How can read section from HL7 document

Question

I want to parse a HL7 document from XML file. So I have this XML file:

<?xml-stylesheet type="text/xsl" href="CCD.xsl"?>
<ClinicalDocument xmlns="urn:hl7-org:v3" xmlns:voc="urn:hl7-org:v3/voc" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="urn:hl7-org:v3 CDA.xsd">

    <typeId extension="POCD_HD000040" root="2.16.840.1.113883.1.3"/>
    <templateId root="2.16.840.1.113883.10.20.1"/> <!-- CCD v1.0 Templates Root -->
    <id root="db734647-fc99-424c-a864-7e3cda82e703"/>
    <code code="34133-9" codeSystem="2.16.840.1.113883.6.1" displayName="Summarization of episode note"/>
    <title>Decipher Test PHR</title>
    <effectiveTime value="20151118103315+0200"/>
    <confidentialityCode code="N" codeSystem="2.16.840.1.113883.5.25"/>
    <languageCode code="en-US"/>
    <recordTarget>
        <patientRole>
            <id extension="160785-9739" root="2.16.840.1.113883.19.5"/>
            <patient>
                <name>
                    <given>Alain</given>
                    <family>Smith</family>
                </name>
                <administrativeGenderCode code="M" codeSystem="2.16.840.1.113883.5.1"/>
                <birthTime value="19850716"/> 
            </patient>
            <providerOrganization>
                <id root="2.16.840.1.113883.19.5"/>
                <name>Good Health Clinic</name>
            </providerOrganization>
        </patientRole>
    </recordTarget>
    <author>
        <time value="20151117114330+0200"/>
        <assignedAuthor>
            <id root="20cf14fb-b65c-4c8c-a54d-b0cca834c18c"/>
            <assignedPerson>
                <name>
                    <prefix>Dr.</prefix>
                    <given>Robert</given>
                    <family>Dolin</family>
                </name>
            </assignedPerson>
            <representedOrganization>
                <id root="2.16.840.1.113883.19.5"/>
                <name>Good Health Clinic</name>
            </representedOrganization>
        </assignedAuthor>
    </author>
    <informant>
        <assignedEntity>
            <id nullFlavor="NI"/>
            <representedOrganization>
                <id root="2.16.840.1.113883.19.5"/>
                <name>Good Health Clinic</name>
            </representedOrganization>
        </assignedEntity>
    </informant>
    <custodian>
        <assignedCustodian>
            <representedCustodianOrganization>
                <id root="2.16.840.1.113883.19.5"/>
                <name>Good Health Clinic</name>
            </representedCustodianOrganization>
        </assignedCustodian>
    </custodian>
    <legalAuthenticator>
        <time value="20151117114330+0200"/>
        <signatureCode code="S"/>
        <assignedEntity>
            <id nullFlavor="NI"/>
            <representedOrganization>
                <id root="2.16.840.1.113883.19.5"/>
                <name>Good Health Clinic</name>
            </representedOrganization>
        </assignedEntity>
    </legalAuthenticator>
    <participant typeCode="IND">
        <associatedEntity classCode="GUAR">
            <id root="4ff51570-83a9-47b7-91f2-93ba30373141"/>
            <addr>
                <streetAddressLine/>
                <city/>
                <state/>
                <postalCode/>
            </addr>
            <telecom value="(tel:) "/>
            <associatedPerson>
                <name>
                    <given>Alfred</given>
                    <family>Smith</family>
                </name>
            </associatedPerson>
        </associatedEntity>
    </participant>
    <participant typeCode="IND">
        <associatedEntity classCode="NOK">
            <id root="4ac71514-6a10-4164-9715-f8d96af48e6d"/>
            <code code="66839005" codeSystem="2.16.840.1.113883.6.96" displayName="Father"/>
            <telecom value="(tel:) "/>
            <associatedPerson>
                <name>
                    <given>Alfred</given>
                    <family>Smith</family>
                </name>
            </associatedPerson>
        </associatedEntity>
    </participant>
    <documentationOf>
        <serviceEvent classCode="PCPR">
            <effectiveTime>
                <low value="20151117114330+0200"/>
                <high value="20151118103315+0200"/>
            </effectiveTime>
            <performer typeCode="PRF">
                <functionCode code="PCP" codeSystem="2.16.840.1.113883.5.88"/>
                <time>
                    <low value="1990"/>
                    <high value="20000407"/>
                </time>
                <assignedEntity>
                    <id root="20cf14fb-b65c-4c8c-a54d-b0cca834c18c"/>
                    <assignedPerson>
                        <name>
                            <prefix>Dr.</prefix>
                            <given>Robert</given>
                            <family>Dolin</family>
                        </name>
                    </assignedPerson>
                    <representedOrganization>
                        <id root="2.16.840.1.113883.19.5"/>
                        <name>Good Health Clinic</name>
                    </representedOrganization>
                </assignedEntity>
            </performer>
        </serviceEvent>
    </documentationOf>
    <!-- 
********************************************************
CDA Body
********************************************************
-->
    <component>
        <structuredBody>

