1. Chapter 12 6e Outline Structured, Semistructured,Unstruct Data
XML Hierarchical (Tree) Data Model
XML Documents and XML Schema
Storing and Extracting XML Documents from Databases
XML Languages
Extracting XML Documents from Relational Databases
XML Usage in Biomedical Informatics

2. What is XML? Standards and Usage of XML XML Used in Myriad of Context
Modeling and Information Exchange (XML Schemas and Instances)
Other XML Standards
XACML – Access Control Markup Language
OWL – Web Ontology Language
HL7/CDA

3. What is XML? eXtensible Markup Language HTML on Steroids!
Markup Language for Storing and Transporting Data
Self-Descriptive Language
Send/Receive/Store/Display
Tutorial:

4. XML Example

5. What is XML?
Not HTML!
XML was designed to carry data - with focus on what data is
HTML was designed to display data - with focus on how data looks
XML tags are not predefined like HTML tags are
Common Standard to Exchange Info

6. Sample XML – Original Style – parts.xml

7. Sample XML – Original Style – parts.dtd

8. Sample XML Original– xmlpartstype.xml

9. Sample XML – Current – XML Schema
<xs:element name="note"> <xs:complexType>   <xs:sequence>     <xs:element name="to" type="xs:string"/>     <xs:element name="from" type="xs:string"/>     <xs:element name="heading" type="xs:string"/>     <xs:element name="body" type="xs:string"/>   </xs:sequence> </xs:complexType> </xs:element>

10. Sample XML – XML Instance
<xs:element name="note"> <xs:complexType>   <xs:sequence>     <xs:element name="to" type="xs:string"/>     <xs:element name="from" type="xs:string"/>     <xs:element name="heading" type="xs:string"/>     <xs:element name="body" type="xs:string"/>   </xs:sequence> </xs:complexType> </xs:element>

11. Sample XML - Schema
<?xml version="1.0" encoding="UTF-8" ?> <xs:schema xmlns:xs=" <xs:element name="shiporder">   <xs:complexType>     <xs:sequence>       <xs:element name="orderperson" type="xs:string"/>       <xs:element name="shipto">         <xs:complexType>           <xs:sequence>             <xs:element name="name" type="xs:string"/>             <xs:element name="address" type="xs:string"/>             <xs:element name="city" type="xs:string"/>             <xs:element name="country" type="xs:string"/>           </xs:sequence>         </xs:complexType>       </xs:element>       

12. Sample XML - Schema
      <xs:element name="item" maxOccurs="unbounded">         <xs:complexType>           <xs:sequence>             <xs:element name="title" type="xs:string"/>             <xs:element name="note" type="xs:string" minOccurs="0"/>             <xs:element name="quantity" type="xs:positiveInteger"/>             <xs:element name="price" type="xs:decimal"/>           </xs:sequence>         </xs:complexType>       </xs:element>     </xs:sequence>     <xs:attribute name="orderid" type="xs:string" use="required"/>   </xs:complexType> </xs:element> </xs:schema>

13. Sample XML – Instance
<?xml version="1.0" encoding="UTF-8"?> <shiporder orderid="889923" xmlns:xsi=" xsi:noNamespaceSchemaLocation="shiporder.xsd">   <orderperson>John Smith</orderperson>   <shipto>     <name>Ola Nordmann</name>     <address>Langgt 23</address>     <city>4000 Stavanger</city>     <country>Norway</country>   </shipto>   <item>     <title>Empire Burlesque</title>     <note>Special Edition</note>     <quantity>1</quantity>     <price>10.90</price>   </item>   <item>     <title>Hide your heart</title>     <quantity>1</quantity>     <price>9.90</price>   </item> </shiporder>

14. Sample XML – XML to Relational

15. Usages of XML Data sources Hypertext documents XML data model
Database storing data for Internet applications
Utilized to Store Information for Other Apps
Emerging Standards across Domains
Hypertext documents
Common method of specifying contents and formatting of Web pages
XML data model

16. Promotes Structured Data
XML Schema Defines Structure
Akin to Class or Relational table
Labels or tags on directed edges represent:
Schema names
Names of attributes
Object types (or entity types or classes)
Relationships
XML Instances are Validated Against Schema

17. XML tags
XML tags may have an element field used to store information within the tag or Meta-data
Plain text can be placed between tags and this text is not parsed
CDATA is character data
This means that any string of non-markup characters is legal as part of the attribute
The ENTITY indicates that the attribute will represent an external entity in the document itself
The ID attribute type if you want to specify a unique identifier for each element.

