XML: Basics. Paul V. Biron Permanente Clinical Systems Development Kaiser Permanente, Southern California

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1 XML: Basics Paul V. Biron Permanente Clinical Systems Development Kaiser Permanente, Southern California 09/15/98 1

2 Outline HTML, SGML and XML The World Wide Web Consortium (W3C) HTML as an application of SGML XML: define your own tag set XML vs. "standard" HL7 encoding Document Type Definitions (DTDs) Well-formed vs. valid Elements Attributes Entities 09/15/98 2

3 Outline (cont.) The "XML Family" of Standards XSL XLL Namespaces Next generation schema definition languge Benefits to be gained Representational expansion Wide availability of toolsets Wide availability of trained personnel 09/15/98 3

4 HTML, SGML, XML HTML: HyperText Markup Language Recommendation of the World Wide Web Consortium (W3C) an application of SGML (the HTML DTD ) SGML: Standard Generalized Markup Language ISO 8879:1986(E) XML is a proper subset of SGML XML and SGML are metalanguages Language for defining other languages Recommendation of the W3C Formally Adopted on 10-February /15/98 4

5 HTML is SGML (although not XML) <h2>patient Information</h2> <ul> <li><b>name:</b>henry Levin, the 7th</li> <li><b>mrn:</b> </li> <li><b>dob:</b> May 13, 1923</li> </ul> <h2>clinical Data</h2> <p>history of smoking for 40 years.</p> <h2>procedure</h2> <p>chest X-ray</p> <h2>findings</h2> <p>comparison is made with a chest-x-ray </p> Radiology Report - Chest X-Ray Patient Information Name: Henry Levin, the 7th MRN: DOB: May 13, 1923 Clinical Data History of smoking for 40 years. Procedure Chest X-Ray Findings Comparison is made with a chest x-ray... <h2>impressions</h2> Impressions <p>rll nodule, suggestive of malignancy. Compared RLL nodule, suggestive of malignancy. with a prior CXR from 6 months ago, nodule size hascompared with a prior CXR from 6 increased.</p> months ago, nodule size has increased. <h2>recommendations</h2> Recommendations <p>i notified the ordering physician of this finding byi notified the ordering physician of this phone.</p> finding by phone. 09/15/98 5

6 XML - Define your own tags <RadiologyReport> <PatientInfo> <Name>Henry Levin, the 7th</Name> <MRN> </MRN> <DOB>May 13, 1923</DOB> </PatientInfo> <ClinicalData>History of smoking for 40 years.</clinicaldata> <Procedure>Chest X-ray</Procedure> <Findings> Comparison is made with a chest-x-ray </Findings> Radiology Report - Chest X-Ray Patient Information Name: Henry Levin, the 7th MRN: DOB: May 13, 1923 Clinical Data History of smoking for 40 years. Procedure Chest X-Ray Findings Comparison is made with a chest x-ray... <Impressions> RLL nodule, suggestive of malignancy. Compared with Impressions a prior CXR from 6 months ago, nodule size has increased. RLL nodule, suggestive of malignancy. </Impressions> Compared with a prior CXR from 6 months ago, nodule size has increased. <Recommendations> I notified the ordering physician of this finding by phone. Recommendations </Recommendations> I notified the ordering physician of this </RadiologyReports> finding by phone. 09/15/98 6