            <!-- 
********************************************************
Problems section
********************************************************
-->
            <component>
                <section>
                    <templateId root="2.16.840.1.113883.10.20.1.11"/> <!-- Problem section template -->
                    <code code="11450-4" codeSystem="2.16.840.1.113883.6.1"/> 
                    <title>Problems</title> 
                    <text>
                        <table border="1" width="100%">
                            <thead>
                                <tr>
                                    <th>Condition</th>
                                    <th>Effective Dates</th>
                                    <th>Condition Status</th>
                                </tr>
                            </thead>
                            <tbody>
                                <tr>
                                    <td>Epilepsy</td>
                                    <td>Mar 22, 2005</td>
                                    <td>Active</td>
                                </tr>
                                <tr>
                                    <td>Pneumonia</td>
                                    <td>Jan 15, 2008</td>
                                    <td>Resolved</td>
                                </tr>
                                <tr>
                                    <td>Fracture of upper limb</td>
                                    <td>Jun 30, 2010</td>
                                    <td>Resolved</td>
                                </tr>
                            <tr id="c9d7faff-2992-41c9-baab-fb9849d9dd45">
                  <td>Respiratorytractinfection</td>
                  <td>Jun 15, 2014</td>
                  <td>Active</td>
                </tr>
              <tr id="e882a61d-da51-44e9-8d80-61ead72baa01">
                  <td>Respiratorytractinfection</td>
                  <td>Jun 15, 2014</td>
                  <td>Active</td>
                </tr>
              <tr id="58fce790-a4a7-4830-93ea-14b7d59095dc">
                  <td>Respiratorytractinfection</td>
                  <td>Jun 15, 2014</td>
                  <td>Active</td>
                </tr>
              <tr id="a0fd1b36-9668-4f94-a12e-d0ada0373d74">
                  <td>Respiratorytractinfection</td>
                  <td>Jun 15, 2014</td>
                  <td>Active</td>
                </tr>
              <tr id="a56940e3-e420-4e6b-87eb-b2a5d3b20537">
                  <td>Respiratorytractinfection</td>
                  <td>Jun 15, 2014</td>
                  <td>Active</td>
                </tr>
              <tr id="d98d7f49-d0df-49b7-a640-3c3fbabdc8c8">
                  <td>Respiratorytractinfection</td>
                  <td>Jun 15, 2014</td>
                  <td>Active</td>
                </tr>
              <tr id="04a91966-3d2d-44e0-9608-db612a71ec37">
                  <td>Respiratorytractinfection</td>
                  <td>Jun 15, 2014</td>
                  <td>Active</td>
                </tr>
              <tr id="71a7ecc2-5898-4623-b08f-ac9f57d10f8e">
                  <td>Respiratorytractinfection</td>
                  <td>Jun 15, 2014</td>
                  <td>Active</td>
                </tr>
              <tr id="d052662c-7c44-4904-93cf-2750d3c0985a">
                  <td>Respiratorytractinfection</td>
                  <td>Jun 15, 2014</td>
                  <td>Active</td>
                </tr>
              </tbody>
                        </table>
                    </text>
                    <entry typeCode="DRIV">
                        <act classCode="ACT" moodCode="EVN">
                            <templateId root="2.16.840.1.113883.10.20.1.27"/> <!-- Problem act template -->
                            <id root="6a2fa88d-4174-4909-aece-db44b60a3abb"/>
                            <code nullFlavor="NA"/>
                            <entryRelationship typeCode="SUBJ">
                                <observation classCode="OBS" moodCode="EVN">
                                    <templateId root="2.16.840.1.113883.10.20.1.28"/> <!-- Problem observation template -->
                                    <id root="d11275e7-67ae-11db-bd13-0800200c9a66"/>
                                    <code code="ASSERTION" codeSystem="2.16.840.1.113883.5.4"/>                 
                                    <statusCode code="completed"/> 
                                    <effectiveTime>
                                        <low value="20050322"/>
                                    </effectiveTime>
                                    <value code="84757009" codeSystem="2.16.840.1.113883.6.96" displayName="Epilepsy" xsi:type="CD"/>
                                    <entryRelationship typeCode="REFR">
                                        <observation classCode="OBS" moodCode="EVN">
                                            <templateId root="2.16.840.1.113883.10.20.1.50"/> <!-- Problem status observation template -->
                                            <code code="33999-4" codeSystem="2.16.840.1.113883.6.1" displayName="Status"/>
                                            <statusCode code="completed"/>
                                            <value code="55561003" codeSystem="2.16.840.1.113883.6.96" displayName="Active" xsi:type="CE"/>
                                        </observation>
                                    </entryRelationship>
                                </observation>
                            </entryRelationship>
                        </act>  
                    </entry>