18. XML Schema The structure of an XML document is defined by its schema.
Dozens of languages to define XML schema:
DTD
W3C (XSD)‏
NG - Relax
This file can validate any instance of an XML document against it self.
This file, or schema also defines allowable tags.

19. XML Instances

20. Sample XML Structure
XML employees a tree structure model for representing data (previous slide)‏
shiporder
shipto
orderperson
orderid
address
name
city
country
item
title
name
quantity
price

21. Schema Example (XSD)‏
<?xml version="1.0" encoding="ISO " ?>
<xs:schema xmlns:xs="
<xs:element name="shiporder">
<xs:complexType>
<xs:sequence>
<xs:element name="orderperson" type="xs:string"/>
<xs:element name="shipto">
<xs:element name="name" type="xs:string"/>
<xs:element name="address" type="xs:string"/>
<xs:element name="city" type="xs:string"/>
<xs:element name="country" type="xs:string"/>
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="item" maxOccurs="unbounded">
<xs:element name="title" type="xs:string"/>
<xs:element name="note" type="xs:string" minOccurs="0"/>
<xs:element name="quantity" type="xs:positiveInteger"/>
<xs:element name="price" type="xs:decimal"/>
<xs:attribute name="orderid" type="xs:string" use="required"/>
</xs:schema>

22. Contrasts with HTML HTML uses a large number of predefined tags
HTML documents
Do not include schema information about type of data
Static HTML page
All information to be displayed explicitly spelled out as fixed text in HTML file

24. XML Hierarchical Data Model
Elements and attributes
Main structuring concepts used to construct an XML document
Complex elements
Constructed from other elements hierarchically
Simple elements
Contain data values
XML tag names
Describe the meaning of the data elements in the document

26. XML Hierarchical Data Model
Tree model or hierarchical model
Main types of XML documents
Data-centric XML documents
Document-centric XML documents
Hybrid XML documents
Schemaless XML documents
Do not follow a predefined schema of element names and corresponding tree structure

27. XML Hierarchical Data Model
XML attributes
Describe properties and characteristics of the elements (tags) within which they appear
May reference another element in another part of the XML document
Common to use attribute values in one element as the references

28. XML Documents and Schema
Well formed
Has XML declaration
Indicates version of XML being used as well as any other relevant attributes
Every element must matching pair of start and end tags
Within start and end tags of parent element

29. XML Documents and Schema
Valid
Document must be well formed
Document must follow a particular schema
Start and end tag pairs must follow structure specified in separate XML DTD (Document Type Definition) file or XML schema file
DTD is Outmoded in Current Usage
Show Examples …
Schemas Now Dominate ..

30. DTD for Projects
continued on next slide

31. DTD for Company

32. XML Schema XML schema language
Standard for specifying the structure of XML documents
Uses same syntax rules as regular XML documents
Same processors can be used on both

34. XML Schema
Identify specific set of XML schema language elements (tags) being used
Specify a file stored at a Web site location
XML namespace
Defines the set of commands (names) that can be used

35. XML Schema XML schema concepts: Description and XML namespace
Annotations, documentation, language
Elements and types
First level element
Element types, minOccurs, and maxOccurs
Keys
Structures of complex elements
Composite attributes

36. An XML schema file called company.
continued on next slide

37. An XML schema file called company.
continued on next slide

38. An XML schema file called company.
continued on next slide

39. An XML schema file called company.
continued on next slide

40. An XML schema file called company.

41. An XML schema file called company.

42. Storing and Extracting XML Documents from Databases
Most common approaches
Using a DBMS to store the documents as text
Can be used if DBMS has a special module for document processing
Using a DBMS to store document contents as data elements
Require mapping algorithms to design a database schema that is compatible with XML document structure

43. Storing and Extracting XML Documents from Databases
Designing a specialized system for storing native XML data
Called Native XML DBMSs
Creating or publishing customized XML documents from preexisting relational databases
Use a separate middleware software layer to handle conversions

44. XML Languages Two query language standards XPath XQuery
Specify path expressions to identify certain nodes (elements) or attributes within an XML document that match specific patterns
XQuery
Uses XPath expressions but has additional constructs

