10/11/2015

LifeasaHealthcareCIO:APrimeronXML,RDF,JSON,andMetadata

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LIFEASAHEALTHCARECIO
EVERY DAY I EXPERIENCE LIFE IN THE WORLD OF HEALTHCARE IT, SUPPORTING 3000
DOCTORS, 18000 FACULTY, AND 3 MILLION PATIENTS. IN THIS BLOG I RECORD MY
EXPERIENCES WITH INFRASTRUCTURE, APPLICATIONS, POLICIES, MANAGEMENT, AND
GOVERNANCE AS WELL AS MUSE ON SUCH TOPICS SUCH AS REDUCING OUR CARBON FOOTPRINT,
STANDARDIZING DATA IN HEALTHCARE, AND LIVING LIFE TO ITS FULLEST.

TUESDAY, JANUARY 11, 2011

SiteFeed

APrimeronXML,RDF,JSON,andMetadata
Anewworkgroup,formedundertheauspicesoftheHITPolicy
CommitteeandtheHITStandardsCommitteeisbeginningitsworkto
helpONCanalyzepubliccommentsonthePresidentsCouncilof
AdvisorsonScienceandTechnology(PCAST)report,discussthe
implicationsofthereportoncurrentONCstrategies,assessthe

LifeasaCIOBlogbyJohnD.
HalamkaMDislicensedundera
CreativeCommonsAttribution
NoncommercialShareAlike3.0
UnitedStatesLicense

feasibilityandimpactofthePCASTreportonONCprograms,and
elaborateonhowtheserecommendationscouldbeintegratedintothe
ONCstrategicframework.

BLOG ARCHIVE

Membershipincludes:

2015(91)

PaulEgerman,Entrepreneur,Chair

2014(118)

WilliamSteadVanderbiltUniversity,ViceChair

2013(148)

DixieBaker,SAIC
HuntBlair,VermontHIE
TimElwell,MisysOpenSource

2012(224)
2011(252)

CarlA.Gunter,UniversityofIllinois

December(21)

JohnHalamka,BethIsraelDeaconessMedicalCenter,HMS

November(20)

LeslieHarris,CenterforDemocracy&Technology
StanHuff,IntermountainHealthcare

October(21)

RobertKahn,CorporationforNationalResearchInitiatives

September(21)

GaryMarchionini,UniversityofNorthCarolina

August(23)

StephenOndra,OfficeofScience&TechnologyPolicy
JonathanPerlin,HospitalCorporationofAmerica
RichardPlatt,HarvardMedicalSchool

July(19)
June(19)

WesRishel,Gartner

May(21)

MarkRothstein,UniversityofLouisville

April(22)

SteveStack,AmericanMedicalAssociation
EileenTwiggs,PlannedParenthood
ToadviseONCaboutthereport'srecommendations,workgroup
membersneedtounderstandtermssuchXML,RDF,JSONand
Metadataaswellaslearnaboutthestandardseffortstodatetocreate
http://geekdoctor.blogspot.com/2011/01/primeronxmlrdfjsonandmetadata.html

March(24)
February(20)
January(21)
PQRIXMLSubmissions
RequiredforCertification
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LifeasaHealthcareCIO:APrimeronXML,RDF,JSON,andMetadata

humanreadableandcomputabledataelementsforhealthcare.
XMLisanabbreviationforExtensibleMarkupLanguage,asetofrules
forencodingdocumentsinmachinereadableform.Here'sanexample
ofdataaboutmeinXML,whichisbothhumanreadableand
computable
<name><fullname>JohnDavidHalamka,M.D.</fullname><firstname
>John</firstname><lastname>Halamka</lastname></name>
<address>
<address1>BethIsraelDeaconessMedCtr</address1><address2>I
nformationSystems,6thFl</address2><address3>1135TremontS
t</address3><address4>RoxburyCrossing,MA02120</address4>
<telephone>617/7548002</telephone><fax>617/7548015</fax><la
titude>42.33555200000000</latitude><longitude>71.08822700000

