XML and Standards in BMI
CSE
5810
Prof. Steven A. Demurjian, Sr.
Computer Science & Engineering Department
The University of Connecticut
371 Fairfield Road, Box U-255
Storrs, CT 06269-2155
steve@engr.uconn.edu
http://www.engr.uconn.edu/~steve
(860) 486 - 4818
XML-STDS-1
Overview

CSE

5810

What is XML? How is it Used Today?
HL7 and CDA, CCR
Other Standards
 MeSH
 Unified Medical Language System
 ICD9 and ICD9-CM (Intl. Classification Diseases)
 ICD10 and ICD10-CM
 SNOMED-CT (Clinical Terms)
 National Drug Codes (NDC)
XML-STDS-2
What is one Possible Solution?

CSE
5810

Standards and Usage of XML
XML Used in Myriad of Context
 Modeling and Information Exchange (XML
Schemas and Instances)
 XML Standards
 XACML – Access Control Markup Language
 OWL – Web Ontology Language
 HL7/CDA

What is/will be its Eventual Role in BMI?
XML-STDS-3
Overview of XML

CSE

5810




XML Overview, Tags, schema.
XML Query Languages: XPath &XQuery
XML Data Models
Biomedical Information and Databases
BMI Standards and Examples: HL7 and CDA
Survey of Technology
XML-STDS-4
XML Overview Continued
 eXtensible
CSE
5810
Markup Language
 Similar to HTML
 Meta-language that describes the content of the
document (self-describing)
 XML is primarily used as a data storage and interchange
medium
 XML exists in plain text format, however it may be
compressed, or altered for transfer
XML-STDS-5
XML Overview Continued
 There
CSE
5810
are no predefined data (tags), or grammer
inherently in XML
 XML tags give an XML document structure and
meaning
 Available tags are defined by a schema.
 All tags in an XML document come in pairs, open and
close
 Tags are completely nested, and there is no ambiguity in
their order
XML-STDS-6
XML: Extensible Markup Language

CSE
5810


Data sources
 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
XML-STDS-7
Structured & Semistructured Data

CSE
5810

Structured data
 Represented in a strict format
 Example: information stored in databases
Semistructured data
 Has a certain structure
 Not all information collected will have identical
structure
XML-STDS-8
Sample XML Structure
CSE
5810
XML-STDS-9
CSE
5810
XML-STDS-10
XML Tags

CSE
5810




XML tags may have an element field which is 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 attribute type 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.
XML-STDS-11
XML Schemas

CSE

5810

Schema information mixed in with data values
Self-describing data
May be displayed as a directed graph
 Labels or tags on directed edges represent:




Schema names
Names of attributes
Object types (or entity types or classes)
Relationships
XML-STDS-12
XML Schema
 The
CSE
5810
structure of an XML document is defined by its
schema.
 Dozens on 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.
XML-STDS-13
Schema Example (XSD)
CSE
5810
<?xml version="1.0" encoding="ISO-8859-1" ?>
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
<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>
<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>
XML-STDS-14
Sample XML Structure
CSE
5810
 XML
employs a tree structure model for representing
data
shiporder
shipto
orderperson
orderid
name
address
city
country
item
title
name
quantity
price
XML-STDS-15
XML Hierarchical Data Model

CSE
5810



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
XML-STDS-16
CSE
5810
XML-STDS-17
XML Hierarchical Data Model

CSE

5810



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
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
XML-STDS-18
XML Documents and Schema

CSE
5810
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

DOM (Document Object Model)
 Manipulate resulting tree representation
corresponding to a well-formed XML document
XML-STDS-19
XML Documents and Schema

CSE
5810
SAX (Simple API for XML)
 Processing of XML documents on the fly
• Notifies processing program through callbacks
whenever a start or end tag is encountered


Makes it easier to process large documents
Allows for streaming
XML-STDS-20
XML Schema

CSE
5810

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
XML-STDS-21
XML Schema

CSE
5810
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
XML-STDS-22
CSE
5810
XML-STDS-23
Sample XML Structure
CSE
5810
XML-STDS-24
XML Documents and Schema

CSE
5810
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
 Schemas Dominate ..

