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Semantic Metadata Registry/Repository SRDC. Common Data Elements…  Common Data Element (CDE)  common definitions and structures so that information.

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Presentation on theme: "Semantic Metadata Registry/Repository SRDC. Common Data Elements…  Common Data Element (CDE)  common definitions and structures so that information."— Presentation transcript:

1 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 ... 2

3 SALUS Project Semantic Meta- data Registry 3

4 SALUS Common Data Elements  The total number of the identified CDEs is 199 Data Element NameDescription Patient.ID.IIIdentifier of the patient Patient.Title.StringTitle/prefix of the patient Patient.GivenName.StringGiven name of the patient Patient.FamilyName.StringFamily name of the patient Patient.Gender.CDGender of the patient Allergy.AdverseEventType.CD Coded type of the allergy / intolerance / adverse event (e.g. drug allergy, food intolerance) Allergy.TimeInterval.IVLTS Effective 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 4

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 5

6 ISO/IEC  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

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… MDR ISO/IEC Any other Metadata 7

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 8

9 Semantic MDR SKOS:exactMatch SKOS: closeMatch Bioportal Terminology Servers LOINC SNOMED-CT ICD-10 … WHOART HITSP OMOP CDISC SHARE FDA Semantic MDR WHO SKOS: closeMatch Rest Services for each MDR: SPARQL Endpoint CDE Endpoint CDE search Retrieve Semantic Links Retrieve Extraction Specifications

10 HITSP Semantic MDR CS nameCCD/ICSR typeExtractionSpecification CSI typeXPATH valueXpath Expression containing CDE = ' '] /cda:value classifiedBy LB.LBORRES.Char CDE Result.value.PQ OC Result CS nameSNOMED-CT typeBioPortal CSI typeowl:sameAs valueURI containing classifiedBy LOD

11 DEC AE OC AEREL P Text VDVD CDE CDISC Semantic MDR CS nameBRIDG typeSKOS BRIDG Semantic MDR CDE OC P P CSI typeskos:exactMatch valueContext{…;URI; …} CSI typeskos:closeMatch valueContext{…;URI; …} CSI typeskos:exactMatch valueContext{…;URI; …} … containing classifiedBy Context = {AdverseEvent > AdverseEventCausalRelationship > EvaluatedActivityRelationship; WHERE EvaluatedActivityRelationship > PerformedActivity > PlannedActivity > DefinedActivity.nameCode=“administer treatment”} LOD

12 Design & Implementation JENA RDF/OWL API

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