CoolTechnologyoftheWeek
TheBirdsinmyBackyard
GeneralPrinciplesofa
UniversalExchange
Languag...
ReflectionsontheCertification
Experience
ObtainingMeaningfulUse
StimulusPayments
CoolTechnologyoftheWeek
WinterBootsandTraction
StandardsValidationfor
Certification

It'samachinefriendlyformofmyHarvardCatalystProfileswebpage

TheProposedStage2and3
MeaningfulUseRecommen...

withdiscretedataelementsthatanycomputerlanguagecaninterpret

TheBookmarkedFinalRules

andsearch.ThecompleteXMLdocumentaboutmeisavailablehere.

AUniversalExchangeLanguage
Example

XMLhasbeenusedtodescribehealthcaredatabyHL7usingthe
ClinicalDocumentArchitecture(CDA)andbyASTMusingthe
ContinuityofCareRecord(CCR)
Here'sanexampleofCDAthatillustratesimmunizations
<informationsource><author><authortimevalue="20000407130000+
0500"><authorname><prefix>Dr.</prefix><given>Robert</given><f
amily>Dolin</family></authorname></authortime></author></info
rmationsource>
<immunizations><immunization><administereddatevalue="199911"
><medicationinformation><codedproductnamecode="88"codesyste
m="2.16.840.1.113883.6.59"displayname="Influenzavirusvacci
ne"><freetextproductname>Influenzavirusvaccine</freetextpro

Metadatais"dataaboutdata"thedetailsbehindthisdatasuchaswho
gatheredit,when,andforwhatpurpose.

TheJanuaryMeetingoftheHIT
StandardsCommittee...
CyberInsuranceIsitWorth
It?
APrimeronXML,RDF,JSON,
andMetadata
EarlyExperienceswithHospital
Certification
CoolTechnologyoftheWeek
WeatherStationLessons
Learned
AHealthcareInformation
ServicesProviderBusines...
MyNewYear'sResolutions
2011
BIDMC'sMeaningfulUseEmail

ThemetadataintheCDAexampleincludesanObjectIdentifier(OID)
of2.16.840.1.113883.6.59whichisacodefortheCenterforDisease
Control'sCVXimmunizationvocabulary.Code88istheCVXcodefor
Influenzavirusvaccine.ThevaccinewasadministeredinNovemberof
1999.TheinformationsourceisBobDolin.ThefullCDAsummaryis
availablehere.

http://geekdoctor.blogspot.com/2011/01/primeronxmlrdfjsonandmetadata.html

2010(256)
2009(250)
2008(241)
2007(56)

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Here'sanexampleofCCRthatillustratesimmunizations

ABOUT ME
JO H N H A LA MK A

<actor><actorobjectid>AA0001</actorobjectid><person><name><cu

JohnD.Halamka,

rrentname><given>John</given><middle>David</middle><family>Ha

MD,MS,isChief

lamka</family></currentname></name><dateofbirth><exactdatetim

InformationOfficerof

e>19620523T04:00:00Z</exactdatetime></dateofbirth><gender><
text>M</text></gender></person></actor>
<address>
<type><text>Home</text></type><line1>11AldenRoad</line1><ci
ty>Wellesley</city><state>MA</state><postalcode>02481</postal

BethIsraelDeaconess
MedicalCenter,ChairmanoftheNew
EnglandHealthcareExchange
Network(NEHEN),CoChairofthe
HITStandardsCommittee,afull
ProfessoratHarvardMedicalSchool,

ThemetadataintheCCRexampleincludesthatthepatientisJohn

andapracticingEmergency

Halamka,born5/23/1962,Male,livesinWellesley.Additional

Physician.

metadataidentifiesthatatetanusshotexistsintherecord.The
concept"Tetanusshot"isdescribedusingtheCenterforDisease