        </section>
            </component>

        </structuredBody>
    </component>
</ClinicalDocument>

Now, I have find Everest framework to parse it (but I don't know if this framework is the good framework to do this or not). So I have this code to parse the file:

using (XmlStateReader xr = new XmlStateReader(XmlReader.Create(@"C:\Users\michele.castriotta\Desktop\document.xml")))
    {
    var fmtr = new XmlIts1Formatter();
    fmtr.ValidateConformance = false;
    fmtr.GraphAides.Add(new ClinicalDocumentDatatypeFormatter());
    var parseResult = fmtr.Parse(xr, typeof(ClinicalDocument));
    // There is a variable called structure which will contain your
    var cda = parseResult.Structure as ClinicalDocument;

    }

This code works but I don't know how can I find for example problem section or anothe section from the ClinicalDocument Onject

Did you check this http://stackoverflow.com/q/31033112/5089204? Your sample could be from there. Well, as this Everes Framework is specialised for this purpose it should be worth to try it. But you question is far to unspecific to give you an answer... — Shnugo, Nov 27 '15 at 11:16
Ok I don't far to unspecific Everest Framework but I'm not able to access at the information of some section — bircastri, Nov 27 '15 at 11:41
I don't know this specific framework. There is a lot of documentation online, just search for Everest and ClinicalDocument... Secondly you might set a stop mark in your code and explore the structure and content of the variable `cda` with shift+F9. — Shnugo, Nov 27 '15 at 11:48

score 1 · Answer 1 · answered Nov 30 '15 at 08:23

Why not parsing Xpaht directly? I am not aware of Everest, but for me using XPath is simpler, more efficient and platform/programming language neutral.

Two sample queries should be: - Get all sections text:

//hl7:section/hl7:text/text()

Get problems section:

//hl7:section[hl7:code[@code='11450-4' and @codeSystem='2.16.840.1.113883.6.1']]

How can read section from HL7 document

1 Answers1