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Bioinform."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We present SHACLens, an interactive visualization workflow\u2014developed with a major pharmaceutical partner\u2014that 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Evaluation and implications<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fbinf.2026.1756507","type":"journal-article","created":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T09:05:31Z","timestamp":1774256731000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["SHACLens: a visualization workflow for SHACL violation exploration in knowledge graphs"],"prefix":"10.3389","volume":"6","author":[{"given":"Christian A.","family":"Steinparz","sequence":"first","affiliation":[{"name":"Visual Data Science Lab, Johannes Kepler University","place":["Linz, Austria"]}]},{"given":"Andreas","family":"Hinterreiter","sequence":"additional","affiliation":[{"name":"Visual Data Science Lab, Johannes Kepler University","place":["Linz, Austria"]}]},{"given":"Labinot","family":"Bajraktari","sequence":"additional","affiliation":[{"name":"Boehringer Ingelheim RCV GmbH & Co KG","place":["Vienna, Austria"]}]},{"given":"Vitaly","family":"Sedlyarov","sequence":"additional","affiliation":[{"name":"Boehringer Ingelheim RCV GmbH & Co KG","place":["Vienna, Austria"]}]},{"given":"Markus J.","family":"Bauer","sequence":"additional","affiliation":[{"name":"Boehringer Ingelheim RCV GmbH & Co KG","place":["Vienna, Austria"]}]},{"given":"Thomas","family":"Zichner","sequence":"additional","affiliation":[{"name":"Boehringer Ingelheim RCV GmbH & Co KG","place":["Vienna, Austria"]}]},{"given":"Marc","family":"Streit","sequence":"additional","affiliation":[{"name":"Visual Data Science Lab, Johannes Kepler University","place":["Linz, Austria"]}]}],"member":"1965","published-online":{"date-parts":[[2026,3,23]]},"reference":[{"key":"B1","article-title":"TGVizTab: an ontology visualisation extension for prot\u00e9g\u00e9","volume-title":"Knowledge capture, workshop on visualization information in knowledge engineering","author":"Alani","year":"2003"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.15488\/11944","article-title":"A library for visualizing SHACL over knowledge graphs","author":"Alom","year":"2022","journal-title":"Master\u2019s Thesis, Gottfried Wilhelm Leibniz Univ. 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