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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