45. XPath: Specifying Path Expressions in XML
XPath expression
Returns a sequence of items that satisfy a certain pattern as specified by the expression
Either values (from leaf nodes) or elements or attributes
Qualifier conditions
Further restrict nodes that satisfy pattern
Separators used when specifying a path:
Single slash (/) and double slash (//)

46. XPath: Specifying Path Expressions in XML

47. XPath: Specifying Path Expressions in XML
Attribute name prefixed by symbol
Wildcard symbol *
Stands for any element
Example: /company/*

48. XPath: Specifying Path Expressions in XML
Axes
Move in multiple directions from current node in path expression
Include self, child, descendent, attribute, parent, ancestor, previous sibling, and next sibling

49. XPath: Specifying Path Expressions in XML
Main restriction of XPath path expressions
Path that specifies the pattern also specifies the items to be retrieved
Difficult to specify certain conditions on the pattern while separately specifying which result items should be retrieved

50. Querying XML - XPath Many languages to query XML
XPath and XQuery are W3C standards
Xpath is a compact method of traversing previous tree
Designed to facilitate use via URL/URI's
/shiporder/item/name ← view all items' names
Extensible to add user defined behaviors
Treats each tag as a node in the tree

51. Querying XML - XQuery Functional extension of XPath
XML equivalent of SQL
Navigate and manipulate document nodes.
Works on collections of documents, or even fragments.
FOR $b IN document("bib.xml")//book
WHERE $b/publisher = "Morgan Kaufmann"
AND $b/year = "1998"
RETURN $b/title

52. XQuery: Specifying Queries in XML
XQuery FLWR expression
Four main clauses of XQuery
Form:
FOR <variable bindings to individual nodes (elements)>
LET <variable bindings to collections of nodes (elements)>
WHERE <qualifier conditions>
RETURN <query result specification>
Zero or more instances of FOR and LET clauses

54. XQuery: Specifying Queries in XML
XQuery contains powerful constructs to specify complex queries
Contains documents describing the latest standards related to XML and XQuery

55. Additonal XML Examples
Present an Entire Company Instance
Departments: Headquarters, Admin, Reseach, Software, Hardware, Sales
Employees: Franklin Wong, James E Borg, etc
Total of 20 in Instance

56. Company Instance with Departments
<?xml version="1.0" ?>
<companyDB xsi:noNamespaceSchemaLocation="company.xsd" xmlns:xsi="
<departments>
<department dno="1">
<dname>Headquarters</dname>
<locations>
<location>Houston</location>
</locations>
<manager mssn=" ">
<startDate>19-JUN-1971</startDate>
</manager>
<employees essns=" "/>
<projectsControlled pnos="20"/>
</department>
<department dno="4">
<dname>Administration</dname>
<location>Stafford</location>
<manager mssn=" ">
<startDate>01-JAN-1985</startDate>
<employees essns=" "/>
<projectsControlled pnos="10 30"/>

57. Some Employees
<employee ssn=" " worksFor="5" supervisor=" " manages="5">
<fname>Franklin</fname>
<minit>T</minit>
<lname>Wong</lname>
<dob>08-DEC-45</dob>
<address>638 Voss, Houston, TX</address>
<sex>M</sex>
<salary>40000</salary>
<dependents>
<dependent>
<dependentName>Alice</dependentName>
<sex>F</sex>
<dob>05-APR-1976</dob>
<relationship>Daughter</relationship>
</dependent>
<dependentName>Theodore</dependentName>
<dob>25-OCT-1973</dob>
<relationship>Son</relationship>
<dependentName>Joy</dependentName>
<dob>03-MAY-1948</dob>
<relationship>Spouse</relationship>
</dependents>
<supervisees essns=" "/>
<projects>
<worksOn pno="2" hours="10.0"/>
<worksOn pno="3" hours="10.0"/>
<worksOn pno="10" hours="10.0"/>
<worksOn pno="20" hours="10.0"/>
</projects>
</employee>

58. Some Employees
<employee ssn=" " worksFor="1" manages="1">
<fname>James</fname>
<minit>E</minit>
<lname>Borg</lname>
<dob>10-NOV-27</dob>
<address>450 Stone, Houston, TX</address>
<sex>M</sex>
<salary>55000</salary>
<supervisees essns=" "/>
<projects>
<worksOn pno="20" hours="0.0"/>
</projects>
</employee>