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
XML-STDS-25
XML Languages

CSE
5810
Two query language standards
 XPath
• 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
XML-STDS-26
XPath: Specifying Path Expressions in XML

CSE
5810
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 (//)
XML-STDS-27
XPath: Specifying Path Expressions in XML

CSE

5810
Attribute name prefixed by the @ symbol
Wildcard symbol *
 Stands for any element
 Example: /company/*
XML-STDS-28
XPath: Specifying Path Expressions in XML

CSE
5810

Axes
 Move in multiple directions from current node in
path expression
 Include self, child, descendent, attribute, parent,
ancestor, previous sibling, and next sibling
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
XML-STDS-29
Querying XML - XPath
 Many
CSE
5810
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
XML-STDS-30
Querying XML - XQuery
 Functional
CSE
5810
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
XML-STDS-31
XQuery: Specifying Queries in XML

CSE
5810
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
XML-STDS-32
CSE
5810
XML-STDS-33
XML Models
 Naively
CSE
5810
there are two models of XML use:
 Data-centric
 Document-centric
 In reality, most XML use is a hybrid of the two
 More important is the database strategy used with XML
 Relational
 Content Managment
 Native XML
XML-STDS-34
XML as Data Exchange Medium

CSE

5810



Widespread Usage Across Computing
UML Tools have Standardized on XML Schema
 Export Given UML Design to XML Instances
 Track Both Design Data and Graphical Data
Database Interactions via XML
 Import from XML into a Relational Schema
 Export form a Relational DB into XML Schema
and Instances
Web Services
 Exchange of Information
 SOAP, WSDL, and UDDI
Facilitates Information Exchange and Portability
XML-STDS-35
XML References

CSE
5810 










“Canonical XML Version 1.0”, John Boyer. 15 March 2001.
W3C
“XML Path Language (Xpath) 2.0”. W3C working Draft. 2
May 2003. W3C
“XML Schema”. XML Schema Working Group. 1 January
2008. W3C
<http://www.w3.org/XML/Schema>
“XML Schema: Formal Description” Brown, Fuchs, et. al. 25
September 2001. W3C
<http://www.w3.org/TR/xmlschema-formal/>
“Extensible Markup Language (XML)”. 1 January 2008. W3C
<http://www.w3.org/XML/>
http://www.25hoursaday.com/StoringAndQueryingXML.html
http://www.nih.gov/about/director/060399.htm
http://www.research.ibm.com/journal/sj/452/shabo.html
“Overview of the CDISC Operational Data Model”. 26 April
2002. CDISC
XML-STDS-36
Medical Data Model
 Medical
CSE
5810
data is non-homogeneous
 But, there exists general trends in medical data:
 Fine grain data such as dates, times, images
 Documents and human generated descriptions and
observations
 Human interaction creates semi-structured data
 Ability to transfer information is esential
 Medical data fits into hybrid model
XML-STDS-37
XML Usage in BMI

CSE

5810
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 relieson efficient storage and transfer of
information