VI EW M Y C OMP LET E P R OFI LE

Control'sCVXimmunizationvocabulary,theSNOMEDCTvocabulary,
andtheNationalLibraryofMedicineMetathesaurusvocabulary.
Metadataaboutthereliabilityoftheinformationincludeswho
reportedthetetanusshotandwhenitwasreported.Themetadatain
myrecorddescribesmeasthesourceofthereportedinformation,
updatedJanuary8,2011.ThefullCCRsummaryisavailablehere.
XMLisaverygeneralconstruct.Anyonecancreateanytagsfordata
andmetadata.HL7haschosentocreateaReferenceInformation

CROSSLINKED BLOGS

HSPH'sLeadershipStrategiesfor
InformationTechnologyinHealth
Care

STATCOUNTER

Model(RIM)todescribethemeaningofitstagsandmetadata.ASTM
hascreatedawelldescribedfixedsetofdataelements.Thechallenge
thatdifferentXMLtaggingcreatesisthatyouhavetofigureoutwhere
tolookfortheinformationyouwant.FortheXMLexampleabove

GEEKDOCTOR WEATHER STATION

aboutmynameandaddress,everyonecreatingapersondirectory
couldcreatetheXMLdifferently.Inonedirectory,aperson's
"lastName"couldberootelement,inanotheritcouldbeachildofan
elementcalled"name",inanotheritcouldanattributeofa"person"
element.TheXMLbelowisjustasvalidawaytodescribemyaddress
astheexampleabove
<addresscity="Boston"postalcode="02120"state="MA"streetad
dress="1135Tremont">
<phonenumbers></phonenumbers>
<phonenumbernumber="6177548002"type="home"></phonenum
ber>
<phonenumbernumber="6177548015"type="fax"></phonenum
ber>
</address>

TheResourceDescriptionFramework(RDF)isametadatamodelthat
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LifeasaHealthcareCIO:APrimeronXML,RDF,JSON,andMetadata

providesastandardizedapproachtodescribingwebresources.The
generalideaistoprovideasubjectpredicateobjectmodelsuchthat
thepredicateincludesofdefinitionofwhatisbeingdescribed.RDF
wascreatedtosolvetheproblemoforganizationsimplementingXML
tagsheterogeneously.
Here'sanRDFdescriptionofme
<rdf:descriptionrdf:about="http://connects.catalyst.harvard.
edu/profiles/profile/person/46034/viewas/rdf"xmlns:bibo="htt
p://purl.org/ontology/bibo/"xmlns:core="http://vivoweb.org/o
ntology/core#"xmlns:fn="http://www.w3.org/2005/xpathfunctio
ns"xmlns:foaf="http://xmlns.com/foaf/0.1/"xmlns:owl="http:/
/www.w3.org/2002/07/owl#"xmlns:rdf="http://www.w3.org/1999/0
2/22rdfsyntaxns#"xmlns:rdfs="http://www.w3.org/2000/01/rd
fschema#"xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/v

ThesubjectismyHarvardCatalystProfilesPage.
Thepredicatesinclude"thesubjecthaslastname,afirstname,anda
preferredtitle"
TheobjectsareHalamka,John,andAssociateProfessor.
Thedefinitionsoflastname,firstname,andpreferredtitlearefoundin
twoplacesthefriendofafrienddefinitionsiteandtheVIVOsite.
ThecompleteRDFdocumentaboutmeisavailablehere.
Thus,RDFprovidesameansofdisplayingmetadatawhilealso
enablingeasyaccesstothedefinitionsofdataelementsused.
WithRDF,dataisalwaysrepresentedassubjects,predicates,and
objects,soreading,parsing,andstoringitisconsistentacrossall
applications.Italsoenablesqueryofdifferentsystemsviaacommon
approach.Forexample,ifIexistasafacultymemberinProfilesandas
aproviderinaclinicalsystemthatusesRDF,itshouldbepossibleto
queryfortopicswhereIhavebothfacultyandclinicalexpertise,
withouthavingtotransformonedatasourceintotheother'sschema.
Similarly,ifthegovernmentmakesallgrants,publications,trials,etc.
availableinRDF,thenthesethingsshouldautomaticallybeavailableto
toolslikeProfiles,withouthavingtowriteanyadditionalcode.
ThereisastandardquerylanguagecalledSPARQLthatcanbeusedto
searchRDFresources.