59. Xpath Expressions /companyDB/departments/department
/companyDB/employees/employee/lname/text()
/companyDB/employees/employee/*
//dob
/companyDB/employees/employee[7]
/companyDB/employees/employee[1]/dependents/dependent[2]
/companyDB/employees/employee[1]/dependents/dependent[last()]

60. Xpath Expressions /companyDB/employees/employee[position()<=3]
/companyDB/employees/employee[minit="E"]
/companyDB/employees/employee[starts-with(lname,"S")]
/companyDB/employees/employee[contains(address,"Philadelphia")]
and sex="M" and dependents/dependent[sex="M"]]
/companyDB/departments/department/dname/text() |
/companyDB/projects/project/pname/text()

61. Xquery expressions Query 1: Get all projects.
let $d:=doc("/Users/raj/company.xml")
for $p in $d/companyDB/projects/project
return $p
Query 2: Get distinct project numbers of projects in which employees work.
<projects> {
for $p in distinct-values(
return
<project>{$p}</project> }
</projects>

62. Xquery expressions Query 5: Get employees who work more than 40 hours.
let $d:=doc("/Users/raj/company.xml")
for $e in $d/companyDB/employees/employee
where
return
<OverWorkedEmp>{$e/lname}
</TotalHours>
</OverWorkedEmp>
Query 6: Get department names and the total number of employees
working in the department.
for $r in $d/companyDB/departments/department
<deptNumEmps>{$r/dname}
</numEmps>
</deptNumEmps>

63. Other Languages and Protocols Related to XML
Extensible Stylesheet Language (XSL)
Define how a document should be rendered for display by a Web browser
Extensible Stylesheet Language for Transformations (XSLT)
Transform one structure into different structure
Web Services Description Language (WSDL)
Description of Web Services in XML

64. Other Languages and Protocols Related to XML
Simple Object Access Protocol (SOAP)
Platform-independent and programming language-independent protocol for messaging and remote procedure calls
Resource Description Framework (RDF)
Languages and tools for exchanging and processing of meta-data (schema) descriptions and specifications over the Web

65. Other Languages and Protocols Related to XML
OWL Web Ontology Language
Towards Representing Semantic/Content
Three variants: OWL Lite, OWL DL, and OWL Full
eXtensible Access Control Markup Language (XACML)
Ability to Define Security Policies
Authentication Policies Defined in XML

66. Other Steps for Extracting XML Documents from Databases
Create correct query in SQL to extract desired information for XML document
Restructure query result from flat relational form to XML tree structure
Customize query to select either a single object or multiple objects into document

67. Other Usages of XML Wide Range of Standards for Domains
health care (with HL7)
finance (with FpML and xBRL)
e-commerce (with cXML)
legal document exchange (with LegalXML)
law enforcement (with MMUCC)
commercial banking (with MISMO),

68. A Complete Example University ER Diagram Subset of the Database
Hierarchical Organization of Course
XML Schema for Course
Hierarchical Organization of Student
XML Schema for Student
Other Views

69. An ER schema diagram for a simplified UNIVERSITY database.

70. Subset of the UNIVERSITY database schema needed for XML document extraction.

71. Hierarchical (tree) view with COURSE as the root.

72. XML schema document with course as the root.

73. Hierarchical (tree) view with STUDENT as the root.

74. XML schema document with student as the root.

75. Course_name Hierarchical (tree) view with SECTION as the root.

76. Converting a graph with cycles into a hierarchical (tree) structure.

77. XML Usage in BMI The convergence of computation and biomedicine
The NIH BMI Science and Tech Initiative:
Define biomedical computing as a science
Many sources of information:
Clinical, surgical, genetics, drug design, biology
Standardization in software
Algorithm development, high speed computing
All relies on efficient storage and transfer of information

78. XML in Clinical Data HL7 standards organization.
V2: ASCII bar format. example:
HL7V3|1|2.02
Message| ^CNTRL-3456| ^- --->
06:00||3.0| ^POLB_IN004410||P|I|ER|ER
respondTo|RSP|tel: ^^WP
entit yRsp|||{FAM^^Hippocrates~GIV^^Harold~GIV^^H~SFX^AC^MD}|tel: ^^WP
sender|SND|nfs:
device|| ^GHH LAB|{GIV^^An Entit y Name}^L|||tel: ^^H
agencyFor
representedOrganization||\NOTH\
location||| ^ELAB-3|{^^GHH Lab}^TN
receiver|RCV|nfs:
device||| ^GHH O E|{GIV^^An Entit y Name}^L|||tel: ^^H
representedOrganization||| |{^^GHH Outpatient Clinic}^TN
location||| ^BLDG4|{^^GHH Outpatient Clinic}^TN
Awkward, inflexible, unclear meaning of values.