7 XML - Define your tag arrangement <RadiologyReport> <PatientInfo> <Name>Henry Levin, the 7th</Name> <MRN> </MRN> <DOB>May 13, 1923</DOB> </PatientInfo> <!ELEMENT RadiologyReport (PatientInfo, ClinicalData, Procedure, Findings, Impressions, Recommendations)> <!ELEMENT PatientInfo (Name, MRN, DOB)> <!ELEMENT Name (#PCDATA)> <ClinicalData>History of smoking for 40 years. <!ELEMENT MRN (#PCDATA)> </ClinicalData> <!ELEMENT DOB (#PCDATA)> <Procedure>Chest X-ray</Procedure> <!ELEMENT ClinicalData (#PCDATA)> <!ELEMENT Procedure (#PCDATA)> <Findings> <!ELEMENT Findings (#PCDATA)> Comparison is made with a chest-x-ray <!ELEMENT Impressions (#PCDATA)> </Findings> <!ELEMENT Recommendations (#PCDATA)> <Impressions> RLL nodule, suggestive of malignancy. Compared with a prior CXR from 6 months ago, nodule size has increased. </Impressions> <Recommendations> I notified the ordering physician of this finding by phone. </Recommendations> </RadiologyReports> 09/15/98 7

8 XML vs. Standard Encoding <RadiologyReport> <PatientInfo> <Name>Henry Levin, the 7th</Name> <MRN> </MRN> <DOB>May 13, 1923</DOB> </PatientInfo> <ClinicalData>History of smoking for 40 years.</clinicaldata> <Procedure>Chest X-ray</Procedure> <Findings> Comparison is made with a chest-x-ray </Findings> <Impressions> RLL nodule, suggestive of malignancy. Compared with a prior CXR from 6 months ago, nodule size has increased. </Impressions> MSH <cr> PID Levin^Henry^^the 7th <cr> OBR 1 ^Chest X-ray<cr> HL7 Message OBX 1 TX 71020&GDT Clinical data: History of smoking for 40 years.<cr> OBX 2 TX 71020&GDT Findings: Comparison is made with a chest-xray <cr> OBX 3 CE 71020&IMP ^RLL nodule, suggestive of malignancy. Compared with a prior CXR from 6 months ago, nodule size has increased.<cr> <Recommendations> I notified the ordering physician of this finding by phone. OBX 4 CE 71020&REC ^I notified the </Recommendations> ordering physician of this finding by </RadiologyReports> phone. <cr> 09/15/98 8

9 XML vs. Standard Encoding <?xml version="1.0"?> <!DOCTYPE ORU.R01 SYSTEM "hl7_v23.dtd"> <ORU.R01> <MSH> </MSH> <PID PID.1="1"> <PID.3 CX.1=" "/> MSH <cr> <PID.5 XPN.1="Levin" XPN.2="Henry" XPN.3="the 7th"/> <PID.7 TS.1=" "/> </PID> <OBR OBR.1="1"> <OBR.4 CE.2"Chest X-ray"/> </OBR> OBR 1 ^Chest X-ray<cr> <OBX OBX.1="1" OBX.2="TX"> <OBX.3 CE.1="71020" SUB="GDT"/> <OBX.5 TX.1="Clinical data: History of..."/> </OBX> <OBX OBX.1="2" OBX.2="TX"> <OBX.3 CE.1="71020" SUB="GDT"/> OBX 2 TX 71020&GDT Findings: <OBX.5 TX.1="Findings: Comparison is made "/> Comparison is made <cr> </OBX> <OBX OBX.1="3" OBX.2="CE"> <OBX.3 CE.1="71020" SUB="IMP"/> <OBX.5 CE.2="RLL nodule, suggestive of..."/> </OBX> <OBX OBX.1="4" OBX.2="CE"> <OBX.3 CE.1="71020" SUB="REC"/> <OBX.5 CE.2="I notified the ordering physician... "/> </OBX> </ORU.R01> 09/15/98 9 HL7 Message PID Levin^Henry^^the 7th <cr> OBX 1 TX 71020&GDT Clinical data: History of... <cr> OBX 3 CE 71020&IMP ^RLL nodule, suggestive of... <cr> OBX 4 CE 71020&REC ^I notified the ordering physician... <cr>

10 Document Type Definitions Document Type Definitions also referred to as DTD s Provide a "schema" for a class of documents A "schema" defines certain semantic and structural constraints, including A set of element declarations Documentation Optional supporting specifications, such as style sheets DTDs are one language for writing schemas for both SGML and XML documents Recent proposals (e.g., Document Content Descriptors, submission to W3C) have been made 09/15/98 10

