XML2RDF Transformation of CDA Patient Documents

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XML2RDF Transformation


import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.httpclient.methods.PostMethod;
import org.apache.commons.httpclient.params.HttpMethodParams;

public class XML2RDFJavaClient { 
    public static final String PROD_URL = "http://rhizomik.net/redefer-services/xml2rdf";

    public static final String XML_URL = "Your XML URL";
	
    public static void main( String[] args ) {
        try {
            HttpClient client = new HttpClient();
             
            PostMethod method = new PostMethod(PROD_URL);
            
            // Configure the form parameters
            method.addParameter("xml",XML_URL);

            // Execute the POST method
            int statusCode = client.executeMethod(method);
            
            if( statusCode != -1 ) {
                String contents = method.getResponseBodyAsString();
                method.releaseConnection();
                System.out.println(contents);
 
            }
        }
        catch( Exception e ){
            e.printStackTrace();
        }
    }
}


RDF Example


<rdf:RDF
    xmlns:xl="http://rhizomik.net/ontologies/2007/11/xl-2003-12-31.owl#"
    xmlns:xlink="http://rhizomik.net/ontologies/2007/11/xlink-2003-12-31.owl#"
    xmlns:usfr-pte="http://rhizomik.net/ontologies/2008/07/usfr-pte-2005-02-28.owl#"
    xmlns:pfif="http://rhizomik.net/ontologies/2010/03/pfif-1.2.owl#"
    xmlns:usfr-mda="http://rhizomik.net/ontologies/2008/07/usfr-mda-2004-08-15.owl#"
    xmlns:j.0="urn:hl7-org:v3#"
    xmlns:us-types="http://rhizomik.net/ontologies/2008/07/us-types-2008-03-31.owl#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:xbrli="http://rhizomik.net/ontologies/2007/11/xbrl-instance-2003-12-31.owl#"
    xmlns:adbe20080530="http://rhizomik.net/html/ontologies/bizontos/xbrl-edgar/adbe-20080530.owl#"
    xmlns:mpeg7="http://rhizomik.net/ontologies/2005/03/Mpeg7-2001.owl#"
    xmlns:link="http://rhizomik.net/ontologies/2007/11/xbrl-linkbase-2003-12-31.owl#"
    xmlns:us-gaap-ci="http://rhizomik.net/ontologies/2008/07/us-gaap-ci-2005-02-28.owl#"
    xmlns:usfr-ptr="http://rhizomik.net/ontologies/2008/07/usfr-ptr-2005-02-28.owl#"
    xmlns:adbe20080829="http://rhizomik.net/html/ontologies/bizontos/xbrl-edgar/adbe-20080829.owl#"
    xmlns:xbrldt="http://rhizomik.net/ontologies/2008/07/xbrldt-2005.owl#">
  <rdf:Description rdf:about="https://github.com/projectcypress/test-deck/blob/master/patients/c32/101_Selena_Roth.xml">
    <j.0:custodian rdf:parseType="Resource">
      <j.0:assignedCustodian rdf:parseType="Resource">
        <j.0:representedCustodianOrganization rdf:parseType="Resource">
          <j.0:addr rdf:parseType="Resource">
            <j.0:postalCode>01730</j.0:postalCode>
            <j.0:state>MA</j.0:state>
            <j.0:city>Bedford</j.0:city>
            <j.0:streetAddressLine>202 Burlington Rd.</j.0:streetAddressLine>
          </j.0:addr>
          <j.0:telecom rdf:parseType="Resource">
            <j.0:value>tel:+1-781-271-3000</j.0:value>
          </j.0:telecom>
          <j.0:name>Cypress</j.0:name>
          <j.0:id rdf:parseType="Resource">
          </j.0:id>
        </j.0:representedCustodianOrganization>
      </j.0:assignedCustodian>
    </j.0:custodian>
    <j.0:realmCode rdf:parseType="Resource">
      <j.0:code>US</j.0:code>
    </j.0:realmCode>
    <j.0:author rdf:parseType="Resource">
      <j.0:assignedAuthor rdf:parseType="Resource">
        <j.0:assignedPerson rdf:parseType="Resource">
          <j.0:name>Auto Generated</j.0:name>
        </j.0:assignedPerson>
        <j.0:telecom rdf:parseType="Resource">
          <j.0:value>tel:+1-781-271-3000</j.0:value>
        </j.0:telecom>
        <j.0:addr rdf:parseType="Resource">
        </j.0:addr>
        <j.0:id rdf:parseType="Resource">
        </j.0:id>
      </j.0:assignedAuthor>
      <j.0:time rdf:parseType="Resource">
        <j.0:value>20120706201850</j.0:value>
      </j.0:time>
    </j.0:author>
    <j.0:code rdf:parseType="Resource">
      <j.0:displayName>Summarization of episode note</j.0:displayName>
