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FromEHRstoLinkedData:
represen5ngandminingencounter
dataforclinicalexper5se
evalua5on
CarloTorniai
ShahimEssaid,ChrisBarnes,MikeConlon,StephenWilliams,JanosHajagos,ErichBremer,JonCorson-Rikert,MelissaHaendel
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www.ctsaconnect.orgCTSAconnect
Reveal Connections. Realize Potential.
CTSAConnectProject
Goals: Iden?fypoten?alcollaborators,relevantresources,and
exper?seacrossscien?ficdisciplines
Assembletransla?onalteamsofscien?ststoaddressspecificresearchques?ons
Approach:
Createaseman?crepresenta?onofclinicianandbasicscience
researcherexper?setoenable
Broadandcomputablerepresenta?onoftransla?onalexper?se
Publica?onofexper?seasLinkedData(LD)foruseinotherapplica?ons
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4/5/13 3
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Reveal Connections. Realize Potential.
MergingVIVOandeagle-i
eagle-iisanontology-drivenapplica?on...forcollec?ngandsearchingresearchresources.
VIVOisanontology-drivenapplica?on...forcollec?nganddisplayinginforma?onaboutpeople.
BothpublishLinkedData.Neitheraddressesclinicalexper5se.
CTSAconnectwillproduceasingleIntegratedSeman5cFramework,amodularcollec?onofontologiesthatalso
includesclinicalexper?se
eagle-i
Resources
VIVO
People
Coordina?on
eagle-i
VIVO
Seman5c
Clinical
ac5vi5es
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ISFClinicalmodule
ARG:Agents,Resources,Grantsontology
CM:Clinicalmodule
IAO:Informa?onAr?factOntologyOBI:OntologyforBiomedical
Inves?ga?ons
OGMS:OntologyforGeneralMedical
Science
FOAF:FriendofaFriendvocabulary
BFO:BasicFormalOntology
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ISFClinicalmodule:encounter
ARG:Agents,Resources,Grantsontology
CM:Clinicalmodule
OGMS:OntologyforGeneralMedical
Science
FOAF:FriendofaFriendvocabulary
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ISFClinicalmodule:encounteroutput
CM:ClinicalmoduleOBI:OntologyforBiomedical
Inves?ga?ons
OGMS:OntologyforGeneral
MedicalScience
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ISF:Clinicalexper5serepresenta5on
Leveragingbillingcodestorepresentclinicalexper?se-exper?seasweightsassociatedtobillingcodes
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Compu5ngandpublishingclinical
exper5se
Step1Aggregate
ClinicalData
Step2Compute
Exper5se
Step4Publish
LinkedData
Step3MapDatato
ISF
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Aggregateclinicaldata
Step1Aggregate
ClinicalData
Step2Compute
Exper5se
Step4Publish
LinkedData
Step3MapDatato
ISF
Provider
ID
ICD
CodeValue
Code
Count
UniquePa5ent
Count CodeLabel
1234567 552.00 1 1Unilateralorunspecifiedfemoralhernia
withobstruc?on(ICD9CM552.00)
1234567 553.02 8 6Bilateralfemoralherniawithoutmen?on
ofobstruc?onorgangrene(ICD9CM
553.02)
1234567 555.1 4 1Regionalenteri?soflargeintes?ne
(ICD9CM555.1)
1234568 745.12 10 5Correctedtransposi?onofgreatvessels
(ICD9CM745.12)
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Computeexper5se:weigh5ngthecodes
Step1Aggregate
ClinicalData
Step4Publish
LinkedData
Step2Compute
Exper5se
Step3MapDatato
ISF
CodeWeight=codefrequency*percentageofpa5ents
Aproviderwith500pa?entshasusedSyndactyly(ICD9:755.12)for30
uniquepa?ents75 ?mes
Percentageofpa?entswithcode:6%
Codefrequency:75/30=2.5Codeweight:6*2.5=15
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Computeexper5se:footprint
Step1Aggregate
ClinicalData
Step4Publish
LinkedData
WegroupthecodesaccordingtothetoplevelICDcodeandgetthe
top10codestogeneratetheexper?sefootprintforeachprac??oner
Step3MapDatato
ISF
Step2Compute
Exper5se
ICDcode Weight
366.1 24.42
250 24
366.9 18.4
250.2 19.2
. .
ICDcode Weight
250 43.2
366 42.82
. .
. .
. .
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PublishLinkedData
Step1Aggregate
ClinicalData
Step2MapDatato
ISF
Step4Publish
LinkedData
Step3Compute
Exper5se
LinkedData
cloud
SPARQL
Endpoints
OtherAPIs
TripleStoresSeveralmeans
toaccessand
querydata
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Whatcanbedonewiththepublished
datasetSELECT ?expertise ?label ?weight!WHERE!{!obo:BFO_0000086 ?expertise.!!!!!?expertise_measurement obo:IAO_0000221 ?expertise.!!!!?expertise_measurement obo:ARG_2000012 ?label.!?expertise_measurement obo:IAO_0000004 ?weight. !!}!
Selecttheexper?sefor
provider
hp://ohsu.dev.eagle-i.net/i/1235281379
Selecttheweightandthelabel
formeasurementsrela?vetotheexper?se
Selecttheweightandthelabel
formeasurements
Theinforma?onisenoughtorepresentclinicalexper?seasa
tagcloud
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SampleencounterdatapublishedasLOD
InferredTypes
Annota5onsand
Proper5es
HealthCareEncounter
InstanceURI
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Queryingthesampleencounterdata
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Nextsteps:enhanceexper5se
representa5onbymappingICD9toMeSH
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Nextsteps:enhanceexper5secalcula5on
Moresophis?catedalgorithmleveragingMeSHhierarchy
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Beyondexper5se
Exper5selinkedtoMeSHwillenablemeaningfulconnec5ons
betweenclinicians,basicresearchers,andbiomedicalknowledge
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Team
CTSA10-001:100928SB23
PROJECT#:00921-0001
OHSU:
MelissaHaendel,CarloTorniai,NicoleVasilevsky,Shahim
Essaid,EricOrwoll
CornellUniversity:
JonCorson-Rikert,DeanKra,
BrianLowe
UniversityofFlorida:
MikeConlon,ChrisBarnes,
NicholasRejack
StonyBrookUniversity:
MoisesEisenberg,Erich
Bremer,JanosHajagos
HarvardUniversity:
DanielaBourges-Waldegg
SophiaCheng
ShareCenter:
ChrisKelleher,WillCorbe,RanjitDas,Ben
Sharma
UniversityatBuffalo:
BarrySmith,Dagobert
Soergel
CTSAconnectproject
ctsaconnect.org
Theclinicalmodulesource:
hp://bit.ly/clinical-isf
CTSAconnectontologysourcehp://code.google.com/p/connect-isf/
Datasetandqueriesdocumenta5onhps://code.google.com/p/ctsaconnect/w/list
Resources
Support : NCATS through Booz Allen
Hamilton
CTSA 10-001: 100928SB23