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I am trying to parse some clinical information from XML file that is standardized to HL7 V3 CDA standard .
Xml file :
<?xml version="1.0" encoding="UTF-8"?><?xml-stylesheet href="http://www.accessdata.fda.gov/spl/stylesheet/spl.xsl" type="text/xsl"?>
<document xmlns="urn:hl7-org:v3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="urn:hl7-org:v3 http://www.accessdata.fda.gov/spl/schema/spl.xsd">
<id root="9bcbe9e4-a541-4ee7-856d-1aacf7f7298f"/>
<code code="34391-3" codeSystem="2.16.840.1.113883.6.1" displayName="HUMAN PRESCRIPTION DRUG LABEL"/>
<title>Amlodipine Besylate 5 mg</title>
<effectiveTime value="20101104"/>
<setId root="9abf41f1-66f9-4be4-a6d7-6c9aa0d5d387"/>
<versionNumber value="448"/>
<author>
<time/>
<assignedEntity>
<representedOrganization>
<id extension="831276758" root="1.3.6.1.4.1.519.1"/>
<name>Lake Erie Medical DBA Quality Care Products LLC</name>
<assignedEntity>
<assignedOrganization>
<assignedEntity>
<assignedOrganization>
<id extension="831276758" root="1.3.6.1.4.1.519.1"/>
<name>Lake Erie Medical DBA Quality Care Products LLC</name>
</assignedOrganization>
<performance>
<actDefinition>
<code code="C73607" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="relabel"/>
</actDefinition>
</performance>
</assignedEntity>
<assignedEntity>
<assignedOrganization>
<id extension="915628612" root="1.3.6.1.4.1.519.1"/>
<name>Alkem Laboratories Limited</name>
</assignedOrganization>
<performance>
<actDefinition>
<code code="C43360" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="manufacture"/>
</actDefinition>
</performance>
</assignedEntity>
</assignedOrganization>
</assignedEntity>
</representedOrganization>
</assignedEntity>
</author>
<component>
<structuredBody>
<component>
<section>
<id root="5e90ce61-5d11-4acf-8a5b-f99cb10b60f4"/>
<code code="48780-1" codeSystem="2.16.840.1.113883.6.1" displayName="SPL listing data elements section"/>
<effectiveTime value="20101103"/>
<subject>
<manufacturedProduct>
<manufacturedProduct>
<code code="35356-059" codeSystem="2.16.840.1.113883.6.69"/>
<name>Amlodipine Besylate <suffix/>
</name>
<formCode code="C42998" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="TABLET"/>
<asEntityWithGeneric>
<genericMedicine>
<name>Amlodipine Besylate </name>
</genericMedicine>
</asEntityWithGeneric>
<asEquivalentEntity classCode="EQUIV">
<code code="C64637" codeSystem="2.16.840.1.113883.3.26.1.1"/>
<definingMaterialKind>
<code code="51991-667" codeSystem="2.16.840.1.113883.6.69"/>
</definingMaterialKind>
</asEquivalentEntity>
<ingredient classCode="ACTIB">
<quantity>
<numerator value="5" unit="mg"/>
<denominator value="1" unit="1"/>
</quantity>
<ingredientSubstance>
<code code="864V2Q084H" codeSystem="2.16.840.1.113883.4.9"/>
<name>AMLODIPINE BESYLATE</name>
<activeMoiety>
<activeMoiety>
<code code="1J444QC288" codeSystem="2.16.840.1.113883.4.9"/>
<name>AMLODIPINE</name>
</activeMoiety>
</activeMoiety>
</ingredientSubstance>
</ingredient>
<ingredient classCode="IACT">
<ingredientSubstance>
<code code="OP1R32D61U" codeSystem="2.16.840.1.113883.4.9"/>
<name>CELLULOSE, MICROCRYSTALLINE</name>
</ingredientSubstance>
</ingredient>
<ingredient classCode="IACT">
<ingredientSubstance>
<code code="L11K75P92J" codeSystem="2.16.840.1.113883.4.9"/>
<name>ANHYDROUS DIBASIC CALCIUM PHOSPHATE</name>
</ingredientSubstance>
</ingredient>
<ingredient classCode="IACT">
<ingredientSubstance>
<code code="5856J3G2A2" codeSystem="2.16.840.1.113883.4.9"/>
<name>SODIUM STARCH GLYCOLATE TYPE A POTATO</name>
</ingredientSubstance>
</ingredient>
<ingredient classCode="IACT">
<ingredientSubstance>
<code code="ETJ7Z6XBU4" codeSystem="2.16.840.1.113883.4.9"/>
<name>SILICON DIOXIDE</name>
</ingredientSubstance>
</ingredient>
<ingredient classCode="IACT">
<ingredientSubstance>
<code code="70097M6I30" codeSystem="2.16.840.1.113883.4.9"/>