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Finally,thereisanemergingalternativetoXMLcalledJavascript
ObjectNotation(JSON)thatismorecompactthatXMLandeasierfor
computerlanguagestomanipulatethanXML.Here'sanexampleof
myaddressinformationinJSON
{
"firstName":"John",
"lastName":"Halamka",
"age":48,
"address":
{
"streetAddress":"1135Tremont",
"city":"Boston",

JSONhasreplacedXMLasadatainterchangeformatinmanysocial
networkingapplications.ItdoeshavethesameissueasXMLthat
authorscancreatearbitraryformats,sotherecouldbeapersonobject
containingfirstnameandlastnameorlastnamecouldbeanobjectyou
havetoknowthewaytheauthororganizedthedatabeforeyoucanuse
it.
Insummary,CDAandCCRalreadyprovideXMLdataforhealthcare
thatis"dataatomic",metadatarich,andsearchableusingstandard
tools.RDFisastandardizedwayofdescribingmetadata.JSONisan
efficientwayofrepresenting,transmitting,andinterpretingdatathatis
similarbutmorecompactthanXML.
OurreportisdueinApril.IwelcomethediscussionwiththePCAST
workgroupoverthenext3months!
POST ED BY JOH N H ALAM KA AT 3: 00 AM

Recommend this on Google

14COMMENTS:
DavidC.Kibbe,MDMBAsaid...
Bravo!DCK
JA N UA RY 1 1, 2011 A T 6 :38 AM
TheRoadofLifesaid...
ExcellentPrimer.ThePCASTreporthasbroughtalotof
differentconceptstogethertotackletheHealthcaresystems,
especiallyforDAES(DataAccessElementServices).
http://geekdoctor.blogspot.com/2011/01/primeronxmlrdfjsonandmetadata.html

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JA N UA RY 1 1, 2011 A T 8 :05 A M
caregrafsaid...
awhileback,IputDrHalamka'sCCDintoRDF(demo,RDF).
RDFisasuccinctandveryflexiblewayofrepresentinga
patient'srecordandiseasytoserializeasaCCD.Itisidealfor
healthcaredatawhichtakestheformof"directedgraphs"
wherenodespointtoothernodes.Asaresult,it'sanaturalfit
fordatainsystem'sliketheVA'sVistA(SemanticVistA).
Thisisgreatnews,thatitisunderconsiderationbytheONC.
JA N UA RY 1 1, 2011 A T 9 :28 A M
RayHoltsaid...
Anythingrelatedtotheefficiencyandaccuracyintransmission
ofpatientdataisgoodnews!
JA N UA RY 1 1, 2011 A T 1 0:39 A M
KeithW.Boonesaid...
John,Iamgratefulthatyouareavailabletoprovidethis
expertisetothecommittee.But,Ihavetoadmittogreatalarm
thatsuchaprimerisneeded.
JA N UA RY 1 1, 2011 A T 1 1: 25 A M
PBsaid...
Conciseyetcomprehensive!
ThanksDrHalamka.
JA N UA RY 1 1, 2011 A T 2 : 42 PM
JoelAmoussousaid...
Brilliant!RDFandOWLopenupnewpossibilitiesintermsof
modelconsistencycheckingandreasoning.Theycanalsohelp
withknowledgeintegration(forexampleintranslational
medicinethroughtheRDFmergingorlinkingofgenomicand
clinicaldata).LinkedOpenData(LOD)principlescanbe
helpfulhereaswell.
JA N UA RY 1 1, 2011 A T 3 : 17 PM
Kristinasaid...
http://geekdoctor.blogspot.com/2011/01/primeronxmlrdfjsonandmetadata.html