79. HL7 V3 Specification Entity, Role, Participation, and Act
Built around Reference Information Model:
Entity, Role, Participation, and Act
Utilizes dedicated vocabularites and data types.
Every specification must begin from RIM.
Clinical Document Architecture
Utilizes XML with tags like ”observation, code, value and id”.
<observation classCode="OBS" moodCode="EVN">
<id root=" "/>
<code code=" " codeSystem=" "
codeSystemName="SNOMED CT" displayName="Peak flow"/>
<effectiveTime value=" "/>
<value xsi:type="RTO_PQ_PQ">
<numerator value="260" unit="l"/>
<denominator value="1" unit="min"/>
</value>
</observation>

80. HL7’s CDA Clinical Document Architecture ANSI/HL7 R1-2000, R2-2005
eDocuments for Interoperability
Key component for local, regional, national electronic health records
Gentle on-ramp to information exchange
Everyone uses documents
EMR compatible, no EMR required
All types of clinical documents
Consult
Discharge
Radiology
Path
Summary
CDA Health chart 80

81. ASTM’s CCR 81

82. HL7 CDA and CCR Standards and Usage of XML
Consider CDA – Clinical Document Architecture
Standard for Clinical (Provider) Medical Recor

83. HL7 CDA and CCR Clinical Record Organized as:
<patient_encounter> - location
<legal_authenticator> - MD
<originating_organization> and <provider>
<patient> - name, birthdate, gender
<body_confidentiality-”CONF1”> - note
History
Past Medical History
Medications
Allergies
Social History
Physical Exam
Vitals (BP, Resp, Temp, HR)
Etc...

84. What is one Possible Solution?
Let’s Explore this in Greater Detail
Starting with the CDA Header
<?xml version="1.0"?>
<!DOCTYPE levelone PUBLIC "-//HL7//DTD CDA Level One 1.0//EN" "levelone_1.0.dtd">
<levelone>
<clinical_document_header>
<id EX="a123" RT=" "/>
<set_id EX="B" RT=" "/>
<version_nbr V="2"/>
<document_type_cd V=" " S=" "
DN="Consultation note"/>
<origination_dttm V=" "/>
<confidentiality_cd ID="CONF1" V="N" S=" xxx"/>
<confidentiality_cd ID="CONF2" V="R" S=" xxx"/>
<document_relationship>
<document_relationship.type_cd V="RPLC"/>
<related_document>
<id EX="a234" RT=" "/>
<version_nbr V="1"/>
</related_document>
</document_relationship>
<fulfills_order>
<fulfills_order.type_cd V="FLFS"/>
<order><id EX="x23ABC" RT=" "/></order>
<order><id EX="x42CDE" RT=" "/></order>
</fulfills_order>

85. CDA Example - Continued

86. CDA Example - Continued

87. CDA Example - Continued

88. CDA Example - Continued

89. CDA Example - Continued

90. CDA Example - Continued

91. CDA Example - Continued

92. CDA Example - Continued

93. CCR Schema
<xs:schema xmlns="urn:astm-org:CCR" xmlns:xs=" xmlns:ccr="urn:astm-org:CCR" targetNamespace="urn:astm-org:CCR"
elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:import namespace=" schemaLocation="xmldsig-core-schema.xsd" />
<xs:element name="ContinuityOfCareRecord">
<xs:complexType>
<xs:sequence>
<xs:element name="CCRDocumentObjectID" type="xs:string" />
<xs:element name="Language" type="CodedDescriptionType" />
<xs:element name="Version" type="xs:string" />
<xs:element name="DateTime" type="DateTimeType" />
<xs:element name="Patient" maxOccurs="2">
<xs:element name="ActorID" type="xs:string" />
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="From">
<xs:element name="ActorLink" type="ActorReferenceType" maxOccurs="unbounded" /> …

