SPHN Semantic Framework

SPHN framework

• Introduction
  • SPHN Semantic Strategy
  • The Data Problem and Stakeholder Roles
  • SPHN Data Ecosystem for FAIR Data
• SPHN Dataset
  • Introduction
  • Scope of the SPHN Dataset
  • Guiding principles for concept design
  • Specification of a concept
  • Development process
  • Availability and usage rights
• SPHN RDF Schema
  • Scope of the SPHN RDF schema
  • Technical specification of the schema
  • Development process
  • Availability and usage rights
• SHACLer
  • SHACL
  • The SHACLer tool
  • SHACLer internals
  • Validating data with the SHACL file
  • Availability and usage rights
  • Contact
• SPARQLer
  • SPARQL
  • The SPARQLer tool
  • Availability and usage rights
  • Contact
• Quality Assurance Framework
  • The SPHN RDF Quality Check tool
  • Statistical SPARQL queries
  • Data validation with SHACL
  • Availability and usage rights
• Terminology Service
  • External terminologies
  • The SPHN Terminology Service
  • Downloading terminology files
  • Reference

External resources used

• External terminologies
• Naming conventions
• ATC
• CHOP
• ICD-10-GM
• LOINC
• SNOMED CT
• UCUM

User guide - How to?

• Access, read and use of SPHN content
  • Access the SPHN Dataset and the RDF schema
  • Read and use of the SPHN Dataset
  • Read and use of the SPHN RDF schema
• Generate a SPHN project-specific ontology
  • Target Audience
  • 1. Project-specific ontology creation
  • 2. New concepts and modification of existing ones
  • 3. Valuesets as individuals in the RDF schema
  • 4. Best practices when generating the RDF
  • 5. Loading of the project into WebProtégé
  • 6. Reporting back to DCC
• Instantiate data according to the project ontology
  • Target Audience
  • 1. Versioning of the data
  • 2. Instantiation of the data
  • 3. Cardinality of the data
• Improve data quality through validation
  • Target Audience
  • 1. Data quality validation using the Quality Check Tool
  • 2. SPHN SHACL validation in GraphDB
• SHACL constraints in the SHACLer
  • Target Audience
  • 1. Assumptions
  • 2. SHACL constraints implemented for SPHN
  • 3. Template of SHACL constraints
  • 4. Implementation examples
• Visually explore data with GraphDB
  • Target Audience
  • Loading data in the GraphDB triplestore
  • Schema and data visualization
• Query data with SPARQL
  • Target Audience
  • Setup inference in GraphDB
  • Data profiling querying - Summary statistics
  • Data exploration querying
  • References
• Concept Flattening in the SPARQLer
  • Target Audience
  • Definitions
  • Concept flattening
• Use Python and R with RDF data
  • Target Audience
  • Overview
  • Loading data from GraphDB in Python and R
  • Combining results from different queries
  • Further Information
• Download external terminologies from the Terminology Service
  • Target Audience
  • Downloading external terminologies from the BioMedIT portal
  • Downloading external terminologies from the Terminology Server

Examples of Implementation

• CHUV with Oracle
  • Introduction
  • Implementation
  • Example of use

Background information

• RDF in SPHN
  • The history
  • Learn about how to use linked data in SPHN
• Semantic Web in SPHN
  • References
• Resource Description Framework (RDF)
  • Introduction to RDF
  • Data Representation with Triples
  • RDF Terms
  • RDF Storage Formats
  • References
• SHACL
  • SHACL targets
  • SHACL shapes
  • SHACL constraints
  • Validation report
  • SHACL example
• SPARQL
  • Introduction
  • Structure of a query
  • Types of queries
  • Query formation

Other

• Contact Information
• Acknowledgements