XML-STDS-38
BMI Scope

CSE
5810


”Biomedical computing is entering an age where
creative exploration of huge amounts of data will lay
the foundation of hypotheses.” ~NIH Director
Issues:
 Standards: Terminology, Syntax and Semantics to
Support Data Consistent Data Usage/Exchange
 Curation: Repository Checked & Cross-Referenced
to avoid Transitive propagation of error
 Interoperability: Data should be as Consistent as
possible across Repositories for All Stakeholders
Computational and Systems issue:
 Utilize and manipulate information.
 Process large volumes of information.
XML-STDS-39
Data sharing and Semantic Interoperability
 Case
CSE
5810
study: Electronic Health Record
 The development and use of an integrated health
record for a patient
 Collect data from multiple sources
 Hetergenous data, e.g. clinical, clinical-trial, genomic
data
 Primary Obstacles:
 Proprietary data formats
 Identifying same “J. Smith” across repositories
 Uniformity on technical level:
 Exchange in text, csv, CDA, CCR, etc.
 Progress Towards Semantic Interoperation
 Ontologies to unify terms across repositories
XML-STDS-40
XML in Clinical Data
 HL7
CSE
5810
standards organization.
 V2: ASCII bar format. example:
HL7V3|1|2.02
Message|2.16.840.1.113883.1122^CNTRL-3456|2002081614303516^- --->
06:00||3.0|2.16.840.1.113883^POLB_IN004410||P|I|ER|ER
respondTo|RSP|tel:555-555-5555^^WP
entit yRsp|||{FAM^^Hippocrates~GIV^^Harold~GIV^^H~SFX^AC^MD}|tel:555-555-5555^^WP
sender|SND|nfs:127.127.127.255
device||2.16.840.1.113883.1122^GHH LAB|{GIV^^An Entit y Name}^L|||tel:555-555-2005^^H
agencyFor
representedOrganization||\NOTH\
location|||2.16.840.1.113883.1122^ELAB-3|{^^GHH Lab}^TN
receiver|RCV|nfs:127.127.127.0
device|||2.16.840.1.113883.1122^GHH O E|{GIV^^An Entit y Name}^L|||tel:555-555-2005^^H
agencyFor
representedOrganization|||2.16.840.1.113883.19.3.1001|{^^GHH Outpatient Clinic}^TN
location|||2.16.840.1.113883.1122^BLDG4|{^^GHH Outpatient Clinic}^TN

Awkward, inflexible, unclear meaning of values.
XML-STDS-41
HL7 V3 Specification

CSE
5810
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="10.23.4573.15879"/>
<code code="313193002" codeSystem="2.16.840.1.113883.6.96"
codeSystemName="SNOMED CT" displayName="Peak flow"/>
<effectiveTime value="20000407"/>
<value xsi:type="RTO_PQ_PQ">
<numerator value="260" unit="l"/>
<denominator value="1" unit="min"/>
</value>
</observation>
XML-STDS-42
XML BMI Issues

CSE
5810



Clinical information in an EMR can be free text
 How do you query this?
 How do you identify and integrate?
Schemas and models are extremely complex, with
nesting, recursion and compound data types
 Difficult mapping to relational databases
 Different organization of ontologies/semantics
XML instances may be megabtypes/gigabytes in size
 What database solutions exist to handle such large
files?
How would you Search a
 Individual CDA or CCR Instance?
 Set of CDA or CCR Instances?
XML-STDS-43
XML References

CSE
5810 










“Canonical XML Version 1.0”, John Boyer. 15 March 2001.
W3C
“XML Path Language (Xpath) 2.0”. W3C working Draft. 2
May 2003. W3C
“XML Schema”. XML Schema Working Group. 1 January
2008. W3C
<http://www.w3.org/XML/Schema>
“XML Schema: Formal Description” Brown, Fuchs, et. al. 25
September 2001. W3C
<http://www.w3.org/TR/xmlschema-formal/>
“Extensible Markup Language (XML)”. 1 January 2008. W3C
<http://www.w3.org/XML/>
http://www.25hoursaday.com/StoringAndQueryingXML.html
http://www.nih.gov/about/director/060399.htm
http://www.research.ibm.com/journal/sj/452/shabo.html
“Overview of the CDISC Operational Data Model”. 26 April
2002. CDISC
XML-STDS-44
HL7’s CDA
CSE
5810


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
45
CDA
Health
chartXML-STDS-45
ASTM’s CCR
CSE
5810
46
XML-STDS-46
HL7 CDA and CCR

CSE
5810

Standards and Usage of XML
 Consider CDA – Clinical Document Architecture
 Standard for Clinical (Provider) Medical Record
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...
XML-STDS-48
What is one Possible Solution?

