Semantic Metadata Registry/Repository

SRDC

2

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 ...

3

SALUS Project Semantic Meta-data Registry

4

SALUS Common Data Elements

The total number of the identified CDEs is 199

Data Element

Name DescriptionPatient.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

5

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

6

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

7

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

NameSurnameBirth DateSex

Patient

FirstnameSurnameDate of BirthGender

Patient

First nameLast nameDate of BirthSex

MDR ISO/IEC 11179

Any other Metadata

8

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 XPATHvalue

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

AERELP

TextVD

CDE

CDISC Semantic MDR

CS name BRIDGtype SKOS

BRIDG Semantic MDR

CDECDECDE

OC

OC

PP

CSI type

skos:exactMatch

value

Context{…;URI;…}CS

Itype

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