SemanticMDR

Report
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
...
2
SALUS Project
Semantic Metadata Registry
3
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
4
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
5
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
6
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
7
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
8
•
•
•
•
•
Bioportal
Rest Services for each MDR:
•
SPARQL Endpoint
•
CDE Endpoint
•
CDE search
•
Retrieve Semantic Links
•
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:[email protected] =
'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

similar documents