Semantic Metadata Registry/Repository SRDC. Common Data Elements… Common Data Element (CDE) ...
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Transcript of Semantic Metadata Registry/Repository SRDC. Common Data Elements… Common Data Element (CDE) ...
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Common Data Elements… Common Data Element (CDE)
common definitions and structures so that information can be exchanged across different domains/applications/studies
Data vs. Metadata “John”
Patient Name “Istanbul”
What does it mean? Patient – City of Residence Patient – City of Birth Biggest city of Turkey ...
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SALUS Common Data Elements
The total number of the identified CDEs is 199
Data Element
Name Description
Patient.ID.II Identifier of the patientPatient.Title.String Title/prefix of the patientPatient.GivenName.String Given name of the patientPatient.FamilyName.String Family name of the patientPatient.Gender.CD Gender of the patient
Allergy.AdverseEventType.CD
Coded type of the allergy / intolerance / adverse event (e.g. drug allergy, food intolerance)
Allergy.TimeInterval.IVLTSEffective time interval of the allergy / intolerance / adverse event
Allergy.Product.CD
Product (i.e. substance) that causes the allergy / intolerance / adverse event (e.g. egg protein, dust, nifedipine)
Allergy.Reaction.Condition
The condition which occur as a reaction to the allergy / intolerance / adverse event; can be any condition
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SALUS Semantic MDR The design and implementation of CDE Repository go beyond the
requirements of SALUS interoperability framework Federated Semantic Metadata Repository
During the elicitation of SALUS CDEs several other common data element models have been analysed one of the major deficiencies is that most of them are published through
PDF documents or spread sheets not accessible in a machine-processable way
HITSP C154, C32 FHIM CIM S&I CEDD CDISC CDASH, SDTM BRIDG CDM Intermountain Healthcare CEM Mini-Sentinel CDM i2b2
it is not practical to expect all of these diverse initiatives and projects to stick to the same common model, and to use the same set of CDE
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ISO/IEC 11179 Family of specifications (6 parts) for metadata registries to increase
the interoperability of applications with the use of data elements A relational metamodel
Generic: any data element model can be represented through regardless of the level of granularity
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Semantic Metadata Registry (MDR)
Metadata for Semantic Interoperability annotate the information models of different systems
with the same set of data elements residing in the metadata registries
early approach: bottom-up takes root from several other disciplines like linguistics, compilers
etc…Patient
Name
Surname
Birth Date
Sex
Patient
Firstname
Surname
Date of BirthGender
Patient
First name
Last name
Date of BirthSex
MDRISO/IEC 11179
Any other Metadata
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Federated Semantic MDRs Maintain & Manage
CDEs the relations between CDEs the components of CDEs the relations between the components of CDEs
Different CDEs from different Content Models their relations and mappings are managed semantically
A set of CDEs with lots of relations – Semantic Resource Set
The relations can be through the LOD cloud
The relations may point to native representations of the Content Models Extraction Specification IHE DEX Profile
Semantic MDR
SKOS:exactMatch
SKOS: closeMatch
Bioportal
Terminology Servers
• LOINC• SNOMED-CT• ICD-10• …• WHOART
http://purl.bioontology.org/ontology/SNOMEDCT/394617004
http://hitsp.org/ontology/C154/ResultValue
HITSP
OMOP
CDISC SHARE
http://cdisc.org/share/ontology/BIRDG/PAPO/RESULT
http://cdisc.org/share/ontology/SDTM/LB/LBORRES
FDA
Semantic MDR
WHO
SKOS: closeMatch
Rest Services for each MDR:• SPARQL Endpoint• CDE Endpoint• CDE search• Retrieve Semantic Links• Retrieve Extraction Specifications
HITSP Semantic MDR
CS name
CCD/ICSR
type ExtractionSpecification
CSI
type XPATH
value
Xpath Expression
containing
CDE
//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.1.31'] /cda:value
classifiedBy
LB.LBORRES.CharCDE
Result.value.PQ
OC Result
CS name
SNOMED-CT
type BioPortal
CSI type
owl:sameAs
value
URI
containing
http://purl.bioontology.org/ontology/SNOMEDCT/394617004
classifiedBy
LOD
LOD
DEC
AEOC
AEREL
P
TextVD
CDE
CDISC Semantic MDR
CS name BRIDG
type SKOS
BRIDG Semantic MDR
CDE
CDE
CDE
OC
OC
P
P
CSI type
skos:exactMatch
value
Context{…;URI;…}
CSI
type
skos:closeMatch
value
Context{…;URI;…}
CSI
type
skos:exactMatch
value
Context{…;URI;…}
…
containing
classifiedBy
classifiedBy
Context = {AdverseEvent > AdverseEventCausalRelationship > EvaluatedActivityRelationship; http://mdr.bridg.org/resource/cde/AdverseEventRelation; WHERE EvaluatedActivityRelationship > PerformedActivity > PlannedActivity > DefinedActivity.nameCode=“administer treatment”}
LOD
Design & Implementation
Triple Store(Jena TDB | Virtuoso)
CDE Knowledge Base
Semantic Data Manipulation API(Pure ISO 11179 Mapping)
MDR API(Easy-to-use Semantic ISO 11179 Mapping)
Java API REST API
Data
Semantic MDR
JENA RDF/OWL API