Transcript SemanticMDR
Semantic Metadata
Registry/Repository
SRDC
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 Project
Semantic Metadata Registry
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SALUS Common Data Elements
The total number of the identified CDEs is 199
Data Element
Name
Description
Patient.ID.II
Patient.Title.String
Patient.GivenName.String
Patient.FamilyName.String
Patient.Gender.CD
Identifier of the patient
Title/prefix of the patient
Given name of the patient
Family name of the patient
Gender of the patient
Allergy.AdverseEventType.CD
Allergy.TimeInterval.IVLTS
Allergy.Product.CD
Allergy.Reaction.Condition
Coded type of the allergy / intolerance / adverse
event (e.g. drug allergy, food intolerance)
Effective time interval of the allergy / intolerance /
adverse event
Product (i.e. substance) that causes the allergy /
intolerance / adverse event (e.g. egg protein, dust,
nifedipine)
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
MDR
Birth Date
Sex
Patient
First name
ISO/IEC
11179
Any other
Metadata
Last name
Patient
Firstname
Date of Birth
Surname
Sex
Date of Birth
Gender
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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
A set of CDEs with lots of relations – Semantic Resource Set
their relations and mappings are managed semantically
The relations can be through the LOD cloud
The relations may point to native representations of the Content Models
Extraction Specification
IHE DEX Profile
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Bioportal
Rest Services for each MDR:
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SPARQL Endpoint
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CDE Endpoint
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CDE search
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Retrieve Semantic Links
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Retrieve Extraction Specifications
LOINC
SNOMED-CT
ICD-10
…
WHOART
http://purl.bioontology.org/ontology/SNOMEDCT/394617004
Terminology Servers
HITSP
SKOS: closeMatch
FDA
CDISC SHARE
http://hitsp.org/ontology/C154/ResultValue
SKOS: closeMatch
SKOS:exactMatch
Semantic
MDR
WHO
OMOP
http://cdisc.org/share/ontology/SDTM/LB/LBORRES
http://cdisc.org/share/ontology/BIRDG/PAPO/RESULT
Semantic
MDR
classifiedBy
CDE
CS name
type
Result.value.PQ
OC Result
CCD/ICSR
ExtractionSpecification
containing
CSI type
value
XPATH
Xpath Expression
//cda:observation[cda:templateId/@root =
'2.16.840.1.113883.10.20.1.31'] /cda:value
classifiedBy
CS
LOD
name
SNOMED-CT
type
BioPortal
containing
CSI type
value
owl:sameAs
URI
HITSP Semantic MDR
LOD
CDE
LB.LBORRES.Char
http://purl.bioontology.org/ontology/SNOMEDCT/394617004
BRIDG Semantic
MDR
classifiedBy
CDE
CS name
BRIDG
type
DEC
OC classifiedBy
AE
CSI type
Text
Context{…;URI;
…}
CSI type
skos:closeMatch
CSI type
CDE
Context{…;URI;
…}
…
value
CDISC Semantic MDR
CDE
OC
skos:exactMatch
value
value
V
D
OC
LOD
containing
P
AEREL
CDE
SKOS
skos:exactMatch
Context{…;URI;
…}
Context = {AdverseEvent >
AdverseEventCausalRelationship >
EvaluatedActivityRelationship;
http://mdr.bridg.org/resource/cde/AdverseEventRelation;
WHERE EvaluatedActivityRelationship >
PerformedActivity > PlannedActivity >
DefinedActivity.nameCode=“administer treatment”}
P
P
Design & Implementation
Java API
REST API
CDE Knowledge Base
Semantic MDR
MDR API
(Easy-to-use Semantic ISO 11179 Mapping)
Semantic Data Manipulation API
(Pure ISO 11179 Mapping)
JENA RDF/OWL API
Triple Store
(Jena TDB | Virtuoso)
Data