94. CCR Instance <ContinuityOfCareRecord xmlns='urn:astm-org:CCR'>
<CCRDocumentObjectID>Doc</CCRDocumentObjectID>
<Language><Text>English</Text></Language>
<Version>V1.0</Version>
<DateTime><ExactDateTime>2008</ExactDateTime></DateTime>
<Patient><ActorID>Patient</ActorID></Patient>
<Body>
<Problems>
<Problem>
<DateTime>
<Type>
<Text>Start date</Text>
</Type>
<ExactDateTime> T07:00:00Z</ExactDateTime>
</DateTime>
<Text>Stop date</Text>
<ExactDateTime> T07:00:00Z</ExactDateTime>
<Description>
<Code>
<Value>346.80</Value>
<CodingSystem>ICD9</CodingSystem>
<Version>2004</Version>
</Code> …

95. Introduction to FHIR Grahame Grieve Aug 19, 2014

96. This presentation
Is licensed for use under the Creative Commons, specifically:
Creative Commons Attribution 3.0 Unported License
(Do with it as you wish, so long as you give credit)

97. The “FHIR” Acronym F – Fast (to design & to implement) H – Health
I – Interoperable
R – Resources (Building blocks)
There is more on Resources to follow
“Fast” is relative – no technology can make integration as fast as we’d like
“FHIR” (pronouced “Fire”) is a fertile source of puns etc. Feel free to make your own
9:25

98. What is FHIR? A set of modular components called “Resources”
Resources refer to each other using URLs
Build a web to support healthcare process
Exchange resources between systems
Using a RESTful API (e.g. web approach)
As a bundle of resources (messages, documents)

99. Genesis of FHIR
There has been a need to share healthcare information electronically for a long time
HL7 v2 is over 25 years old
Increasing pressure to broaden scope of sharing
Across organizations, disciplines, even borders
Mobile & cloud-based applications
Faster – integration in days or weeks, not months or years
Who

100. Genesis of FHIR HL7 did not have much to offer in this space?
V2 Old, and limited by it’s own rules
V3 too slow and too hard
CDA has success, but both limited and too hard
Different contexts of interoperability  different representations that aren’t compatible
Nothing suitable for light-weight integration, or for Health 2.0
No other Organization so well situated

101. Genesis of FHIR HL7 undertook a “Fresh look”
What would healthcare exchange look like if we started from scratch using modern approaches?
Web search for success markers led to RESTful based APIs
An exemplar: Highrise from “37 Signals)
Drafted a healthcare exchange API based on this approach

102. Resources

103. Resources

104. Resources

105. Available Resources

106. Available Resources

107. Resources Conceptually

108. Resources Conceptually

109. Resources Conceptually

110. Resources Conceptually

111. Resources Conceptually

112. Representing Resources in Different Formats
The resources are described in several different ways:
a hierarchical table that presents a logical view of the content
a UML diagram that summarizes the content graphically
a pseudo-XML syntax that provides a visual sense of what the end resource instances will look like in XML
a pseudo-JSON syntax that provides a visual sense of what the end resource instances will look like in JSON

113. XML vs. JSON

114. XML vs. JSON

115. XML vs. JSON

116. JSON vs. RDF { "resourceType" : "Observation", "code" : { "coding" : {
"system" : [ fhir:uri.value "
"code" : [ fhir:code.value " "],
"display" : [ fhir:string.value "Rh immune globulin given Qualitative"] },
"text" : "Rh immune globulin" }
@prefix loinc: < .
:resource a fhir:Observation;
fhir:Observation.code [
a loinc: ;
fhir:CodeableConcept.coding [
fhir:Coding.system [ fhir:uri.value < ;
fhir:Coding.code [ fhir:code.value " " ];
fhir:Coding.display [ fhir:string.value "Rh immune globulin given Qualitative"]; ];
fhir:CodeableConcept.text [ fhir:string.value "Rh immune globulin" ]; ].

117. Standard and Databases
Many Applications Have Standards
Finance (with FpML and xBRL), e-commerce (with cXML), legal document exchange (with LegalXML), law enforcement (with MMUCC), commercial banking (with MISMO)
DBs Apps must Interact with Standards
Standard Values and Codes Stored in DB
Need to be Searchable by Various Codes
Values/Codes Transmitted to other Systems and Organizations
Health Care has a Large Set of Standards

118. Health Care Standards of Note
MeSH
Unified Medical Language System
ICD9 and ICD9-CM (Intl. Classification Diseases)
ICD10 and ICD10-CM
SNOMED-CT (Clinical Terms)
National Drug Codes (NDC)

119. MeSH
The Medical Subject Headings (MeSH®) thesaurus is a controlled vocabulary produced by the National Library of Medicine and used for indexing, cataloging, and searching for biomedical and health-related information and documents.
2011 MeSH includes the subject descriptors appearing in MEDLINE®/PubMed®, the NLM catalog database, and other NLM databases.
Many synonyms, near-synonyms, and closely related concepts are included as entry terms to help users find the most relevant MeSH descriptor for the concept they are seeking.

