SPHN Semantic Interoperability Framework

SPHN framework

• Introduction
  • SPHN Semantic Interoperability Strategy
  • The Stakeholder Roles
  • SPHN Data Ecosystem for FAIR Data
  • Reference
• 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
  • Further reading
• SPHN Schema Scope
  • Basic overview
  • Control elements
  • Graph and metadata display
  • Availability and usage rights
• SPHN Schema Forge
  • Usage
  • Tools integrated in SPHN Schema Forge
  • Availability and usage rights
• SPHN Connector
  • Introduction
  • Overview, architecture & Workflow
  • Distinguished features of the SPHN Connector
  • SPHN tools used in SPHN Connector
  • Availability and usage rights
• Terminology Service
  • The DCC Terminology Service
  • Downloading terminology files
  • Versioning strategy of terminologies
  • Availability and usage rights
  • References
• SPHN Mocker
  • SPHN Sampler
  • Availability and usage rights

External terminologies used

• External terminologies
• Versions used in SPHN
• Naming conventions for terminologies not in RDF

User guide - How to?

• Generate a project-specific RDF Schema
  • Target Audience
  • Introduction
  • Procedure to update the semantics
  • Option 1: Produce an RDF Schema from the SPHN Dataset Template
  • Option 2: Generate an RDF Schema using an ontology editor
  • Reporting back to DCC
• Generate data according to a RDF schema
  • Target Audience
  • 1. Versioning of the data
  • 2. Instantiation of the data
  • 3. Special case of shared identifier
  • 4. Cardinality of the data
• Validate data with SHACL rules
  • Target Audience
  • SHACL validation in GraphDB
• Managing your GraphDB instance
  • Setting up your GraphDB instance
  • Managing graphs within a GraphDB repository
• Loading data into GraphDB
  • GraphDB Workbench
  • RDF4J API
  • GraphDB ImportRDF
• Extract subsets of a graph
  • Simple approach
  • Advanced approach
• Visually explore data with GraphDB
  • Target Audience
  • Schema and data visualization
  • Availability
• Query data with SPARQL
  • Target Audience
  • Data profiling querying - Summary statistics
  • Data exploration querying
  • Setup inference in GraphDB
  • References
• 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
• FAIRify external terminologies in RDF
  • Target audience
  • Identify the terminology of interest
  • Define metadata of interest
  • Translate terminology to RDF
  • Hands on example

Concepts guidelines

• Assessment concepts
  • Concept design
  • Examples for data delivery
  • Guideline for data delivery
  • Example for semantic inheritance
• Lab concepts
  • Concept design
  • Examples for data delivery
  • Guideline for data delivery
• Measurement concepts
  • Concept design
  • Examples for data delivery
  • Guideline for data delivery
• Omics concepts
  • Concept design
  • Examples of data delivery
  • Example of semantic inheritance
• Representation of genetic variants
  • Concept design
  • Variant Descriptor
  • Genomic Variation
  • Examples for data delivery
  • Guidelines for data delivery
• Provenance concepts
  • Overview
  • Concept design
  • Example for data delivery
  • Guideline for data delivery
• Drug and related concepts
  • Concept design
  • Examples for data delivery
  • Guideline for data delivery

Examples of Implementation

• CHUV implementation of SPHN
  • CHUV research ecosystem
  • SPHN Data Provisioning Process
  • Data standarization
  • Data de-identification
  • CHUV pipeline and SPHN Connector
  • Federated Query System and Einstein
• HUG implementation of SPHN
  • HUG DATA LAKE
  • SPHN pipeline
  • TI4Health / DEAS / Einstein component FQS (Federated Query System)
• Insel implementation of SPHN
• USB implementation of SPHN
  • Data Warehouse at the University Hospital Basel
  • SPHN related infrastructure at the University Hospital Basel
• USZ implementation of SPHN
  • Data Aggregation
  • ONTOCAT
  • DeidMaster
  • Data Transformation and De-Identification
  • SPHN Connector
  • Einstein and Federated Query

Background information

• RDF in SPHN
  • 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
• RDF Quads
  • Formats
  • Quads in SPHN
  • Querying with Quads
• SHACL
  • SHACL targets
  • SHACL shapes
  • SHACL constraints
  • Validation report
  • SHACL example
• SPARQL
  • Introduction
  • Structure of a query
  • Types of queries
  • Query formation
  • Advanced queries

Other

• Contact Information
• Acknowledgements