SHACLens: a visualization workflow for SHACL violation exploration in knowledge graphs

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.