Part of the Institute of Computer Graphics @ Johannes Kepler University Linz, Austria

SHACLens: A Visualization Workflow for SHACL Violation Exploration in Knowledge Graphs

SHACLens Teaser

Abstract

Introduction: Validating large knowledge graphs with the Shapes Constraint Language (SHACL) often yields violation reports too large to interpret and trace to root causes, especially in industry-scale datasets such as pharmaceutical omics pipelines. Methods: We present SHACLens, an interactive visualization workflow developed with a major pharmaceutical partner that links ontology, instance data, and violation reports across multiple coordinated views. We contribute a practitioner-informed workflow co-designed with pharmaceutical data-analysis experts. A Node-Link View combines ontology and groups of equivalent violations, a projection view reveals clusters of nodes with similar errors, a LineUp table combines instance data with violation information, a Class Tree offers a class-hierarchy overview, and an integrated LLM assistant provides contextual explanations and can operate the system via natural-language commands. Results: Within this workflow, selections and filters propagate across views, exposing co-occurring errors and their likely upstream causes. Analysts iteratively identify violation clusters, inspect correlations, and trace the detailed cause of errors. Evaluation and implications: We evaluated SHACLens through an iterative expert-in-the-loop design process with the partner team and a qualitative study on a transcriptomics dataset containing 5,203 violating nodes with the same experts. In this study, SHACLens efficiently surfaced repeated sets of errors due to missing objects and schema inconsistencies, supporting goal-oriented analysis and serendipitous findings.


Citation

Christian A. Steinparz, Andreas Hinterreiter, Labinot Bajraktari, Vitaly Sedlyarov, Markus J. Bauer, Thomas Zichner, Marc Streit
SHACLens: A Visualization Workflow for SHACL Violation Exploration in Knowledge Graphs
Frontiers in Bioinformatics, 6: 1756507, doi:10.3389/fbinf.2026.1756507, 2026.

BibTeX

@article{2026_frontiers_shaclens,
    title = {SHACLens: A Visualization Workflow for SHACL Violation Exploration in Knowledge Graphs},
    author = {Christian A. Steinparz and Andreas Hinterreiter and Labinot Bajraktari and Vitaly Sedlyarov and Markus J. Bauer and Thomas Zichner and Marc Streit},
    journal = {Frontiers in Bioinformatics},
    doi = {10.3389/fbinf.2026.1756507},
    url = {https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1756507},
    volume = {6},
    pages = {1756507},
    month = {March},
    year = {2026}
}