TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual
Li, L. X.; Bleker, C.; Soliman, S.; Calzone, L.; Hiroi, N.; Helikar, T.; Konig, M.; Ladeira, L.; Monteiro, P. T.; Noel, V.; Pastva, S.; Salazar, A.; Safranek, D.; Thieffry, D.; Tsirvouli, E.; Niarakis, A.; Gennari, J.
Show 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.
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