Health Data IntegrationHealth Data Integration

Farrokh Alemi, Ph.D.Francisco Loaiza Ph.D.Vikas Arya

Essential XML ConceptsEssential XML Concepts

• XML Syntax

XML - instance document

Essential XML ConceptsEssential XML Concepts

• XML Syntax

• XML - instance document

BloodPressure units="mmHg"

XML Tag Name XML Tag Attribute XML Attribute Value

Start and End Delimiters

< >

< >BloodPressure units="mmHg" 128

< >/BloodPressure

XML Closing Tag

XML Tag Content

Structure of XML TagStructure of XML Tag

Sample XML DocumentSample XML Document

Sample XML DocumentSample XML Document

XML Declaration

XML DeclarationXML Declaration

XML Declaration

Processinginstruction

endProcessinginstruction

start

Comment TagsComment Tags

XML Comment

Comment endComment

start

Comment TagsComment Tags

XML Comment

Comment endComment

start

Opening & Closing Tags for Opening & Closing Tags for PersonPerson

XML commands

Closing tag

Opening tag

Opening & Closing Tags for Opening & Closing Tags for PersonNamePersonName

XML commands

Closing tag

Opening tag

Opening & Closing Tags for Opening & Closing Tags for BloodPressureBloodPressure

XML commands

Closing tag

Opening tag

Root TagRoot Tag

Root Tag

Root TagRoot Tag

Tag for Table name

Root TagRoot Tag

Attributes/Fieldsin Table

Another ExampleAnother Example

<?xml version="1.0" encoding="ASCII" ?>

Declaration StatementDeclaration Statement

<?xml version="1.0" encoding="ASCII" ?><!-- data from public health agencies on influenza outbreak in 2002 -->

Comment StatementComment Statement

<?xml version="1.0" encoding="ASCII" ?><!-- data from public health agencies on influenza outbreak in 2002 --> <Influenza_2002></Influenza_2002>

Root TagRoot Tag

<?xml version="1.0" encoding="ASCII" ?><!-- data from public health agencies on influenza outbreak in 2002 --><Influenza_2002>   <Report>      <cityName>Atlanta</cityName>      <patientQuantity>2,138</patientQuantity>      <hospitalStay unit="days">8</hospitalStay>      <casualtyQuantity>14</casualtyQuantity>   </Report>   <Report>      <cityName>Los Angeles</cityName>      <patientQuantity>15,764</patientQuantity>      <hospitalStay unit="days">5</hospitalStay>      <casualtyQuantity>77</casualtyQuantity>   </Report>   <Report>    <cityName>New York</cityName>       <patientQuantity>22,349</patientQuantity>      <hospitalStay unit="days">7</hospitalStay>      <casualtyQuantity>146</casualtyQuantity>   </Report>   </Influenza_2002>