      <j.0:codeSystemName>LOINC</j.0:codeSystemName>
      <j.0:codeSystem>2.16.840.1.113883.6.1</j.0:codeSystem>
      <j.0:code>34133-9</j.0:code>
    </j.0:code>
    <j.0:templateId rdf:parseType="Resource">
      <j.0:root>2.16.840.1.113883.3.88.11.32.1</j.0:root>
      <j.0:assigningAuthorityName>HITSP/C32</j.0:assigningAuthorityName>
    </j.0:templateId>
    <j.0:templateId rdf:parseType="Resource">
      <j.0:root>2.16.840.1.113883.3.27.1776</j.0:root>
      <j.0:assigningAuthorityName>CDA/R2</j.0:assigningAuthorityName>
    </j.0:templateId>
    <j.0:component rdf:parseType="Resource">
      <j.0:structuredBody rdf:parseType="Resource">
        <j.0:component rdf:parseType="Resource">
          <j.0:section rdf:parseType="Resource">
            <j.0:entry rdf:parseType="Resource">
              <j.0:organizer rdf:parseType="Resource">
                <j.0:component rdf:parseType="Resource">
                  <j.0:observation rdf:parseType="Resource">
                    <j.0:classCode>OBS</j.0:classCode>
                    <j.0:moodCode>EVN</j.0:moodCode>
                    <j.0:id rdf:parseType="Resource">
                      <j.0:root>b94f0a90-a9d5-012f-03d7-000c297b3103</j.0:root>
                    </j.0:id>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.10.20.1.31</j.0:root>
                      <j.0:assigningAuthorityName>CCD</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:value>
                      <j.0:PQ>
                        <j.0:value></j.0:value>
                      </j.0:PQ>
                    </j.0:value>
                    <j.0:code rdf:parseType="Resource">
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.96</j.0:codeSystem>
                        <j.0:code>171234009</j.0:code>
                      </j.0:translation>
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.12</j.0:codeSystem>
                        <j.0:code>90935</j.0:code>
                      </j.0:translation>
                      <j.0:originalText>Nephropathy Screening</j.0:originalText>
                      <j.0:codeSystem>2.16.840.1.113883.6.1</j.0:codeSystem>
                      <j.0:code>1754-1</j.0:code>
                    </j.0:code>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>1.3.6.1.4.1.19376.1.5.3.1.4.13</j.0:root>
                      <j.0:assigningAuthorityName>IHE PCC</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:effectiveTime rdf:parseType="Resource">
                      <j.0:value>20100331040000</j.0:value>
                    </j.0:effectiveTime>
                    <j.0:statusCode rdf:parseType="Resource">
                      <j.0:code>completed</j.0:code>
                    </j.0:statusCode>
                    <j.0:text rdf:parseType="Resource">
                      <j.0:reference rdf:parseType="Resource">
                        <j.0:value>#results-desc-7</j.0:value>
                      </j.0:reference>
                    </j.0:text>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.3.88.11.83.15.1</j.0:root>
                      <j.0:assigningAuthorityName>HITSP C83</j.0:assigningAuthorityName>
                    </j.0:templateId>
                  </j.0:observation>
                </j.0:component>
                <j.0:effectiveTime rdf:parseType="Resource">
                  <j.0:value>20120706201850</j.0:value>
                </j.0:effectiveTime>
                <j.0:code rdf:parseType="Resource">
                  <j.0:nullFlavor>NA</j.0:nullFlavor>
                </j.0:code>
                <j.0:classCode>BATTERY</j.0:classCode>
                <j.0:component rdf:parseType="Resource">
                  <j.0:observation rdf:parseType="Resource">
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.10.20.1.31</j.0:root>
                      <j.0:assigningAuthorityName>CCD</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.3.88.11.83.15.1</j.0:root>
                      <j.0:assigningAuthorityName>HITSP C83</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:statusCode rdf:parseType="Resource">
                      <j.0:code>completed</j.0:code>
