TabularQual: a spreadsheet-based format for annotating and curating logical models in SBML-qual
Year: 2026
Type: article
Abstract: Logical models are widely used to study regulatory and signaling systems, yet their reuse, annotation, and exchange across tools remain challenging. Although SBML Level 3 Qualitative Models (SBML-qual) provides a standard representation, its XML-based syntax is difficult to inspect and edit directly. Here we introduce TabularQual, a spreadsheet-based, community-driven representation for Boolean and multi-valued logical models, together with a bidirectional converter between spreadsheets and SBML-qual. The converter is accessible programmatically and via a web interface to support diverse user workflows. We further describe two integration strategies that enable existing modeling tools to operate with TabularQual, either through SBML-qual exchange or via direct support. Case studies using the Stress Knowledge Map and CaSQ demonstrate how this integration supports model construction, curation, and reuse. TabularQual provides a practical bridge between human-readable model representations and standardized executable formats, supporting reproducibility, interoperability, and community-driven model development.
Institutions: University of Washington, National Institute of Biology, Centre Inria de Saclay, Inserm, Université Paris Sciences et Lettres, École Nationale Supérieure des Mines de Paris, Institut Curie, Kanagawa Institute of Technology, Keio University, University of Nebraska–Lincoln, Humboldt-Universität zu Berlin, University Hospital Schleswig-Holstein, University of Liège, Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento, University of Lisbon, Masaryk University, University of Konstanz, École Normale Supérieure - PSL, Institut de Biologie de l'École Normale Supérieure, Norwegian University of Science and Technology, Centre National de la Recherche Scientifique, Université Toulouse III - Paul Sabatier, Université de Toulouse, Unité de biologie Moléculaire, Cellulaire et du Développement, Centre de Biologie Intégrative de Toulouse
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,490
Funders: European Commission, Deutsche Forschungsgemeinschaft, Agence Nationale de la Recherche, Bundesministerium für Bildung und Forschung, Javna Agencija za Raziskovalno Dejavnost RS, National Institutes of Health, Fundação para a Ciência e a Tecnologia, National Institute of General Medical Sciences, National Institute of Biomedical Imaging and Bioengineering
OpenAlex ID: W7223347565