Browsing by Subject "Data Standards"
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Item Development Of Semi-Automated Tools To Map Cancer Research Common Data Elements To The Biomedical Research Integrated Domain Group Model(2020-03) Renner, RobinetteWhile using data standards can facilitate research by making it easier to share data, manually mapping to data standards creates an obstacle to their adoption. Semi-automated mapping strategies can reduce the manual mapping burden. This research addresses the mapping dilemma by applying well-established and emerging techniques to a real-world use case. First, machine learning approaches were used and evaluated to map Common Data Elements (CDEs) from the National Cancer Institute’s (NCI) cancer Data Standards Registry and Repository to the Biomedical Research Integrated Domain Group (BRIDG) model. Second, a graph database that incorporates the CDEs, BRIDG Model, and the NCI Thesaurus was developed and evaluated. A shortest path algorithm was then used to predict mappings from CDEs to classes in the BRIDG model. Finally, analysis was conducted to: determine the strengths and weaknesses of each approach; highlight data quality issues; and determine when either approach or a combination of the approaches provides the optimal results. The results indicate that an artificial neural network-based mapping tool is able to predict CDE to BRIDG class mappings with between 34 - 94% accuracy but is limited by the availability of training data. The results also show that a graph database can be used to map CDEs to BRIDG classes but is limited by the subjective nature of the mapping process. An optimal mapping tool combines machine learning and graph database techniques with the knowledge and experience of a human subject matter expert.Item Shape Expressions (ShEx) Schemas for HL7 FHIR R5 Specification(2023-12) Sharma, DeepakThe Shape Expressions (ShEx), a W3C standard, is a human-readable and machineprocessable language for describing RDF data. ShEx is an effective way to describe how data should be represented in RDF, and to define structural constraints. ShEx can both be used to define and validate RDF data. The Fast Healthcare Information Resources (FHIR) standard, which forms a foundation for healthcare related data interchange, has added ShEx as an official representational form alongside XML and JSON. Our initial efforts of modeling FHIR profiles into ShEx Schemas proved that ShEx is very useful for describing a standard model of FHIR RDF data by translating FHIR resources into ShEx Schemas. After demonstrating the success and importance of the results of initial algorithmictransformations from FHIR DSTU3 model to ShEx schemas, we continued our study and expanded the prototypical implementation to the official HL7 FHIR R5 version We resolved about dozen issues in initial implementation with consensus from semantic web community - the HL7 ITS/W3C RDF Task Force. We extended our implementation to transform the FHIR R5 specification into ShEx schema. We also developed an enhanced validation mechanism (includes constraints,terminology bindings along with structural properties) of FHIR RDF data using ShEx schema language. First FHIR resource examples were transformed into FHIR RDF instance data. These ShEx schemas and FHIR RDF examples are now part of published FHIR R5. The validation mechanism evaluated these ShEx schemas for completeness and their application on instance data. First, we made sure that schemas have valid structure, cardinality, invariants, value domains and term-bindings. Second, we applied these ShEx schemas to validate the official FHIR RDF examples. The enhanced validation tooling proved critical to ascertain their structural and semantic completeness. We demonstrated that ShEx provides nearly complete coverage of all the FHIR resources.