                    </j.0:statusCode>
                    <j.0:effectiveTime rdf:parseType="Resource">
                      <j.0:value>20100331040000</j.0:value>
                    </j.0:effectiveTime>
                    <j.0:id rdf:parseType="Resource">
                      <j.0:root>b94eef20-a9d5-012f-03d7-000c297b3103</j.0:root>
                    </j.0:id>
                    <j.0:code rdf:parseType="Resource">
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.96</j.0:codeSystem>
                        <j.0:code>113079009</j.0:code>
                      </j.0:translation>
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.12</j.0:codeSystem>
                        <j.0:code>83721</j.0:code>
                      </j.0:translation>
                      <j.0:originalText>LDL</j.0:originalText>
                      <j.0:codeSystem>2.16.840.1.113883.6.1</j.0:codeSystem>
                      <j.0:code>2089-1</j.0:code>
                    </j.0:code>
                    <j.0:classCode>OBS</j.0:classCode>
                    <j.0:moodCode>EVN</j.0:moodCode>
                    <j.0:text rdf:parseType="Resource">
                      <j.0:reference rdf:parseType="Resource">
                        <j.0:value>#results-desc-3</j.0:value>
                      </j.0:reference>
                    </j.0:text>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>1.3.6.1.4.1.19376.1.5.3.1.4.13</j.0:root>
                      <j.0:assigningAuthorityName>IHE PCC</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:value>
                      <j.0:PQ>
                        <j.0:value></j.0:value>
                      </j.0:PQ>
                    </j.0:value>
                  </j.0:observation>
                </j.0:component>
                <j.0:statusCode rdf:parseType="Resource">
                  <j.0:code>completed</j.0:code>
                </j.0:statusCode>
                <j.0:id rdf:parseType="Resource">
                  <j.0:root>b94ed830-a9d5-012f-03d7-000c297b3103</j.0:root>
                </j.0:id>
                <j.0:component rdf:parseType="Resource">
                  <j.0:observation rdf:parseType="Resource">
                    <j.0:id rdf:parseType="Resource">
                      <j.0:root>b94ee250-a9d5-012f-03d7-000c297b3103</j.0:root>
                    </j.0:id>
                    <j.0:moodCode>EVN</j.0:moodCode>
                    <j.0:statusCode rdf:parseType="Resource">
                      <j.0:code>completed</j.0:code>
                    </j.0:statusCode>
                    <j.0:effectiveTime rdf:parseType="Resource">
                      <j.0:value>20100719040000</j.0:value>
                    </j.0:effectiveTime>
                    <j.0:classCode>OBS</j.0:classCode>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.10.20.1.31</j.0:root>
                      <j.0:assigningAuthorityName>CCD</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:value>
                      <j.0:PQ>
                        <j.0:value></j.0:value>
                      </j.0:PQ>
                    </j.0:value>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>1.3.6.1.4.1.19376.1.5.3.1.4.13</j.0:root>
                      <j.0:assigningAuthorityName>IHE PCC</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:text rdf:parseType="Resource">
                      <j.0:reference rdf:parseType="Resource">
                        <j.0:value>#results-desc-1</j.0:value>
                      </j.0:reference>
                    </j.0:text>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.3.88.11.83.15.1</j.0:root>
                      <j.0:assigningAuthorityName>HITSP C83</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:code rdf:parseType="Resource">
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.96</j.0:codeSystem>
                        <j.0:code>43396009</j.0:code>
                      </j.0:translation>
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.12</j.0:codeSystem>
                        <j.0:code>83036</j.0:code>
                      </j.0:translation>
                      <j.0:originalText>HbA1c test</j.0:originalText>
