A visual SPARQL query builder for bioimaging metadata, built with Sparnatural. Developed as part of the foundingGIDE project.
The demo lets you explore study-level metadata from the Image Data Resource (IDR) and other GIDE sources. Metadata is converted to RDF via RO-Crate and served through SPARQL endpoints on TriplyDB.
For the broader rationale and search strategy, see BioImage-Archive/gide-search.
https://german-bioimaging.github.io/gide-sparnatural/
- The SHACL configuration (
idr_studies_shacl.ttl) defines which classes and properties appear in the query builder. - Users compose queries visually; Sparnatural translates them to SPARQL.
- SPARQL queries are run against TriplyDB endpoints that host a dump of the metadata triples enriched with FBbi and NCBITaxon terms.
- Results are displayed with YASGUI.
This project builds on sparnatural-mpi by Mariana Meireles, which provided Sparnatural-based navigation for OMERO datasets related to the Pseudomonas fluorescens SBW25 Knowledge Hub.
It gradually evolved to a study-level search for the GIDE project.
- RO-Crates for SSBD and BIA provided by Koji Kyoda and François Sherwood respectively. See the gide-crate-combine repository for details.
- Supported by German BioImaging.
- OMERO-ONTOP sandbox originally provided by Carsten Fortmann-Grote.
- Built with Sparnatural (LGPL-3.0) and YASGUI.