XML-STDS-1 CSE 5810 XML and Standards in BMI Prof. Steven A. Demurjian, Sr. Computer Science & Engineering Department The University of Connecticut 371

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XML and Standards in BMIXML and Standards in BMI

Prof. Steven A. Demurjian, Sr.Computer Science & Engineering Department

The University of Connecticut371 Fairfield Road, Box U-255

Storrs, CT 06269-2155

[email protected]://www.engr.uconn.edu/

~steve(860) 486 - 4818

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Overview Overview What is XML? How is it Used Today?What is XML? How is it Used Today? HL7 and CDA, CCRHL7 and CDA, CCR Other StandardsOther 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)

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What is one Possible Solution?What is one Possible Solution? Standards and Usage of XMLStandards and Usage of XML XML Used in Myriad of ContextXML 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

XML Databases What is/will be its Eventual Role in BMI?What is/will be its Eventual Role in BMI?

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Overview of XMLOverview of XML XML Overview, Tags, schema.XML Overview, Tags, schema. XML Query Languages: XPath &XQueryXML Query Languages: XPath &XQuery XML Data ModelsXML Data Models Storage Strategy + XML DBMS:Storage Strategy + XML DBMS:

Relational, CMS, native Native XML DBMS: Pros/Cons.Native XML DBMS: Pros/Cons. Biomedical Information and DatabasesBiomedical Information and Databases BMI Standards and Examples: HL7 and CDABMI Standards and Examples: HL7 and CDA Survey of TechnologySurvey of Technology

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XML overviewXML overview eXtensible Markup LanguageeXtensible Markup Language Similar to HTMLSimilar to HTML Meta-language that describes the content of the Meta-language that describes the content of the

document (self-describing)document (self-describing) XML is primarily used as a data storage and interchange XML is primarily used as a data storage and interchange

mediummedium XML exists in plain text format, however it may be XML exists in plain text format, however it may be

compressed, or altered for transfercompressed, or altered for transfer

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XML overview cont.XML overview cont. There are no predefined data (tags), or grammer There are no predefined data (tags), or grammer

inherently in XMLinherently in XML XML tags give an XML document structure and XML tags give an XML document structure and

meaningmeaning Available tags are defined by a schema.Available tags are defined by a schema. All tags in an XML document come in pairs, open and All tags in an XML document come in pairs, open and

closeclose Tags are completely nested, and there is no ambiguity in Tags are completely nested, and there is no ambiguity in

their ordertheir order

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XML tagsXML tags XML tags may have an element field which is used to XML tags may have an element field which is used to

store information within the tag or Meta-datastore information within the tag or Meta-data Plain text can be placed between tags and this text is Plain text can be placed between tags and this text is

not parsednot parsed CDATA is character dataCDATA 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 The ENTITY attribute type indicates that the attribute will represent an external entity in the document itselfwill represent an external entity in the document itself

The ID attribute type if you want to specify a unique The ID attribute type if you want to specify a unique identifier for each element.identifier for each element.

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XML SchemaXML Schema The structure of an XML document is defined by its The structure of an XML document is defined by its

schema.schema. Dozens on languages to define XML schema:Dozens on languages to define XML schema:

DTD W3C (XSD) NG - Relax

This file can validate any instance of an XML document This file can validate any instance of an XML document against it self.against it self.

This file, or schema also defines allowable tags.This file, or schema also defines allowable tags.

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Sample XML StructureSample XML Structure XML employees a tree structure model for XML employees a tree structure model for

representing data (previous slide)representing data (previous slide)

shiporder

orderperson

shipto

name address city country

item

title name quantity price

orderid

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Schema Example (XSD)Schema Example (XSD)

<?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>

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Querying XML - XPathQuerying XML - XPath Many languages to query XMLMany languages to query XML

XPath and XQuery are W3C standards Xpath is a compact method of traversing previous treeXpath 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 behaviorsExtensible to add user defined behaviors Treats each tag as a node in the treeTreats each tag as a node in the tree

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Querying XML - XQueryQuerying XML - XQuery Functional extension of XPath Functional extension of XPath XML equivalent of SQLXML equivalent of SQL Navigate and manipulate document nodes.Navigate and manipulate document nodes. Works on collections of documents, or even fragments.Works on collections of documents, or even fragments.