CSE

5810
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="2.16.840.1.113883.3.933"/>
<set_id EX="B" RT="2.16.840.1.113883.3.933"/>
<version_nbr V="2"/>
<document_type_cd V="11488-4" S="2.16.840.1.113883.6.1"
DN="Consultation note"/>
<origination_dttm V="2000-04-07"/>
<confidentiality_cd ID="CONF1" V="N" S="2.16.840.1.113883.5.1xxx"/>
<confidentiality_cd ID="CONF2" V="R" S="2.16.840.1.113883.5.1xxx"/>
<document_relationship>
<document_relationship.type_cd V="RPLC"/>
<related_document>
<id EX="a234" RT="2.16.840.1.113883.3.933"/>
<set_id EX="B" RT="2.16.840.1.113883.3.933"/>
<version_nbr V="1"/>
</related_document>
</document_relationship>
<fulfills_order>
<fulfills_order.type_cd V="FLFS"/>
<order><id EX="x23ABC" RT="2.16.840.1.113883.3.933"/></order>
<order><id EX="x42CDE" RT="2.16.840.1.113883.3.933"/></order>
</fulfills_order>
XML-STDS-49
CDA Example - Continued
CSE
5810
XML-STDS-50
CDA Example - Continued
CSE
5810
XML-STDS-51
CDA Example - Continued
CSE
5810
XML-STDS-52
CDA Example - Continued
CSE
5810
XML-STDS-53
CDA Example - Continued
CSE
5810
XML-STDS-54
CDA Example - Continued
CSE
5810
XML-STDS-55
CDA Example - Continued
CSE
5810
XML-STDS-56
CDA Example - Continued
CSE
5810
XML-STDS-57
CCR Schema
CSE
5810
<xs:schema xmlns="urn:astm-org:CCR" xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:ccr="urn:astm-org:CCR" targetNamespace="urn:astm-org:CCR"
elementFormDefault="qualified" attributeFormDefault="unqualified">
<xs:import namespace="http://www.w3.org/2000/09/xmldsig#"
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:complexType>
<xs:sequence>
<xs:element name="ActorID" type="xs:string" />
</xs:sequence>
</xs:complexType>
</xs:element>
<xs:element name="From">
<xs:complexType>
<xs:sequence>
<xs:element name="ActorLink" type="ActorReferenceType"
maxOccurs="unbounded" />
</xs:sequence>
</xs:complexType>
</xs:element>
…
XML-STDS-58
CCR Instance
CSE
5810
<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>2007-04-04T07:00:00Z</ExactDateTime>
</DateTime>
<DateTime>
<Type>
<Text>Stop date</Text>
</Type>
<ExactDateTime>2008-07-20T07:00:00Z</ExactDateTime>
</DateTime>
<Description>
<Code>
<Value>346.80</Value>
<CodingSystem>ICD9</CodingSystem>
<Version>2004</Version>
</Code>
…
XML-STDS-59
Standard and Databases

CSE
5810


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
XML-STDS-60
Health Care Standards of Note

CSE

5810




MeSH
Unified Medical Language System
ICD9 and ICD9-CM (Intl. Classification Diseases)
ICD10 and ICD10-CM
SNOMED-CT (Clinical Terms)
National Drug Codes (NDC)
XML-STDS-61
MeSH