                      <j.0:codeSystem>2.16.840.1.113883.6.1</j.0:codeSystem>
                      <j.0:code>4548-4</j.0:code>
                    </j.0:code>
                  </j.0:observation>
                </j.0:component>
                <j.0:component rdf:parseType="Resource">
                  <j.0:procedure rdf:parseType="Resource">
                    <j.0:effectiveTime rdf:parseType="Resource">
                      <j.0:nullFlavor>UNK</j.0:nullFlavor>
                    </j.0:effectiveTime>
                    <j.0:statusCode rdf:parseType="Resource">
                      <j.0:code>completed</j.0:code>
                    </j.0:statusCode>
                    <j.0:id rdf:parseType="Resource">
                      <j.0:root>b94eda20-a9d5-012f-03d7-000c297b3103</j.0:root>
                    </j.0:id>
                    <j.0:text rdf:parseType="Resource">
                      <j.0:reference rdf:parseType="Resource">
                        <j.0:value>Unknown</j.0:value>
                      </j.0:reference>
                    </j.0:text>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.3.88.11.83.17</j.0:root>
                      <j.0:assigningAuthorityName>HITSP C83</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.10.20.1.29</j.0:root>
                      <j.0:assigningAuthorityName>CCD</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:classCode>PROC</j.0:classCode>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>1.3.6.1.4.1.19376.1.5.3.1.4.19</j.0:root>
                      <j.0:assigningAuthorityName>IHE PCC</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:moodCode>EVN</j.0:moodCode>
                    <j.0:code rdf:parseType="Resource">
                      <j.0:originalText rdf:parseType="Resource">
                        <j.0:reference rdf:parseType="Resource">
                          <j.0:value>Unknown</j.0:value>
                        </j.0:reference>
                      </j.0:originalText>
                      <j.0:nullFlavor>UNK</j.0:nullFlavor>
                    </j.0:code>
                  </j.0:procedure>
                </j.0:component>
                <j.0:component rdf:parseType="Resource">
                  <j.0:observation rdf:parseType="Resource">
                    <j.0:effectiveTime rdf:parseType="Resource">
                      <j.0:value>20100331040000</j.0:value>
                    </j.0:effectiveTime>
                    <j.0:classCode>OBS</j.0:classCode>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.3.88.11.83.15.1</j.0:root>
                      <j.0:assigningAuthorityName>HITSP C83</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:statusCode rdf:parseType="Resource">
                      <j.0:code>completed</j.0:code>
                    </j.0:statusCode>
                    <j.0:code rdf:parseType="Resource">
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.96</j.0:codeSystem>
                        <j.0:code>28036006</j.0:code>
                      </j.0:translation>
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.12</j.0:codeSystem>
                        <j.0:code>83701</j.0:code>
                      </j.0:translation>
                      <j.0:originalText>High Density Lipoprotein (HDL)</j.0:originalText>
                      <j.0:codeSystem>2.16.840.1.113883.6.1</j.0:codeSystem>
                      <j.0:code>14646-4</j.0:code>
                    </j.0:code>
                    <j.0:text rdf:parseType="Resource">
                      <j.0:reference rdf:parseType="Resource">
                        <j.0:value>#results-desc-6</j.0:value>
                      </j.0:reference>
                    </j.0:text>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>1.3.6.1.4.1.19376.1.5.3.1.4.13</j.0:root>
                      <j.0:assigningAuthorityName>IHE PCC</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:id rdf:parseType="Resource">
                      <j.0:root>b94f04a0-a9d5-012f-03d7-000c297b3103</j.0:root>
                    </j.0:id>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.10.20.1.31</j.0:root>