FOR $b IN document("bib.xml")//bookWHERE $b/publisher = "Morgan Kaufmann"AND $b/year = "1998"RETURN $b/title

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XML ModelsXML Models Naively there are two models of XML use:Naively there are two models of XML use:

Data-centric Document-centric

In reality, most XML use is a hybrid of the twoIn reality, most XML use is a hybrid of the two More important is the database strategy used with XMLMore important is the database strategy used with XML

Relational Content Managment Native XML

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Data – Centric ModelData – Centric Model Information is generally stored in a relational databaseInformation is generally stored in a relational database XML is transport medium, nothing moreXML is transport medium, nothing more Irrelevent to application that data exists as XML for Irrelevent to application that data exists as XML for

some period of timesome period of time Characteristics:Characteristics:

Fine grained data. Data relationship is insignificant. Need to transfer relational information. Means of storing new information.

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Document – Centric ModelDocument – Centric Model When XML is utilized soley as a documentWhen XML is utilized soley as a document

This pesentation in Open Office The documents in part, or in full are stored and retrieved The documents in part, or in full are stored and retrieved Does not originate from relational databaseDoes not originate from relational database Document used for human consumptionDocument used for human consumption Usually information written by hand in a language like Usually information written by hand in a language like

PDF, RTF then converted to XMLPDF, RTF then converted to XML

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Reality: Hybrid ModelReality: Hybrid Model Most documents like a PDF will also contain small Most documents like a PDF will also contain small

grained information (last edited date, character set)grained information (last edited date, character set) Data from a relational DB may even be a document, or Data from a relational DB may even be a document, or

require self descriptionrequire self description Various database technologies support all modelsVarious database technologies support all models Important to understand your data, and choose db Important to understand your data, and choose db

technology that is most compatibletechnology that is most compatible

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XML as Data Exchange MediumXML as Data Exchange Medium Widespread Usage Across ComputingWidespread Usage Across Computing UML Tools have Standardized on XML SchemaUML Tools have Standardized on XML Schema

Export Given UML Design to XML Instances Track Both Design Data and Graphical Data

Database Interactions via XMLDatabase Interactions via XML Import from XML into a Relational Schema Export form a Relational DB into XML Schema

and Instances Web ServicesWeb Services

Exchange of Information SOAP, WSDL, and UDDI

Facilitates Information Exchange and PortabilityFacilitates Information Exchange and Portability

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Medical Data ModelMedical Data Model Medical data is non-homogeneousMedical data is non-homogeneous But, there exists general trends in medical data: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 esentialAbility to transfer information is esential Medical data fits into hybrid modelMedical data fits into hybrid model

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Data – Centric ComparisonData – Centric Comparison Advantages:Advantages:

Utlizes existing database software. (IBM, Oracle, SqlServer) Quick ( existing db's are already fast) Dual role (not limited only to XML) Many even support XQuery

Disadvantages:Disadvantages: More configuration (mapping relational -> XML) Slower when creating complex XML files due to middle step

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Document – Centric ComparisonDocument – Centric Comparison Advantages:Advantages:

Good integration into workflow Document managment made easy Collaboration, and web publishing

Disadvantages:Disadvantages: Not able to extract data from document directly Not designed for high availability, high load systems Non-uniformity in implementations

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Storage Strategy: RelationalStorage Strategy: Relational Utilizing a relational database to store XML documents Utilizing a relational database to store XML documents

and data is very popularand data is very popular In a very data – centric application this approach is In a very data – centric application this approach is

intuitiveintuitive Most top tier database applications support XML in Most top tier database applications support XML in

some waysome way Oracle, SQL server, IBM, etc...

Software is highly supported and well developed.Software is highly supported and well developed.