11 Well-Formed vs. Valid XML Document prolog element Misc* A well-formed document must match the production labeled document In common usage, this often translates to: The elements, delimited by start- and end-tags, nest properly within each other An XML document is valid if it has an associated document type declaration and if the document complies with the constraints expressed in it 09/15/98 11

12 Overview of XML DTD's Elements Entities Attributes Content Models Occurrence Indicators Grouping Operators Types Occurrence Indicators Default Values Parameter General 09/15/98 12

13 Elements Element Only other elements may be present in the element s content XML Document You can control the order of these sub-elements <!ELEMENT ORU (OBR, OBX*)>... <ORU> <OBR OBR.1="1"> <OBR.4 CE.1="80004" CE.2="ELECTROLYTES"/> </OBR> <OBX OBX.1="1" OBX.5="150" OBX.11="F"> <OBX.3 CE.1="84295" CE.2="NA"/> <OBX.6 CE.1="mmol/l"/> </OBX> </ORU> 09/15/98 13

14 Attributes String (CDATA) String (or CDATA) attributes may take any literal string as a value, including whitespace characters CDATA (character data) <!ATTLIST OBX.3 CE.1 CDATA #IMPLIED CE.2 CDATA #IMPLIED CE.3 CDATA #IMPLIED>... <ORU> <OBR OBR.1="1"> <OBR.4 CE.1="80004" CE.2="ELECTROLYTES"/> </OBR> <OBX OBX.1="1" OBX.5="150" OBX.11="F"> <OBX.3 CE.1="84295" CE.2="NA"/> <OBX.6 CE.1="mmol/l"/> </OBX> </ORU> XML Document 09/15/98 14

15 Entities XML Document prolog General and Parameter Entity Definitions Parameter Entity References element General Entity References Type Referenced Example Parameter Prolog <!ENTITY % HL7.Table.0008 AA AE AR CA CE CR > General Document's Element Content <!ENTITY entity replacement text > 09/15/98 15

16 The "XML Family" of Standards XSL: Extensible Style Language Declarative language for "screen rendering" and transformation Will allow a single XML file to be "rendered" in multiple formats viewing HL7 messages in a standard web browser W3C V1.0 "working draft" released August 18, 1998 XLL: Extensible Link Language Inter/Intra document linking specifications HTML's <a href=" "> on steroids Xlink W3C working draft released March 3, 1998 Xpointer W3C working draft released March 3, /15/98 16

17 The "XML Family" of Standards Namespaces Mechanism for avoiding element/attribute name collisions W3C working draft released August 2, 1998 To be incorporated into a future revision of the XML Specification Next generation "schema" definition languages DTD's on steroids More extensive datatyping Inheritance mechanism(s) W3C working group recently formed Working draft(s)/recommendation(s) at least 1 year away "Document Content Description" W3C submission acknowledged August 10, /15/98 17

18 The Benefits to be Gained Representational expansion Recursive (segment-less) encodings "self-documenting" structures Wide availability of toolsets XML parsers and parser SDKs Stylesheet editors and processors Transformation (conversion) engines Wide availability of trained personnel XML programmers 09/15/98 18

19 Questions prolog element XML Document <?QUESTIONS?> 09/15/98 19

XML: Introduction. !important Declaration... 9:11 #FIXED... 7:5 #IMPLIED... 7:5 #REQUIRED... Directive... 9:11

XML: Introduction. !important Declaration... 9:11 #FIXED... 7:5 #IMPLIED... 7:5 #REQUIRED... Directive... 9:11 !important Declaration... 9:11 #FIXED... 7:5 #IMPLIED... 7:5 #REQUIRED... 7:4 @import Directive... 9:11 A Absolute Units of Length... 9:14 Addressing the First Line... 9:6 Assigning Meaning to XML Tags...