String descriptionFile = "/Users/alo/Downloads/SnomedCT_RF2Release_INT_20170731/Snapshot/Terminology/sct2_Description_Snapshot-en_INT_20170731.txt";
+        String languageFile = "/Users/alo/Downloads/SnomedCT_RF2Release_INT_20170731/Snapshot/Refset/Language/der2_cRefset_LanguageSnapshot-en_INT_20170731.txt";
+//        String textDefinitionFile = "/Users/ar/Downloads/SnomedCT_RF2Release_INT_201601731/Snapshot/Terminology/xsct2_TextDefinition_Snapshot-en_INT_20160131.txt";
+        String textDefinitionFile = null;
+        String iri = "http://snomed.info/id/";
+
+        RF2Parser parser = new RF2Parser(conceptFile, relationshipFile,
+        		descriptionFile,textDefinitionFile,languageFile, outputFile,iri, true);
+//        RF2Parser parser = new RF2Parser(conceptFile, relationshipFile,
+//        		null,null,null, outputFile,iri);
+        parser.parse();
+        System.out.println("Done! The process has generated a new OWL Ontology file: " + outputFile);
+    }
+}