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XML Shema mappingXML Shema mapping Using a relational DB requires mapping XML schema Using a relational DB requires mapping XML schema

to DB schema.to DB schema. Table based:Table based:

Often implemented as a middleware layer Schema structure must follow row-column

convention Object – relational:Object – relational:

XML is a tree of objects Mapped to DB using well established methods Natively supported in some DB apps

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Storage Strategy: CMSStorage Strategy: CMS CMS – Content Management SystemCMS – Content Management System Used in exclusively document-centric modelUsed in exclusively document-centric model Various programs allow indexing, storage, Various programs allow indexing, storage,

manipulation, and publication of XML documentsmanipulation, and publication of XML documents Application specificApplication specific Numerous implementations, most recently Open Numerous implementations, most recently Open

Office and MS Word 2007Office and MS Word 2007 Not very interesting or useful in context of biomedical Not very interesting or useful in context of biomedical

informationinformation

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Native XML DatabasesNative XML Databases Definition:Definition:

”A database that has an XML document as its fundamental unit of (logical) storage and defines a (logical) model for an XML document, as opposed to the data in that document, and stores and retrieves documents according to that model. At a minimum, the model must include elements, attributes, PCDATA, and document order.”

Data types: No support in XML, need a mappingData types: No support in XML, need a mapping Document or database schema can be used External user defined mapping Not necessary when only transfering data

No requirement on underlying medium or No requirement on underlying medium or implementationimplementation

Two architectures; text and model basedTwo architectures; text and model based

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Native: Text-basedNative: Text-based Use any DBUse any DB

Rather than mapping schemas, store entire XML documents

Usually involves saving entire document as a BLOB / Character LOB

Utilize various text field searches to retrieve info from XML document

Some DB text searching are being made XML aware

Speed: Document located on disk preferences full or partial document retrieval

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Native: Model-basedNative: Model-based Internal object model of the document schemaInternal object model of the document schema Store this model in a databaseStore this model in a database

Relational / object-oriented database Proprietary

Performance similar to chosen db enginePerformance similar to chosen db engine Still limited by hierachy of XML dataStill limited by hierachy of XML data

Retrieve all orderid's from hundreds of docs slow Support for common XML query languagesSupport for common XML query languages

XPath, XQuery, etc...

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XML Usage in BMIXML Usage in BMI The convergence of computation and biomedicineThe convergence of computation and biomedicine The NIH BMI Science and Tech Initiative: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 All relieson efficient storage and transfer of informationinformation

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BMI ScopeBMI Scope ””Biomedical computing is entering an age where Biomedical computing is entering an age where

creative exploration of huge amounts of data will lay creative exploration of huge amounts of data will lay the foundation of hypotheses.” ~NIH Directorthe foundation of hypotheses.” ~NIH Director

Issues: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:Computational and Systems issue:

Utilize and manipulate information. Process large volumes of information.

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Data sharing and Semantic InteroperabilityData sharing and Semantic Interoperability Case study: Electronic Health RecordCase 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: Primary Obstacles:

Proprietary data formats Identifying same “J. Smith” across repositories

Uniformity on technical level: Uniformity on technical level: Exchange in text, csv, CDA, CCR, etc.

Progress Towards Semantic InteroperationProgress Towards Semantic Interoperation Ontologies to unify terms across repositories

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XML in Clinical DataXML in Clinical Data HL7 standards organization.HL7 standards organization.

V2: ASCII bar format. example:

HL7V3|1|2.02Message|2.16.840.1.113883.1122^CNTRL-3456|2002081614303516^- ---> 06:00||3.0|2.16.840.1.113883^POLB_IN004410||P|I|ER|ERrespondTo|RSP|tel:555-555-5555^^WP entit yRsp|||{FAM^^Hippocrates~GIV^^Harold~GIV^^H~SFXÂC^MD}|tel:555-555-5555^^WPsender|SND|nfs:127.127.127.255 device||2.16.840.1.113883.1122^GHH LAB|{GIV^Ân Entit y Name}^L|||tel:555-555-2005^^H agencyFor representedOrganization||\NOTH\ location|||2.16.840.1.113883.1122ÊLAB-3|{^^GHH Lab}^TNreceiver|RCV|nfs:127.127.127.0 device|||2.16.840.1.113883.1122^GHH O E|{GIV^Ân 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.

