TabularQual: a spreadsheet-based format for annotating and curating logical models in SBML-qual
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 through a public web interface ( https://tabularqual.streamlit.app/ ), supporting 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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BibTeX
@article{li2026tabularqual,
title = {{TabularQual: a spreadsheet-based format for annotating and curating logical models in SBML-qual}},
author = {Luna Xingyu Li and Carissa Bleker and Sylvain Soliman and Laurence Calzone and Noriko Hiroi and Tomáš Helikar and Matthias König and Luiz Ladeira and Pedro T Monteiro and Vincent Noël and Samuel Pastva and Albin Salazar and David Šafránek and Denis Thieffry and Eirini Tsirvouli and Anna Niarakis and John H Gennari},
journal = {npj Systems Biology and Applications},
year = {2026},
month = oct,
doi = {10.1038/s41540-026-00841-w},
url = {https://inria.hal.science/hal-05837659v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - TabularQual: a spreadsheet-based format for annotating and curating logical models in SBML-qual
AU - Luna Xingyu Li
AU - Carissa Bleker
AU - Sylvain Soliman
AU - Laurence Calzone
AU - Noriko Hiroi
AU - Tomáš Helikar
AU - Matthias König
AU - Luiz Ladeira
AU - Pedro T Monteiro
AU - Vincent Noël
AU - Samuel Pastva
AU - Albin Salazar
AU - David Šafránek
AU - Denis Thieffry
AU - Eirini Tsirvouli
AU - Anna Niarakis
AU - John H Gennari
PY - 2026
DA - 2026/10/23
JO - npj Systems Biology and Applications
DO - 10.1038/s41540-026-00841-w
UR - https://inria.hal.science/hal-05837659v1
AB - 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 through a public web interface ( https://tabularqual.streamlit.app/ ), supporting 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.
SN - 2056-7189
ER -