<name>MAGNESIUM STEARATE</name>
</ingredientSubstance>
</ingredient>
<asContent>
<quantity>
<numerator value="90" unit="1">
<translation code="C48477" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="BOTTLE"/>
</numerator>
<denominator value="1"/>
</quantity>
<containerPackagedProduct>
<code code="35356-059-90" codeSystem="2.16.840.1.113883.6.69"/>
<formCode code="C43173" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="BOTTLE, PLASTIC"/>
</containerPackagedProduct>
</asContent>
</manufacturedProduct>
<subjectOf>
<marketingAct>
<code code="C53292" codeSystem="2.16.840.1.113883.3.26.1.1"/>
<statusCode code="active"/>
<effectiveTime>
<low value="20101104"/>
</effectiveTime>
</marketingAct>
</subjectOf>
<subjectOf>
<approval>
<id extension="ANDA078925" root="2.16.840.1.113883.3.150"/>
<code code="C73584" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="ANDA"/>
<author>
<territorialAuthority>
<territory>
<code code="USA" codeSystem="2.16.840.1.113883.5.28"/>
</territory>
</territorialAuthority>
</author>
</approval>
</subjectOf>
<subjectOf>
<characteristic classCode="OBS">
<code code="SPLCOLOR" codeSystem="2.16.840.1.113883.1.11.19255"/>
<value code="C48325" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="white" xsi:type="CE">
<originalText>off whit</originalText>
</value>
</characteristic>
</subjectOf>
<subjectOf>
<characteristic classCode="OBS">
<code code="SPLSCORE" codeSystem="2.16.840.1.113883.1.11.19255"/>
<value value="1" xsi:type="INT"/>
</characteristic>
</subjectOf>
<subjectOf>
<characteristic classCode="OBS">
<code code="SPLSHAPE" codeSystem="2.16.840.1.113883.1.11.19255"/>
<value code="C48348" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="ROUND" xsi:type="CE">
<originalText>flat faced beveled edge</originalText>
</value>
</characteristic>
</subjectOf>
<subjectOf>
<characteristic classCode="OBS">
<code code="SPLIMPRINT" codeSystem="2.16.840.1.113883.1.11.19255"/>
<value xsi:type="ST">210</value>
</characteristic>
</subjectOf>
<subjectOf>
<characteristic classCode="OBS">
<code code="SPLSIZE" codeSystem="2.16.840.1.113883.1.11.19255"/>
<value unit="mm" value="8" xsi:type="PQ"/>
</characteristic>
</subjectOf>
<consumedIn>
<substanceAdministration>
<routeCode code="C38288" codeSystem="2.16.840.1.113883.3.26.1.1" displayName="ORAL"/>
</substanceAdministration>
</consumedIn>
</manufacturedProduct>
</subject>
</section>
</component>
<component>
<section>
<id root="7a474776-2650-40ff-9a8e-22710ed363e4"/>
<code code="34089-3" codeSystem="2.16.840.1.113883.6.1" displayName="DESCRIPTION SECTION"/>
<text>
<linkHtml href=""/>11 DESCRIPTION<br/>Amlodipine besylate is the besylate salt of amlodipine, a long-acting calcium
channel blocker.<br/>Amlodipine besylate is chemically described as
3-Ethyl-5-methyl(±)-2- [(2-aminoethoxy)methyl]-4-(2-chlorophenyl)-1,4-dihydro-6-
methyl-3,5-pyridinedicarboxylate, monobenzenesulphonate. Its empirical formula
is C<sub>20</sub>H<sub>25</sub>ClN<sub>2</sub>O<sub>5</sub>•C<sub>6</sub>H<sub>6</sub>O<sub>3</sub>S, and its structural formula is<br/>
<br/>.<br/>
</text>
<effectiveTime value="20101104"/>
</section>
</component>
<component>
<section>
<id root="82d89368-0995-45fd-85a1-e8cdc0edab97"/>
<code code="34090-1" codeSystem="2.16.840.1.113883.6.1" displayName="CLINICAL PHARMACOLOGY SECTION"/>
<text>
<linkHtml href=""/>12 CLINICAL PHARMACOLOGY<br/>
<linkHtml href=""/>12.1 Mechanism of Action<br/>Amlodipine is a dihydropyridine calcium antagonist (calcium ion antagonist or
slow-channel blocker)
<br/>
<linkHtml href=""/>
<linkHtml href=""/>
<br/>
<linkHtml href=""/>12.2 Pharmacodynamics<br/>
<br/>
<linkHtml href=""/>
<linkHtml href=""/>
<br/>
<linkHtml href=""/>12.3 .<br/>
<br/>
<linkHtml href=""/>12.4 Pediatric Patients<br/>Sixty-two hypertensive patients aged 6 to 17 years received doses of amlodipine