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HL7 V3 SpecificationHL7 V3 Specification Built around Reference Information Model:Built around Reference Information Model:

Entity, Role, Participation, and Act Utilizes dedicated vocabularites and data types. Every specification must begin from RIM.

Clinical Document ArchitectureClinical 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>

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XML BMI IssuesXML BMI Issues Clinical information in an EMR can be free text 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 Schemas and models are extremely complex, with nesting, recursion and compound data typesnesting, recursion and compound data types Difficult mapping to relational databases Different organization of ontologies/semantics

XML instances may be megabtypes/gigabytes in sizeXML instances may be megabtypes/gigabytes in size What database solutions exist to handle such large

files? How would you Search a How would you Search a

Individual CDA or CCR Instance? Set of CDA or CCR Instances?

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XML ReferencesXML References ““Canonical XML Version 1.0”, John Boyer. 15 March 2001. Canonical XML Version 1.0”, John Boyer. 15 March 2001.

W3CW3C ““XML Path Language (Xpath) 2.0”. W3C working Draft. 2 XML Path Language (Xpath) 2.0”. W3C working Draft. 2

May 2003. W3CMay 2003. W3C ““XML Schema”. XML Schema Working Group. 1 January XML Schema”. XML Schema Working Group. 1 January

2008. W3C2008. W3C <http://www.w3.org/XML/Schema> <http://www.w3.org/XML/Schema> ““XML Schema: Formal Description” Brown, Fuchs, et. al. 25 XML Schema: Formal Description” Brown, Fuchs, et. al. 25

September 2001. W3CSeptember 2001. W3C <http://www.w3.org/TR/xmlschema-formal/><http://www.w3.org/TR/xmlschema-formal/> ““Extensible Markup Language (XML)”. 1 January 2008. W3CExtensible Markup Language (XML)”. 1 January 2008. W3C <http://www.w3.org/XML/><http://www.w3.org/XML/> http://www.25hoursaday.com/StoringAndQueryingXML.htmlhttp://www.25hoursaday.com/StoringAndQueryingXML.html http://www.nih.gov/about/director/060399.htmhttp://www.nih.gov/about/director/060399.htm http://www.research.ibm.com/journal/sj/452/shabo.htmlhttp://www.research.ibm.com/journal/sj/452/shabo.html ““Overview of the CDISC Operational Data Model”. 26 April Overview of the CDISC Operational Data Model”. 26 April

2002. CDISC2002. CDISC

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ConsultConsult

HL7’s CDAHL7’s CDA

Clinical Document ArchitectureClinical Document Architecture ANSI/HL7 R1-2000, R2-2005

eDocuments for InteroperabilityeDocuments 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

CDA CDA Health Health chartchart

SummarySummary

PathPathRadiologyRadiology

DischargeDischarge

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3535

ASTM’s CCRASTM’s CCR

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HL7 CDA and CCRHL7 CDA and CCR Standards and Usage of XMLStandards and Usage of XML

Consider CDA – Clinical Document Architecture Standard for Clinical (Provider) Medical Record

Clinical Record Organized as: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...

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What is one Possible Solution?What is one Possible Solution? Let’s Explore this in Greater DetailLet’s Explore this in Greater Detail Starting with the CDA HeaderStarting 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>

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CDA Example - ContinuedCDA Example - Continued

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CCR SchemaCCR Schema<xs:schema xmlns="urn:astm-org:CCR" xmlns:xs="http://www.w3.org/2001/XMLSchema" <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" xmlns:ccr="urn:astm-org:CCR" targetNamespace="urn:astm-org:CCR" elementFormDefault="qualified" attributeFormDefault="unqualified">elementFormDefault="qualified" attributeFormDefault="unqualified">

