RDF as the Healthcare Interchange Language. Charles Mead, M.D., MSc., CoChair W3C Healthcare Life Sciences Work Group

Transcription

1 RDF as the Healthcare Interchange Language Charles Mead, M.D., MSc., CoChair W3C Healthcare Life Sciences Work Group

2 21 st - Century Personalized Medicine Used by permission: NaJonal Cancer InsJtute Cancer BioinformaJcs Grid (cabig)

3 Barriers to Achieving Computable SemanJc Interoperability ( sharing semanjcs ) Non- semanjc RepresentaJon technologies and traceability gaps (design- Jme) SerializaJon brisleness(run- Jme) ImplementaJon technology diversity SemanJc Lack of layered standards SemanJc overlap at standards boundaries

4 Non- SemanJc Barriers to Achieving CSI RepresentaJon technologies and traceability gaps (design- Jme) UML separajon of views of instances from views of classes à modeling of domain content (instance data and schema/metadata) is owen difficult for domain experts Fido a dog Dog rdf:subclassof Mammal UML tools non- standard mechanisms for associajng exemplar but unbounded value sets with class asributes Requirements- to- Design- to- ImplementaJon traceability is difficult Disconnect between analysis- level definijonal semanjcs and their computajonal equivalence when traced through design- Jme logical and run- Jme physical representajons.

5 Non- SemanJc Barriers to Achieving CSI(2) SerializaJon brisleness(run- Jme) XML nested structure can obscure semanjc equivalence Simple example: Students, Classes, Teachers Necessitates one- off Xpath, XSLT transforms for semanjc alignment ImplementaJon technology diversity Different physical data models and/or access technologies for same schema E.G. raison d être for CDISC ODM exchange standard (XML)

6 Why RDF?

7 SemanJcs as a First- Class CiJzen RepresentaJon of data (and metadata) in a RDF- based graph eliminates the problem of semanjcs wrapped in syntacjc structures Transmission of RDF graphs ujlizes exisjng internet standards, e.g. HTTP, REST, etc. ApplicaJon of Linked Data Best PracJces increases the value of data (and metadata) in both intranet- and internet- based communijes.

8 SemanJcs as a First- Class CiJzen (2) Use of SemanJc Web technologies does not magically solve core issues of semanjc ambiguity or cross- graph disagreement. Those issues must sjll be addressed through person- to- person/organizajon- to- organizajon dialogue. Use of SW technologies does, however, enable bo)om- up harmonizajon/semanjc resolujon Siloed ontology development if more amenable to harmonizajon than tradijonal RDBMS or XML siloed development

9 InformaJon Models and Terminology Models: The Perfect World Grade IV anaphylac?c reac?on to Penicillin injec?on. (HL7 Reference Informa?on Model and SNOMED- CT) hsp://

10 Grade IV anaphylac?c reac?on to Penicillin injec?on. (HL7 Reference Informa?on Model and SNOMED- CT) hsp:// InformaJon Models and Terminology Models: The Real World (TermInfo problem)

11 TermInfo Example hsp:// Clinical observajon: Grade IV anaphylac?c reac?on to a penicillin injec?on. RepresentaJon using HL7 Reference InformaJon Model (RIM) and SNOMED- CT terminology RIM is an cross- domain informajon model composijonal capability based on use of instances of Act and ActRelaJonship SNOMED- CT is a healthcare terminology model composijonal capability based on concatenajon of muljple atomic terms from muljple axes.

12 TermInfo Example (2) hsp:// The semanjc boundary between the RIM and SNOMED is not clean à muljple representajons of the same semanjcs Complex RIM model with atomic SNOMED code bindings Simple RIM model with complex SNOMED code bindings ConJnuum of possibilijes between these two extremes Although all representajons are semanjcally equivalent from a clinical perspecjve, they are not a priori CSI because of serializajon differences SW solujon to the problem involves idenjfying and expressing the overlapping semanjc boundaries RIM ontology SNOMED ontology RIM- SNOMED cross ontology boundary mapping

13 The SemanJc Web Value ProposiJon Common design- Jme and run- Jme representajon (RDF graph parerns) Eliminates impedance mismatch that owen occurs between these two contexts SemanJcs as a first- class cijzen Reduces technology barriers SPARQL end- points (a broadly- applicable standard) to query RDBMS (and other) persistence layers Reduces syntax and lexical barriers Single RDF model and syntax à technology- independent schema à immunity to serializa?on brirleness Enables solujons to semanjc CSI barriers Layered metadata Overlapping standards boundaries

14 The SemanJc Web Value ProposiJon(2) Tools and infrastructure designed to promote reuse, discovery, amalgamajon, harmonizajon of data and meta- data from muljple contexts Point- wise (bosom- up) semanjc harmonizajon Decentralized extensibility Reuse made easy: Interoperability emerges from laziness Significant amount of work already done in TMC domains

15 Healthcare Standards and RDF plus a few examples SALUS project hsps://github.com/srdc CDISC2RDF hsp://cdisc2rdf.com HL7 Reference InformaJon Model hsp:// acjon=edit&projectnumber=983 BRIDG Model HCLS demo projects hsp:// hsp:// hsp:// hsp:// hsp:// -