between 1.25 mg and 20 mg. Weight-adjusted clearance and volume of distribution
were similar to values in adults.<linkHtml href=""/>
<linkHtml href=""/>
<br/>
</text>
<effectiveTime value="20101104"/>
</section>
</component>
<component>
<section>
<id root="09519e8a-96a2-405a-bae4-e9a4857c7d43"/>
<code code="34067-9" codeSystem="2.16.840.1.113883.6.1" displayName="INDICATIONS & USAGE SECTION"/>
<text>
<linkHtml href="#section-"/>
<linkHtml href="#section-"/>
<linkHtml href="#section-"/>
<linkHtml href="#section-"/>
<linkHtml href="#section-"/>
<linkHtml href=""/>
<br/>
<linkHtml href=""/>
<linkHtml href=""/>
<linkHtml href=""/>
<linkHtml href=""/>agents.<linkHtml href=""/>
<linkHtml href=""/>
<linkHtml href=""/>1.2 Coronary Artery Disease (CAD)<br/>
<content styleCode="underline">Chronic Stable Angina</content>
<br/>Amlodipine besylate tablets are
indicated for the symptomatic treatment of chronic stable angina. Amlodipine
besylate tablets may be used alone or in combination with other antianginal
agents.<br/>
<br/>
<content styleCode="underline">Vasospastic Angina (Prinzmetal's or Variant
Angina)</content>
<br/>Amlodipine besylate tablets are indicated for the treatment
of confirmed or suspected vasospastic angina. Amlodipine besylate tablets may be
used as monotherapy or in combination with other antianginal
agents.<br/>
<br/>
<content styleCode="underline">Angiographically Documented CAD</content>
<br/>e<br/>
<content styleCode="underline"/>
<br/>
<br/>
</text>
<effectiveTime value="20101104"/>
</section>
</component>
<component>
<section>
<id root="82dcdac1-1a49-4c95-b33d-593a0d7588ae"/>
<code code="34070-3" codeSystem="2.16.840.1.113883.6.1" displayName="CONTRAINDICATIONS SECTION"/>
<text>
<linkHtml href=""/>4 CONTRAINDICATIONS<br/>Amlodipine besylate
tablets are contraindicated in patients with known sensitivity to amlodipine.<linkHtml href=""/>
<linkHtml href=""/>
</text>
<effectiveTime value="20101104"/>
</section>
</component>
<component>
<section>
<id root="d30aa4d2-e468-4ced-9774-7cacb077bbff"/>
<code code="34084-4" codeSystem="2.16.840.1.113883.6.1" displayName="ADVERSE REACTIONS SECTION"/>
<text>
<linkHtml href=""/>6 ADVERSE REACTIONS<linkHtml href=""/>
<linkHtml href=""/>
<linkHtml href=""/>6.1
are headache and edema.</text>
<effectiveTime value="20101104"/>
</section>
</component>
<component>
<section>
<id root="1d54e787-afa3-4931-b9e7-bc3bb021ef15"/>
<code code="34088-5" codeSystem="2.16.840.1.113883.6.1" displayName="OVERDOSAGE SECTION"/>
<text>
<linkHtml href=""/>10 OVERDOSAGE<br/>Overdosage might be expected to cause excessive peripheral vasodilation with
marked hypotension and possibly a reflex tachycardia. In humans, experience with
intentional overdosage of amlodipine is limited.<br/>
<sup>2 </sup>basis) caused a marked peripheral vasodilation and
hypotension.<br/>
<br/>If.<linkHtml href=""/>
<linkHtml href=""/>
<br/>
</text>
<effectiveTime value="20101104"/>
</section>
</component>
<component>
<section>
<id root="706986ac-49d5-4b07-a2b0-d5f75ef311bb"/>
<code code="34068-7" codeSystem="2.16.840.1.113883.6.1" displayName="DOSAGE & ADMINISTRATION SECTION"/>
<text>
<linkHtml href="#section-"/>
<linkHtml href=""/>
<linkHtml href=""/>
<linkHtml href=""/>
<linkHtml href=""/>2.1 Adults<br/>
<content styleCode="italics">[see <linkHtml href="#Section_6">Adverse Reactions (6)</linkHtml>].</content>
<br/>
<content styleCode="italics"/>
<br/>The recommended dose range for patients with
coronary artery disease is 5–10 mg once daily. In clinical studies, the majority
of patients required 10 mg <content styleCode="italics">[see <linkHtml href="#Section_14.4">Clinical Studies (14.4)</linkHtml>]</content>. <br/>
<linkHtml href=""/>
<linkHtml href=""/>
<linkHtml href=""/>2.2 Children<br/>The effective antihypertensive
oral dose in pediatric patients ages 6–17 years is 2.5 mg to 5 mg once daily.