Record TagsRecord Tags

Name Medical Test Date

John Robertson Blood Test 2-Jan-02

Maria Estrada Cholesterol Test 27-Jul-02

Sandy Hellerman X-Ray 13-Mar-02

Julia Moriarty Chest MRI 23-Dec-01

Pedro Martinez EKG 11-Feb-02

Sayeed Rashidi Cholesterol Test 11-Nov-02

Using Excel to Write XML Using Excel to Write XML

  name     MedicalTest

    Date  

<name> John Robertson

</name> <MedTest> BloodTest

</MedTest> <Date> 02-Jan-03 </Date>

<name> Maria Estrada

</name> <MedTest> Cholesterol Test

</MedTest> <Date> 27-Jul-02 </Date>

<name> Sandy Hellerman

</name> <MedTest> X-Ray </MedTest> <Date> 13-Mar-02 </Date>

<name> Julia Moriarty

</name> <MedTest> Chest MRI </MedTest> <Date> 23-Dec-01 </Date>

<name> Pedro Martinez

</name> <MedTest> EKG </MedTest> <Date> 11-Feb-03 </Date>

<name> Sayeed Rashidi

</name> <MedTest> Cholesterol Test

</MedTest> <Date> 11-Nov-02 </Date>

Spreadsheet with Tags Spreadsheet with Tags InsertedInserted

name MedicalTest

Date

<PatRec> <Name> JohnRobertson

</Name> <MedTest> Blood Test </MedTest> <Date> 02-Jan-03 </Date> </PatRec>

<PatRec> <Name> MariaEstrada

</Name> <MedTest> Cholesterol Test

</MedTest> <Date> 27-Jul-02 </Date> </PatRec>

<PatRec> <Name> Sandy Hellerman

</Name> <MedTest> X-Ray </MedTest> <Date> 13-Mar-02 </Date> </PatRec>

<PatRec> <Name> Julia Moriarty

</Name> <MedTest> Chest MRI </MedTest> <Date> 23-Dec-01 </Date> </PatRec>

<PatRec> <Name> Pedro Martinez

</Name> <MedTest> EKG </MedTest> <Date> 11-Feb-03 </Date> </PatRec>

<PatRec> <Name> Sayeed Rashidi

</Name> <MedTest> Cholesterol Test

</MedTest> <Date> 11-Nov-02 </Date> </PatRec>

Inserting Record Delimiter Inserting Record Delimiter TagTag

<PatRec> <Name> JohnRobertson </Name> <MedTest> Blood Test </MedTest> <Date> 02-Jan-03 </Date> </PatRec><PatRec> <Name> MariaEstrada </Name> <MedTest> Cholesterol Test </MedTest> <Date> 27-Jul-02 </Date></PatRec><PatRec> <Name> Sandy Hellerman </Name> <MedTest> X-Ray </MedTest> <Date> 13-Mar-02 </Date> </PatRec><PatRec> <Name> Julia Moriarty </Name> <MedTest> Chest MRI </MedTest> <Date> 23-Dec-01</Date> </PatRec><PatRec> <Name> Pedro Martinez </Name> <MedTest> EKG </MedTest> <Date> 11-Feb-03</Date> </PatRec><PatRec> <Name> Sayeed Rashidi </Name> <MedTest> Cholesterol Test </MedTest> <Date> 11-Nov-02 </Date> </PatRec>

Correcting Syntax in NotepadCorrecting Syntax in Notepad

PatRec><Name>John Robertson</Name><MedTest>Blood Test</MedTest><Date>2002-01-03</Date></PatRec><PatRec><Name>Maria Estrada</Name><MedTest>Cholesterol Test</MedTest><Date>2002-07-27</Date></PatRec><PatRec><Name>Sandy Hellerman</Name><MedTest>X-Ray</MedTest><Date>2002-04-13</Date></PatRec><PatRec><Name>Julia Moriarty</Name><MedTest>Chest MRI</MedTest><Date>2002-12-23</Date></PatRec><PatRec><Name>Pedro Martinez</Name><MedTest>EKG</MedTest><Date>2003-02-11</Date></PatRec><PatRec><Name>Sayeed Rashidi</Name><MedTest>Cholesterol Test</MedTest><Date>2002-11-11</Date></PatRec>

Final ResultFinal Result

<?xml version="1.0" encoding="ASCII" ?><MedRecords><PatRec><Name>John Robertson</Name><MedTest>Blood Test</MedTest><Date>2002-01-03</Date></PatRec><PatRec><Name>Maria Estrada</Name><MedTest>Cholesterol Test</MedTest><Date>2002-07-27</Date></PatRec><PatRec><Name>Sandy Hellerman</Name><MedTest>X-Ray</MedTest><Date>2002-04-13</Date></PatRec><PatRec><Name>Julia Moriarty</Name><MedTest>Chest MRI</MedTest><Date>2002-12-23</Date></PatRec><PatRec><Name>Pedro Martinez</Name><MedTest>EKG</MedTest><Date>2003-02-11</Date></PatRec><PatRec><Name>Sayeed Rashidi</Name><MedTest>Cholesterol Test</MedTest><Date>2002-11-11</Date></PatRec></MedRecords>

Insert Insert DeclarationDeclaration

Saving Document as XMLSaving Document as XML

Take Home LessonTake Home Lesson

XML syntax and structure