<xs:import namespace="http://www.w3.org/2000/09/xmldsig#" <xs:import namespace="http://www.w3.org/2000/09/xmldsig#" schemaLocation="xmldsig-core-schema.xsd" />schemaLocation="xmldsig-core-schema.xsd" /><xs:element name="ContinuityOfCareRecord"><xs:element name="ContinuityOfCareRecord"> <xs:complexType><xs:complexType> <xs:sequence><xs:sequence> <xs:element name="CCRDocumentObjectID" type="xs:string" /><xs:element name="CCRDocumentObjectID" type="xs:string" /> <xs:element name="Language" type="CodedDescriptionType" /><xs:element name="Language" type="CodedDescriptionType" /> <xs:element name="Version" type="xs:string" /><xs:element name="Version" type="xs:string" /> <xs:element name="DateTime" type="DateTimeType" /><xs:element name="DateTime" type="DateTimeType" /> <xs:element name="Patient" maxOccurs="2"><xs:element name="Patient" maxOccurs="2"> <xs:complexType><xs:complexType> <xs:sequence><xs:sequence> <xs:element name="ActorID" type="xs:string" /><xs:element name="ActorID" type="xs:string" /> </xs:sequence></xs:sequence> </xs:complexType></xs:complexType> </xs:element></xs:element> <xs:element name="From"><xs:element name="From"> <xs:complexType><xs:complexType> <xs:sequence><xs:sequence> <xs:element name="ActorLink" type="ActorReferenceType"<xs:element name="ActorLink" type="ActorReferenceType"

maxOccurs="unbounded" />maxOccurs="unbounded" /> </xs:sequence></xs:sequence> </xs:complexType></xs:complexType> </xs:element></xs:element>

……

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CCR InstanceCCR Instance<ContinuityOfCareRecord xmlns='urn:astm-org:CCR'><ContinuityOfCareRecord xmlns='urn:astm-org:CCR'> <CCRDocumentObjectID>Doc</CCRDocumentObjectID><CCRDocumentObjectID>Doc</CCRDocumentObjectID> <Language><Text>English</Text></Language><Language><Text>English</Text></Language> <Version>V1.0</Version><Version>V1.0</Version> <DateTime><ExactDateTime>2008</ExactDateTime></DateTime><DateTime><ExactDateTime>2008</ExactDateTime></DateTime> <Patient><ActorID>Patient</ActorID></Patient><Patient><ActorID>Patient</ActorID></Patient> <Body><Body> <Problems><Problems> <Problem><Problem> <DateTime><DateTime> <Type><Type> <Text>Start date</Text><Text>Start date</Text> </Type></Type> <ExactDateTime>2007-04-04T07:00:00Z</ExactDateTime><ExactDateTime>2007-04-04T07:00:00Z</ExactDateTime> </DateTime></DateTime> <DateTime><DateTime> <Type><Type> <Text>Stop date</Text><Text>Stop date</Text> </Type></Type> <ExactDateTime>2008-07-20T07:00:00Z</ExactDateTime><ExactDateTime>2008-07-20T07:00:00Z</ExactDateTime> </DateTime></DateTime> <Description><Description> <Code><Code> <Value>346.80</Value><Value>346.80</Value> <CodingSystem>ICD9</CodingSystem><CodingSystem>ICD9</CodingSystem> <Version>2004</Version><Version>2004</Version> </Code></Code>

……

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Other Relevant Standards of NoteOther Relevant Standards of Note MeSHMeSH Unified Medical Language SystemUnified Medical Language System ICD9 and ICD9-CM (Intl. Classification Diseases)ICD9 and ICD9-CM (Intl. Classification Diseases) ICD10 and ICD10-CMICD10 and ICD10-CM SNOMED-CT (Clinical Terms)SNOMED-CT (Clinical Terms) National Drug Codes (NDC)National Drug Codes (NDC)

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MeSHMeSH The Medical Subject Headings (MeSH®) thesaurus is The Medical Subject Headings (MeSH®) thesaurus is

a controlled vocabulary produced by the National a controlled vocabulary produced by the National Library of Medicine and used for indexing, cataloging, Library of Medicine and used for indexing, cataloging, and searching for biomedical and health-related and searching for biomedical and health-related information and documents. information and documents.