CSE
5810



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.
http://www.nlm.nih.gov/mesh/
XML-STDS-62
MeSH in ASCII
CSE
5810
*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 = D03.438.221.173
PA = Anti-Bacterial Agents
PA = Ionophores
MH_TH = NLM (1975)
ST = T109
ST = T195
N1 = 4-Benzoxazolecarboxylic acid, 5-(methylamino)-2-((3,9,11trimethyl-8-(1-methyl-2-oxo-2-(1H-pyrrol-2-yl)ethyl)-1,7dioxaspiro(5.5)undec-2-yl)methyl)-, (6S(6alpha(2S*,3S*),8beta(R*),9beta,11alpha))RN = 52665-69-7
PI = Antibiotics (1973-1974)
PI = Carboxylic Acids (1973-1974)
XML-STDS-63
MeSH in ASCII
CSE
5810
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 23187 1975-90
PM = 91; was A 23187 1975-90 (see under ANTIBIOTICS 1975-83)
HN = 91(75); was A 23187 1975-90 (see under ANTIBIOTICS 1975-83)
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
XML-STDS-64
MeSH in XML - desc2011.dtd
<!-- MeSH DTD file for Descriptor records. desc2011.dtd -->
-->
CSE <!-- Author: MeSH
-->
5810 <!-- Effective: 09/01/2010
<!-- #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)">
XML-STDS-65
MeSH in XML - desc2011.dtd
<!ELEMENT DescriptorRecordSet (DescriptorRecord*)>
CSE <!ATTLIST DescriptorRecordSet LanguageCode
5810 (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">
XML-STDS-66
MeSH in XML - desc2011.dtd
<!ELEMENT
CSE <!ELEMENT
5810 <!ELEMENT
<!ELEMENT
<!ELEMENT
<!ELEMENT
<!ELEMENT
<!ELEMENT
<!ELEMENT
<!ELEMENT
<!ELEMENT
<!ELEMENT
ActiveMeSHYearList (Year+)>
AllowableQualifiersList (AllowableQualifier+) >
AllowableQualifier (QualifierReferredTo,Abbreviation )>
Annotation (#PCDATA)>
ConsiderAlso (#PCDATA) >
Day (#PCDATA)>
DescriptorUI (#PCDATA) >
DescriptorName (String) >
DateCreated (%normal.date;) >
DateRevised (%normal.date;) >
DateEstablished (%normal.date;) >
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
XML-STDS-67
dMeSH in XML - Sample
<?xml version="1.0"?>
CSE <!DOCTYPE DescriptorRecordSet SYSTEM "desc2011.dtd">
5810 <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>
XML-STDS-68
dMeSH in XML - Sample
<ActiveMeSHYearList>
<Year>2007</Year>
<Year>2008</Year>
CSE
<Year>2009</Year>
5810
<Year>2011</Year>
</ActiveMeSHYearList>
<AllowableQualifiersList>
<AllowableQualifier>
<QualifierReferredTo>
<QualifierUI>Q000008</QualifierUI>
<QualifierName>
<String>administration &amp; dosage</String>
</QualifierName>
</QualifierReferredTo>
<Abbreviation>AD</Abbreviation>
</AllowableQualifier>
<AllowableQualifier>
<QualifierReferredTo>
<QualifierUI>Q000009</QualifierUI>
<QualifierName>
<String>adverse effects</String>
</QualifierName>
</QualifierReferredTo>
<Abbreviation>AE</Abbreviation>
</AllowableQualifier>
ETC
XML-STDS-69
Unifies Medical Language System

CSE

5810
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.
XML-STDS-70
UMLS Concepts, Semantic Types/Relations
CSE
5810
XML-STDS-71
ICD9 Respiratory Diseases
CSE
5810
XML-STDS-72
ICD10 Respiratory Diseases
CSE
5810
XML-STDS-73
SNOMED-CT

CSE
5810

SNOMED stands for Systemized Nomenclature Of
Medicine Clinical Terms. SNOMED-CT is the result
of merging two ontologies: SNOMED-RT and
Clinical Terms.
http://www.ihtsdo.org/snomed-ct/
75
XML-STDS-75
SNOMED-CT

CSE

5810

Composed of Concepts, Terms, and Relationships
Precisely Represent Clinical Information Across
Scope of Health Care
Content Coverage Divided into Hierarchies
76
XML-STDS-76
SNOMED Example
CSE
5810
XML-STDS-77
National Drug Codes

CSE

5810



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:


http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm
Searchable Database:

http://www.accessdata.fda.gov/scripts/cder/ndc/default.cfm
XML-STDS-78
NDC Examples
CSE
5810
XML-STDS-79
Concluding Remarks: XML/Standards

CSE
5810


Explored Usage of XML Including:
 Basic XML Concepts
 XML Tools and Standards
 XML Databases
 Use of XML in BMI
Reviewed HL7 and CDA
Examined Numerous Standards
XML-STDS-80