                      <j.0:assigningAuthorityName>CCD</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:moodCode>EVN</j.0:moodCode>
                    <j.0:value>
                      <j.0:PQ>
                        <j.0:value></j.0:value>
                      </j.0:PQ>
                    </j.0:value>
                  </j.0:observation>
                </j.0:component>
                <j.0:templateId rdf:parseType="Resource">
                  <j.0:root>2.16.840.1.113883.10.20.1.32</j.0:root>
                </j.0:templateId>
                <j.0:moodCode>EVN</j.0:moodCode>
                <j.0:component rdf:parseType="Resource">
                  <j.0:observation rdf:parseType="Resource">
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>1.3.6.1.4.1.19376.1.5.3.1.4.13</j.0:root>
                      <j.0:assigningAuthorityName>IHE PCC</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:statusCode rdf:parseType="Resource">
                      <j.0:code>completed</j.0:code>
                    </j.0:statusCode>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.3.88.11.83.15.1</j.0:root>
                      <j.0:assigningAuthorityName>HITSP C83</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:moodCode>EVN</j.0:moodCode>
                    <j.0:templateId rdf:parseType="Resource">
                      <j.0:root>2.16.840.1.113883.10.20.1.31</j.0:root>
                      <j.0:assigningAuthorityName>CCD</j.0:assigningAuthorityName>
                    </j.0:templateId>
                    <j.0:effectiveTime rdf:parseType="Resource">
                      <j.0:value>20101207050000</j.0:value>
                    </j.0:effectiveTime>
                    <j.0:classCode>OBS</j.0:classCode>
                    <j.0:code rdf:parseType="Resource">
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.96</j.0:codeSystem>
                        <j.0:code>43396009</j.0:code>
                      </j.0:translation>
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.12</j.0:codeSystem>
                        <j.0:code>83036</j.0:code>
                      </j.0:translation>
                      <j.0:originalText>HbA1c test</j.0:originalText>
                      <j.0:codeSystem>2.16.840.1.113883.6.1</j.0:codeSystem>
                      <j.0:code>4548-4</j.0:code>
                    </j.0:code>
                    <j.0:value>
                      <j.0:PQ>
                        <j.0:value></j.0:value>
                      </j.0:PQ>
                    </j.0:value>
                    <j.0:text rdf:parseType="Resource">
                      <j.0:reference rdf:parseType="Resource">
                        <j.0:value>#results-desc-0</j.0:value>
                      </j.0:reference>
                    </j.0:text>
                    <j.0:id rdf:parseType="Resource">
                      <j.0:root>b94edb20-a9d5-012f-03d7-000c297b3103</j.0:root>
                    </j.0:id>
                  </j.0:observation>
                </j.0:component>
                <j.0:component rdf:parseType="Resource">
                  <j.0:observation rdf:parseType="Resource">
                    <j.0:moodCode>EVN</j.0:moodCode>
                    <j.0:code rdf:parseType="Resource">
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.96</j.0:codeSystem>
                        <j.0:code>121868005</j.0:code>
                      </j.0:translation>
                      <j.0:translation rdf:parseType="Resource">
                        <j.0:codeSystem>2.16.840.1.113883.6.12</j.0:codeSystem>
                        <j.0:code>82465</j.0:code>
                      </j.0:translation>
                      <j.0:originalText>Total Cholesterol</j.0:originalText>
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                      <j.0:i>C0374194:Ophthalmological services: medical examination and evaluation, with initiation or continuation of diagnostic and treatment program; intermediate, established patient;</j.0:i>
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                      <j.0:i>C0428883:Diastolic blood pressure;</j.0:i>
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