2011 MeSH includes the subject descriptors appearing 2011 MeSH includes the subject descriptors appearing in MEDLINE®/PubMed®, the NLM catalog database, in MEDLINE®/PubMed®, the NLM catalog database, and other NLM databases.and other NLM databases.

Many synonyms, near-synonyms, and closely related Many synonyms, near-synonyms, and closely related concepts are included as entry terms to help users find concepts are included as entry terms to help users find the most relevant MeSH descriptor for the concept the most relevant MeSH descriptor for the concept they are seeking. they are seeking.

http://www.nlm.nih.gov/mesh/http://www.nlm.nih.gov/mesh/

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Descriptor Data ElementsDescriptor Data Elements

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Qualifier Data ElementsQualifier Data Elements

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Supplementary ConceptsSupplementary Concepts

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MeSH in ASCIIMeSH in ASCII*NEWRECORD*NEWRECORDRECTYPE = DRECTYPE = DMH = CalcimycinMH = CalcimycinAQ = AA AD AE AG AI AN BI BL CF CH CL CS CT DU EC HI IM IP ME PD 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 URPK PO RE SD ST TO TU URENTRY = A-23187|T109|T195|LAB|NRW|NLM (1991)|900308|abbcdefENTRY = A-23187|T109|T195|LAB|NRW|NLM (1991)|900308|abbcdefENTRY = A23187|T109|T195|LAB|NRW|UNK (19XX)|741111|abbcdefENTRY = A23187|T109|T195|LAB|NRW|UNK (19XX)|741111|abbcdefENTRY = Antibiotic A23187|T109|T195|NON|NRW|NLM (1991)|900308|ENTRY = Antibiotic A23187|T109|T195|NON|NRW|NLM (1991)|900308|abbcdefabbcdefENTRY = A 23187ENTRY = A 23187ENTRY = A23187, AntibioticENTRY = A23187, AntibioticMN = D03.438.221.173MN = D03.438.221.173PA = Anti-Bacterial AgentsPA = Anti-Bacterial AgentsPA = IonophoresPA = IonophoresMH_TH = NLM (1975)MH_TH = NLM (1975)ST = T109ST = T109ST = T195ST = T195N1 = 4-Benzoxazolecarboxylic acid, 5-(methylamino)-2-((3,9,11-N1 = 4-Benzoxazolecarboxylic acid, 5-(methylamino)-2-((3,9,11-trimethyl-8-(1-methyl-2-oxo-2-(1H-pyrrol-2-yl)ethyl)-1,7-trimethyl-8-(1-methyl-2-oxo-2-(1H-pyrrol-2-yl)ethyl)-1,7-dioxaspiro(5.5)undec-2-yl)methyl)-, (6S-dioxaspiro(5.5)undec-2-yl)methyl)-, (6S-(6alpha(2S*,3S*),8beta(R*),9beta,11alpha))-(6alpha(2S*,3S*),8beta(R*),9beta,11alpha))-RN = 52665-69-7RN = 52665-69-7PI = Antibiotics (1973-1974)PI = Antibiotics (1973-1974)PI = Carboxylic Acids (1973-1974)PI = Carboxylic Acids (1973-1974)

XML-STDS-55

CSE5810

MeSH in ASCIIMeSH in ASCII

MS = An ionophorous, polyether antibiotic from Streptomyces MS = An ionophorous, polyether antibiotic from Streptomyces chartreusensis. It binds and transports cations across membranes chartreusensis. It binds and transports cations across membranes and uncouples oxidative phosphorylation while inhibiting ATPase of and uncouples oxidative phosphorylation while inhibiting ATPase of rat liver mitochondria. The substance is used mostly as a rat liver mitochondria. The substance is used mostly as a biochemical tool to study the role of divalent cations in various biochemical tool to study the role of divalent cations in various biological systems.biological systems.OL = use CALCIMYCIN to search A 23187 1975-90OL = use CALCIMYCIN to search A 23187 1975-90PM = 91; was A 23187 1975-90 (see under ANTIBIOTICS 1975-83)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)HN = 91(75); was A 23187 1975-90 (see under ANTIBIOTICS 1975-83)MED = *62MED = *62MED = 847MED = 847M90 = *299M90 = *299M90 = 2405M90 = 2405M85 = *454M85 = *454M85 = 2878M85 = 2878M80 = *316M80 = *316M80 = 1601M80 = 1601M75 = *300M75 = *300M75 = 823M75 = 823M66 = *1M66 = *1M66 = 3M66 = 3ETCETC