120. MeSH in ASCII *NEWRECORD RECTYPE = D MH = Calcimycin
AQ = AA AD AE AG AI AN BI BL CF CH CL CS CT DU EC HI IM IP ME PD PK PO RE SD ST TO TU UR
ENTRY = A-23187|T109|T195|LAB|NRW|NLM (1991)|900308|abbcdef
ENTRY = A23187|T109|T195|LAB|NRW|UNK (19XX)|741111|abbcdef
ENTRY = Antibiotic A23187|T109|T195|NON|NRW|NLM (1991)|900308|abbcdef
ENTRY = A 23187
ENTRY = A23187, Antibiotic
MN = D
PA = Anti-Bacterial Agents
PA = Ionophores
MH_TH = NLM (1975)
ST = T109
ST = T195
N1 = 4-Benzoxazolecarboxylic acid, 5-(methylamino)-2-((3,9,11-trimethyl-8-(1-methyl-2-oxo-2-(1H-pyrrol-2-yl)ethyl)-1,7-dioxaspiro(5.5)undec-2-yl)methyl)-, (6S-(6alpha(2S*,3S*),8beta(R*),9beta,11alpha))-
RN =
PI = Antibiotics ( )
PI = Carboxylic Acids ( )

121. MeSH in ASCII
MS = An ionophorous, polyether antibiotic from Streptomyces chartreusensis. It binds and transports cations across membranes and uncouples oxidative phosphorylation while inhibiting ATPase of rat liver mitochondria. The substance is used mostly as a biochemical tool to study the role of divalent cations in various biological systems.
OL = use CALCIMYCIN to search A
PM = 91; was A (see under ANTIBIOTICS )
HN = 91(75); was A (see under ANTIBIOTICS )
MED = *62
MED = 847
M90 = *299
M90 = 2405
M85 = *454
M85 = 2878
M80 = *316
M80 = 1601
M75 = *300
M75 = 823
M66 = *1
M66 = 3
ETC

122. MeSH in XML - desc2011.dtd
<!-- MeSH DTD file for Descriptor records. desc2011.dtd -->
<!-- Author: MeSH -->
<!-- Effective: 09/01/ >
<!-- #PCDATA: parseable character data = text
occurence indicators (default: required, not repeatable):
?: zero or one occurrence, i.e., at most one (optional)
*: zero or more occurrences (optional, repeatable)
+: one or more occurrences (required, repeatable)
|: choice, one or the other, but not both
-->
<!ENTITY % DescriptorReference "(DescriptorUI, DescriptorName)">
<!ENTITY % normal.date "(Year, Month, Day)">
<!ENTITY % ConceptReference "(ConceptUI,ConceptName,ConceptUMLSUI?)">
<!ENTITY % QualifierReference "(QualifierUI, QualifierName)">
<!ENTITY % TermReference "(TermUI, String)">

123. MeSH in XML - desc2011.dtd
<!ELEMENT DescriptorRecordSet (DescriptorRecord*)>
<!ATTLIST DescriptorRecordSet LanguageCode (cze|dut|eng|fin|fre|ger|ita|jpn|lav|por|scr|slv|spa) #REQUIRED>
<!ELEMENT DescriptorRecord (%DescriptorReference;,
DateCreated,
DateRevised?,
DateEstablished?,
ActiveMeSHYearList,
AllowableQualifiersList?,
Annotation?,
HistoryNote?,
OnlineNote?,
PublicMeSHNote?,
PreviousIndexingList?,
EntryCombinationList?,
SeeRelatedList?,
ConsiderAlso?,
PharmacologicalActionList?,
RunningHead?,
TreeNumberList?,
RecordOriginatorsList,
ConceptList) >
<!ATTLIST DescriptorRecord DescriptorClass (1 | 2 | 3 | 4) "1">

