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Semantic Metadata Registry/Repository

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?

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Semantic Metadata Registry/Repository

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  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 • ...

  3. SALUS Project Semantic Meta-data Registry

  4. SALUS Common Data Elements • The total number of the identified CDEs is 199

  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-processableway • 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… Any other Metadata ISO/IEC 11179 MDR

  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

  9. FDA • Rest Services for each MDR: • SPARQL Endpoint • CDE Endpoint • CDE search • Retrieve Semantic Links • Retrieve Extraction Specifications • LOINC • SNOMED-CT • ICD-10 • … • WHOART Bioportal Semantic MDR http://purl.bioontology.org/ontology/SNOMEDCT/394617004 Terminology Servers OMOP Semantic MDR SKOS: closeMatch SKOS: closeMatch CDISC SHARE SKOS:exactMatch WHO HITSP http://cdisc.org/share/ontology/SDTM/LB/LBORRES http://cdisc.org/share/ontology/BIRDG/PAPO/RESULT http://hitsp.org/ontology/C154/ResultValue

  10. CSI classifiedBy CDE CS Result.value.PQ containing OC Result CSI //cda:observation[cda:templateId/@root ='2.16.840.1.113883.10.20.1.31'] /cda:value classifiedBy CS LOD LOD containing HITSP Semantic MDR CDE LB.LBORRES.Char http://purl.bioontology.org/ontology/SNOMEDCT/394617004

  11. CDE CS DEC CDE BRIDG Semantic MDR OC P CDE OC P OC AE classifiedBy CDE CSI LOD containing classifiedBy P AEREL CSI … Context = {AdverseEvent > AdverseEventCausalRelationship > EvaluatedActivityRelationship; http://mdr.bridg.org/resource/cde/AdverseEventRelation; WHERE EvaluatedActivityRelationship > PerformedActivity > PlannedActivity > DefinedActivity.nameCode=“administer treatment”} CSI VD Text CDISC Semantic MDR

  12. Design & Implementation JENA RDF/OWL API

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