XML-STDS-56

CSE5810

MeSH in XML - MeSH in XML - desc2011.dtddesc2011.dtd-->-->

-->

<!ENTITY % DescriptorReference "(DescriptorUI, DescriptorName)"><!ENTITY % DescriptorReference "(DescriptorUI, DescriptorName)"><!ENTITY % normal.date "(Year, Month, Day)"><!ENTITY % normal.date "(Year, Month, Day)"><!ENTITY % ConceptReference <!ENTITY % ConceptReference "(ConceptUI,ConceptName,ConceptUMLSUI?)">"(ConceptUI,ConceptName,ConceptUMLSUI?)"><!ENTITY % QualifierReference "(QualifierUI, QualifierName)"><!ENTITY % QualifierReference "(QualifierUI, QualifierName)"><!ENTITY % TermReference "(TermUI, String)"><!ENTITY % TermReference "(TermUI, String)">

XML-STDS-57

CSE5810

MeSH in XML - MeSH in XML - desc2011.dtddesc2011.dtd<!ELEMENT DescriptorRecordSet (DescriptorRecord*)><!ELEMENT DescriptorRecordSet (DescriptorRecord*)><!ATTLIST DescriptorRecordSet LanguageCode (cze|dut|eng|fin|fre|ger|<!ATTLIST DescriptorRecordSet LanguageCode (cze|dut|eng|fin|fre|ger|ita|jpn|lav|por|scr|slv|spa) #REQUIRED>ita|jpn|lav|por|scr|slv|spa) #REQUIRED>

<!ELEMENT DescriptorRecord (%DescriptorReference;,<!ELEMENT DescriptorRecord (%DescriptorReference;, DateCreated,DateCreated, DateRevised?,DateRevised?, DateEstablished?,DateEstablished?, ActiveMeSHYearList,ActiveMeSHYearList, AllowableQualifiersList?,AllowableQualifiersList?, Annotation?,Annotation?, HistoryNote?,HistoryNote?, OnlineNote?,OnlineNote?, PublicMeSHNote?,PublicMeSHNote?, PreviousIndexingList?,PreviousIndexingList?, EntryCombinationList?,EntryCombinationList?, SeeRelatedList?,SeeRelatedList?, ConsiderAlso?,ConsiderAlso?, PharmacologicalActionList?,PharmacologicalActionList?, RunningHead?,RunningHead?, TreeNumberList?,TreeNumberList?, RecordOriginatorsList,RecordOriginatorsList, ConceptList) >ConceptList) ><!ATTLIST DescriptorRecord DescriptorClass (1 | 2 | 3 | 4) "1"><!ATTLIST DescriptorRecord DescriptorClass (1 | 2 | 3 | 4) "1">