124. MeSH in XML - desc2011.dtd <!ELEMENT ActiveMeSHYearList (Year+)>
<!ELEMENT AllowableQualifiersList (AllowableQualifier+) >
<!ELEMENT AllowableQualifier (QualifierReferredTo,Abbreviation )>
<!ELEMENT Annotation (#PCDATA)>
<!ELEMENT ConsiderAlso (#PCDATA) >
<!ELEMENT Day (#PCDATA)>
<!ELEMENT DescriptorUI (#PCDATA) >
<!ELEMENT DescriptorName (String) >
<!ELEMENT DateCreated (%normal.date;) >
<!ELEMENT DateRevised (%normal.date;) >
<!ELEMENT DateEstablished (%normal.date;) >
<!ELEMENT DescriptorReferredTo (%DescriptorReference;) >
<!ELEMENT EntryCombinationList (EntryCombination+) >
<!ELEMENT EntryCombination (ECIN,
ECOUT)>
<!ELEMENT ECIN (DescriptorReferredTo,QualifierReferredTo) >
<!ELEMENT ECOUT (DescriptorReferredTo,QualifierReferredTo? ) >
<!ELEMENT HistoryNote (#PCDATA)>
<!ELEMENT Month (#PCDATA)>
<!ELEMENT OnlineNote (#PCDATA)>
ETC

125. dMeSH in XML - Sample <?xml version="1.0"?>
<!DOCTYPE DescriptorRecordSet SYSTEM "desc2011.dtd">
<DescriptorRecordSet LanguageCode = "eng">
<DescriptorRecord DescriptorClass = "1">
<DescriptorUI>D000001</DescriptorUI>
<DescriptorName>
<String>Calcimycin</String>
</DescriptorName>
<DateCreated>
<Year>1974</Year>
<Month>11</Month>
<Day>19</Day>
</DateCreated>
<DateRevised>
<Year>2006</Year>
<Month>07</Month>
<Day>05</Day>
</DateRevised>
<DateEstablished>
<Year>1984</Year>
<Month>01</Month>
<Day>01</Day>
</DateEstablished>

126. dMeSH in XML - Sample <ActiveMeSHYearList>
<Year>2007</Year>
<Year>2008</Year>
<Year>2009</Year>
<Year>2011</Year>
</ActiveMeSHYearList>
<AllowableQualifiersList>
<AllowableQualifier>
<QualifierReferredTo>
<QualifierUI>Q000008</QualifierUI>
<QualifierName>
<String>administration & dosage</String>
</QualifierName>
</QualifierReferredTo>
<Abbreviation>AD</Abbreviation>
</AllowableQualifier>
<QualifierUI>Q000009</QualifierUI>
<String>adverse effects</String>
<Abbreviation>AE</Abbreviation>
ETC

127. Unifies Medical Language System
UMLS acronym for was developed for National Library of Medicine
Disease is semantic type with around 392 relations (109 semantic relations and 22 other relations). Pneumonia categorized under one semantic type Disease, but has hundreds of relations.

128. UMLS Concepts, Semantic Types/Relations

129. ICD9 Respiratory Diseases

130. ICD10 Respiratory Diseases

131. Interesting ICD10 Codes ICD9 had 1 3,000, ICD has 68,000 Codes!
W61.12XA: Struck by macaw, initial encounter.
V97.33XA Sucked into jet engine, initial encounter
V97.33XD: Sucked into jet engine, subsequent encounter.
Spacecraft crash injuring occupant – V9542XA
Hurt walking into a lamppost – W2202XA

132. SNOMED-CT
SNOMED stands for Systemized Nomenclature Of Medicine Clinical Terms. SNOMED-CT is the result of merging two ontologies: SNOMED-RT and Clinical Terms.
133

133. SNOMED-CT Composed of Concepts, Terms, and Relationships
Precisely Represent Clinical Information Across Scope of Health Care
Content Coverage Divided into Hierarchies
134

134. SNOMED Example

135. National Drug Codes Tracking of Drugs (Prescription and OTC)
From Submittal Through Approach
Keeps Track of Many Details on Medication
Each Drug by Manufacturer has Unique NDC Identifier
See:
Searchable Database:
cfm

136. NDC Examples

137. Summary
Three main types of data: structured, semi- structured, and unstructured
XML standard
Tree-structured (hierarchical) data model
XML documents and the languages for specifying the structure of these documents
XPath and XQuery languages
Query XML data