SPHN Schema Forge

The SPHN Schema Forge is a web service for building SPHN-compliant RDF schemas by simply uploading an Excel file as input. It simplifies the process of generating a SPHN-compliant RDF Schema, human-readable HTML representation of the schema as well as SHACL shapes and SPARQL queries which are used for data quality checks.

The web service is available at: https://schemaforge.dcc.sib.swiss.

SchemaForge Homepage

Figure 1. The SPHN Schema Forge web service homepage.

Usage

There are two options to run the web service:

  1. Upload a SPHN-compliant Dataset (one Excel file, template and user guide) to generate the full stack of RDF content from the project-specific RDF Schema to the HTML Visualization

  2. Upload a SPHN-compliant project-specific RDF Schema and the SPHN RDF Schema (two Turtle files, template and user guide) to build the SHACL rules, SPARQL queries and HTML Visualization

In addition, it is possible to upload a SHACL exception file for the SHACL output (JSON file) and to upload concept images for the human-readable HTML representation (PNG files).

Note

When uploading a project-specific Turtle file, please ensure the file name has the structure “prefix_anything.ttl” to differentiate it from the SPHN Turtle file.

The web service will run the Dataset2RDF, the Documentation and Visualization tool, the SPARQLer and the SHACLer in the background, without the need to install any of this tools. After completion, the RDF Schema, the HTML documentation, the SPARQL queries and the SHACL contraints will be generated and can be downloaded.

SchemaForge Workflow

Figure 2. Workflow integrating the SPHN Schema Forge web service in the context of the SPHN Semantic Interoperability Framework.

Tools integrated in SPHN Schema Forge

The following tools are integrated in the SPHN Schema Forge and enable to automatically build the full stack of Semantic Web content in SPHN (RDF schema, HTML visualization, SPARQLs and SHACLs):

SPHN Dataset2RDF Tool: The SPHN Dataset2RDF Tool takes as input an Excel Dataset, compliant with SPHN, and returns the RDF schema as a Turtle file. Further information on this tool will be soon available.

SPHN Schema Visualization Tool & SPARQLer: The SPHN Schema Visualization Tool takes as input the RDF schema and returns a HTML documentation file describing the content of the RDF schema. It currently also generates SPARQL queries for each concept (concept flattening and statistical queries).

Note

The Visualization tool and the SPARQLer are currently interconnected and consist of the same tool generating two different outputs: one being the HTML visualization of the RDF schema and the other being SPARQL queries related to the RDF schema.

Further information on the visualization tool will be soon available. Further information about the SPARQLer can be found at SPARQLer.

SHACLer: The SHACLer takes as input the RDF schema and returns SHACL constraints used for validation of SPHN-related data. Further information on the SHACLer can be found at SHACLer.

Availability and usage rights

© Copyright 2023, Personalized Health Informatics Group (PHI), SIB Swiss Institute of Bioinformatics

The SPHN Schema Forge is available at https://schemaforge.dcc.sib.swiss/ and is licensed under the GPLv3 license.

For any question or comment, please contact the SPHN Data Coordination Center (DCC) at dcc@sib.swiss.