Doses in excess of 5 mg daily have not been studied in pediatric patients <content styleCode="italics">[see <linkHtml href="#Section_12.4">Clinical Pharmacology (12.4)</linkHtml>, <linkHtml href="#Section_14.1">Clinical Studies (14.1)</linkHtml>]</content>.</text>
<effectiveTime value="20101104"/>
</section>
</component>
<component>
<section>
<id root="39f80cec-5fea-490c-a8e9-e4acf96649a4"/>
<code code="34069-5" codeSystem="2.16.840.1.113883.6.1" displayName="HOW SUPPLIED SECTION"/>
<text>
<linkHtml href=""/>16 HOW SUPPLIED/STORAGE AND HANDLING<br/>
<linkHtml href=""/><linkHtml href=""/>
<linkHtml href=""/>
<br/>
<br/>
<linkHtml href=""/>
of 90<linkHtml href=""/>
<linkHtml href=""/>
<br/>
<br/>
<linkHtml href=""/>16.3 10 mg Tablets<br/>Amlodipine besylate
tablets 10 mg (amlodipine besylate equivalent to 10 mg of amlodipine per tablet)
are white to off white, round, flat-faced, beveled edge tablets ‘209’ debossed
on one side and plain on the other side and supplied as follows:<br/>NDC
51991-668-90 Bottle of 90<br/>
<br/>
<br/>
</text>
<effectiveTime value="20101104"/>
</section>
</component>
<component>
<section>
<id root="3211934b-8588-4bca-bc0d-16d89c2152a1"/>
<code code="42230-3" codeSystem="2.16.840.1.113883.6.1" displayName="SPL PATIENT PACKAGE INSERT SECTION"/>
<text>
<linkHtml href=""/>PATIENT PACKAGE INSERT<br/>
<content styleCode="bold">
<content styleCode="bold">AMLODIPINE BESYLATE TABLETS 2.5 mg, 5 mg, and
10 mg</content>
</content>
<br/>
<br/>
<content styleCode="bold">What is amlodipine besylate?</content>
<br/>
<br/>
<content styleCode="bold">High Blood Pressure (hypertension)</content>
<br/>
<br/>
<content styleCode="bold">Angina</content>
<br/>Angina is a pain or discomfort that keeps
coming back when part of your heart does not get enough blood. Angina feels like
a pressing or squeezing pain, usually in your chest under the breastbone.
Sometimes you can feel it in your shoulders, arms, neck, jaws, or back.
Amlodipine besylate <content styleCode="bold"/>can relieve this pain.<br/>
<br/>
<content styleCode="bold">Who should not use amlodipine besylate?</content>
<br/>Do not use
amlodipine besylate if you are allergic to amlodipine (the active ingredient in
amlodipine besylate tablets), or to the inactive ingredients. Your doctor or
pharmacist can give you a list of these ingredients.<br/>
<br/>
<content styleCode="bold">What should I tell my doctor before taking amlodipine besylate?
</content>
<br/>Tell your doctor about any prescription and non-prescription
medicines you are taking, including natural or herbal remedies.<br/>Tell your
doctor if you:
<list listType="unordered" ID="ie2a63721-85e3-4273-8fd9-48d010179dd1">
<item>ever had heart disease</item>
<item>ever had liver problems</item>
<item>are pregnant, or plan to become pregnant. Your doctor will decide if
amlodipine besylate is the best treatment for you.</item>
<item>are breast-feeding. Do not breast-feed while taking amlodipine besylate. You
can stop breast-feeding or take a different medicine.</item>
</list>
<br/>
<content styleCode="bold">How should I take amlodipine besylate?</content>
<list listType="unordered" ID="i1c95c31f-953d-4661-8c5a-317bbc09c96a">
<item></item>
<item>It may be easier to take your dose if you do it at the same time every day,
such as with breakfast or dinner, or at bedtime. Do not take more than one dose
of amlodipine besylate at a time.</item>
<item>If you miss a dose, take it as soon as you remember. Do not take amlodipine
besylate if it has been more than 12 hours since you missed your last dose. Wait
and take the next dose at your regular time.</item>
<item>
<content styleCode="bold">Other medicines:</content> You can use nitroglycerin and
amlodipine besylate together. If you take nitroglycerin for angina, don't stop
taking it while you are taking amlodipine besylate.</item>
<item>While you are taking amlodipine besylate, do not stop taking your other
prescription medicines, including any other blood pressure medicines, without
talking to your doctor.</item>
<item>If you took too much amlodipine besylate, call your doctor or Poison Control
Center, or go to the nearest hospital emergency room right away.</item>
</list>
<br/>
<content styleCode="bold">What should I avoid while taking amlodipine besylate?</content>
<br/>
<list listType="unordered" ID="i7c271fb0-d554-40ae-8bcd-752af260043b">
<item>
<content styleCode="bold">Do not</content> breast-feed. It is not known if amlodipine
besylate will pass through your milk.</item>
<item>
<content styleCode="bold">Do not</content> start any new prescription or
non-prescription medicines or supplements, unless you check with your doctor
first.</item>
</list>
<br/>
<content styleCode="bold">What are the possible side effects of amlodipine
besylate?</content>
<br/>Amlodipine besylate may cause the following side effects.