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Fantastic!!!
JA N UA RY 1 2,2 011 A T 1 : 29 AM
Ragheedsaid...
Nicesummary!
Isuspectpartofthereasonsocialnetworksareamongthefirst
toabandonXMLinfavorofJSONisbecauseatsuchalarge
scalethechallengesassociatedwithgenerating,parsing,and
manipulatingXMLaremagnified.
IfanationalscaleHIEisthevision,weshouldbemindfulof
emergingstandardswhichcansimplifydataexchange.
Ofcourse,JSONmaynotbeagoodfitforalltasks,butIcan
seeitbeingusefulforrelativelysimpleonessuchas
transmittingprescriptionsandlaborders.
JA N UA RY 1 3, 201 1A T 2 :49 PM
HealthPerspectivessaid...
TheprimerisneededbecauseitbringsJSONandRDFintothe
sameconversationasthemoretraditionalapproaches
JA N UA RY 3 1, 201 1A T 1 : 5 2PM
stevesaid...
Thiswasanexcellentpost,butitleftoutoneimportant
differencebetweenJSONandXML.Whileit'scertainly
possibleforcontentproducerstoencodearbitraryelements
usingeach,XML(unlikeJSON)haswelldefinedandwidely
usedmechanismsfordefiningandenforcingdataschemata
(thesetofallowableelementsandthewaysinwhichtheymay
becombined).ThereareseveraldifferenteffortsintheJSON
worldtodothesesortsofthings,butnothing'sgottentoomuch
tractionlargelybecause,IMHO,theactofimposingthatlevel
ofstructureonJSONremovesoneofJSON'sbigadvantages
overXMLitslightweightanddynamicnature.
Thismeansthatit'seasiertoencodesemanticallyrichcontent
(suchashealthrelateddata)inXMLthaninJSON,whichis
reallymoreofadataserializationformatthanadata
interchangeformat.That'snottoknockJSONIuseitallthe
time,andIthinktherearedefinitelypossibleusesforitinHIE
relatedapplications.It'sjustamatterofusingtherighttoolfor
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therightjob.
Incidentally,IpersonallythinkthatRDF+OWLrepresentthe
RightWaytosolvethetechnicalaspectsofofHIE,butI'mnot
holdingmybreathforwidescaleadoption.RDFissucha
simpleconceptsubject/predicate/objectyet,inpractice,it'sa
surprisinglyhardapproachformostprogrammers(myself
included,atfirst)togettheirheadsaround.
M A R CH 3 ,20 11 A T 9:07 PM
EconomyWonksaid...
IthinkweneedtodiscusssomemoredetailedidealsforJSON
andXMLasregardingtheCCD.ThegreatadvantagetheCCD
(andtheCCR)haveisthatinCCDtherearestructureswhich
areverifiedagainstthatforcetheCCDtocomplywithasetof
standardsthatproveusefultothe"enduser"ofthedocument,
namely,thephysician.Iamnotawareofthissameconvenience
availablewithJSON.JSONseemsmuchsimplerforintuitive
understanding,butwhatgoodisitifthereisnostructure
behindtheinstance?
M A R CH 22, 201 1 AT 3:23 P M
Sandeepsaid...
Dr.Halamka,Iwishtodisagreesomewhatfromyour
commentsonHL7ReferenceImplementationModel(RIM).In
awayRIMdoesprovidemeaningtoXMLtags,butXMLisjust
aserialisationformatforinformationencodedinmodel
structureconformingtoRIM.RIMaimstostandardiseonthe
structureandsemanticsofinformationsoastofacilitate
consistentgeneration,transmission,andconsumptionof
informationacrosssystems.InthatsenseRIMgoesbeyond
metadataandisclosertoRDFasfarasstructureofinformation
isconcerned
A PR IL 8, 201 1A T 12: 4 3 AM
TylerTallmansaid...
Wouldyouconsiderdiscussingjsonldinthisorfollowing
posts
F EBR U AR Y 20, 201 2A T 1 1: 5 6A M
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