XML-STDS-58

CSE5810

MeSH in XML - MeSH in XML - desc2011.dtddesc2011.dtd<!ELEMENT ActiveMeSHYearList (Year+)><!ELEMENT ActiveMeSHYearList (Year+)><!ELEMENT AllowableQualifiersList (AllowableQualifier+) ><!ELEMENT AllowableQualifiersList (AllowableQualifier+) ><!ELEMENT AllowableQualifier (QualifierReferredTo,Abbreviation )><!ELEMENT AllowableQualifier (QualifierReferredTo,Abbreviation )><!ELEMENT Annotation (#PCDATA)><!ELEMENT Annotation (#PCDATA)><!ELEMENT ConsiderAlso (#PCDATA) ><!ELEMENT ConsiderAlso (#PCDATA) ><!ELEMENT Day (#PCDATA)><!ELEMENT Day (#PCDATA)><!ELEMENT DescriptorUI (#PCDATA) ><!ELEMENT DescriptorUI (#PCDATA) ><!ELEMENT DescriptorName (String) ><!ELEMENT DescriptorName (String) ><!ELEMENT DateCreated (%normal.date;) ><!ELEMENT DateCreated (%normal.date;) ><!ELEMENT DateRevised (%normal.date;) ><!ELEMENT DateRevised (%normal.date;) ><!ELEMENT DateEstablished (%normal.date;) ><!ELEMENT DateEstablished (%normal.date;) ><!ELEMENT DescriptorReferredTo (%DescriptorReference;) ><!ELEMENT DescriptorReferredTo (%DescriptorReference;) >

<!ELEMENT EntryCombinationList (EntryCombination+) ><!ELEMENT EntryCombinationList (EntryCombination+) ><!ELEMENT EntryCombination (ECIN,<!ELEMENT EntryCombination (ECIN, ECOUT)>ECOUT)><!ELEMENT ECIN (DescriptorReferredTo,QualifierReferredTo) ><!ELEMENT ECIN (DescriptorReferredTo,QualifierReferredTo) ><!ELEMENT ECOUT (DescriptorReferredTo,QualifierReferredTo? ) ><!ELEMENT ECOUT (DescriptorReferredTo,QualifierReferredTo? ) ><!ELEMENT HistoryNote (#PCDATA)><!ELEMENT HistoryNote (#PCDATA)><!ELEMENT Month (#PCDATA)><!ELEMENT Month (#PCDATA)><!ELEMENT OnlineNote (#PCDATA)><!ELEMENT OnlineNote (#PCDATA)>ETCETC

XML-STDS-59

CSE5810

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

XML-STDS-60

CSE5810

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

XML-STDS-61

CSE5810

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.

Unifies Medical Language System UMLS acronym for was developed for National

Library of Medicine

XML-STDS-62

CSE5810

UMLS Concepts, Semantic Types/RelationsUMLS Concepts, Semantic Types/Relations

XML-STDS-63

CSE5810

ICD9 Respiratory DiseasesICD9 Respiratory Diseases

XML-STDS-64

CSE5810

ICD10 Respiratory DiseasesICD10 Respiratory Diseases

XML-STDS-65

CSE5810

65

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.

http://www.ihtsdo.org/snomed-ct/

XML-STDS-66

CSE5810

66

SNOMED-CT Composed of Concepts, Terms, and RelationshipsComposed of Concepts, Terms, and Relationships Precisely Represent Clinical Information Across Precisely Represent Clinical Information Across

Scope of Health CareScope of Health Care Content Coverage Divided into HierarchiesContent Coverage Divided into Hierarchies

XML-STDS-67

CSE5810

SNOMED ExampleSNOMED Example

XML-STDS-68

CSE5810

National Drug CodesNational Drug Codes Tracking of Drugs (Prescription and OTC)Tracking of Drugs (Prescription and OTC) From Submittal Through ApproachFrom Submittal Through Approach Keeps Track of Many Details on MedicationKeeps Track of Many Details on Medication Each Drug by Manufacturer has Unique NDC Each Drug by Manufacturer has Unique NDC

IdentifierIdentifier See:See:

http://www.fda.gov/Drugs/InformationOnDrugs/ucm142438.htm Searchable Database:Searchable Database:

http://www.accessdata.fda.gov/scripts/cder/ndc/default.cfm

XML-STDS-69

CSE5810

NDC ExamplesNDC Examples

XML-STDS-70

CSE5810

Concluding Remarks: XML/StandardsConcluding Remarks: XML/Standards Explored Usage of XML Including:Explored Usage of XML Including:

Basic XML Concepts XML Tools and Standards XML Databases Use of XML in BMI

Reviewed HL7 and CDAReviewed HL7 and CDA Examined Numerous StandardsExamined Numerous Standards