Most side effects are mild or moderate:
<list listType="unordered" ID="i83cb3d3a-99ac-4f4f-8d0b-3bfcb5e29f15">
<item>headache</item>
<item>swelling of your legs or ankles</item>
<item>tiredness, extreme sleepiness</item>
<item>stomach pain, nausea</item>
<item>dizziness</item>
<item>flushing (hot or warm feeling in your face)</item>
<item>arrhythmia (irregular heartbeat)</item>
<item>heart palpitations (very fast heartbeat)</item>
</list>
<br/>It is rare, but when you first start taking amlodipine besylate or increase your
dose, you may have a heart attack or your angina may get worse. If that happens,
call your doctor right away or go directly to a hospital emergency room.<br/>
<br/>Tell your doctor if you are concerned about any side effects you experience.
These are not all the possible side effects of amlodipine besylate. For a
complete list, ask your doctor or pharmacist.<br/>
<br/>
<content styleCode="bold">How do I store amlodipine besylate tablets?</content>
<br/>
<br/>
<content styleCode="bold">General advice about amlodipine besylate</content>
<br/><br/>
<br/>You can ask your pharmacist or doctor for information about amlodipine
besylate.<br/>
<br/>
<br/>
</text>
<effectiveTime value="20101104"/>
</section>
</component>
<component>
<section>
<id root="3c8a283d-3b42-41e7-aacb-ea355b5d948e"/>
<code code="51945-4" codeSystem="2.16.840.1.113883.6.1" displayName="PACKAGE LABEL.PRINCIPAL DISPLAY PANEL"/>
<text>
<paragraph>Image of label<renderMultiMedia referencedObject="MM554"/>
</paragraph>
</text>
<effectiveTime value="20101104"/>
<component>
<observationMedia classCode="OBS" moodCode="EVN" ID="MM554">
<text>Image of label</text>
<value xsi:type="ED" mediaType="image/jpeg">
<reference value="amlodipine besylate 5 mg alkem laboratories limited.jpg"/>
</value>
</observationMedia>
</component>
</section>
</component>
</structuredBody>
</component>
</document>
What is the best library to do this? I have found that Everest Framework (http://everest.codeplex.com/) is grate for such kind of work but I did not find any examples how to achieve this. Does anybody used this framework before?I am looking for an example where I can deserialize this xml file into ClinicalDocument class. Thanks
206
To do this you can use the following code:
using(XmlStateReader xr = new XmlStateReader(XmlReader.Create(@"C:\path-to-file.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;
}
Not sure if that will help you transform, but that will read a CDA into a ClinicalDocument class.
172
I am assuming you're using visual studios. If so this is the easiest solution in my opinion: 1.Create a c# class. 2.Then Copy all of your XML (from one of your CDA's). 3.Then go to that class you created before and go to Edit>paste special>Paste XML as Classes.
This will create a class for you based off that XML. Then all you have to do to parse any xml (CDA) like one you copied, is deserialize it into that class type and it will create an object which you can pull all the information out of. I hope that helps!
EDIT: http://blog.codeinside.eu/2014/09/08/Visual-Studio-2013-Paste-Special-JSON-And-Xml/
Deserialize example: (presuming the class you created is called CDA)
string path = "The Path of the XML file";
XmlSerializer superCereal = new XmlSerializer(typeof(CDA));
StreamReader sr = new StreamReader(path);
CDA doc= (CDA)superCereal.Deserialize(sr);
sr.Close();
Now the object doc will have all the information of the xml inside of it.
42
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