Eprint already available on another site (E-prints, working papers and research blog)
TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual.
Li, Luna Xingyu; Bleker, Carissa; Soliman, Sylvain et al.
2026
 

Files


Full Text
Li et al. - 2026 - TabularQual A spreadsheet-based format for annotating and - bioRxiv.pdf
Author preprint (1.5 MB) Creative Commons License - Attribution
Download

All documents in ORBi are protected by a user license.

Send to



Details



Keywords :
Logical models; Systems biology; Standards; Qualitative models; Format conversion; SBML; SBML-qual; Systems Biology Markup Language
Abstract :
[en] 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.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Li, Luna Xingyu ;  Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, United States
Bleker, Carissa ;  Department of Biotechnology and Systems Biology, National Institute of Biology, Vecna pot 121, 1000 Ljubljana, Slovenia
Soliman, Sylvain ;  Inria, Saclay Center, Lifeware team, France
Calzone, Laurence ;  Institut Curie, Universite PSL, INSERM, U1331, MinesParisTech, F-75005, Paris, France
Hiroi, Noriko ;  Kanagawa Institute of Technology, Keio university school of Medicine
Helikar, Tomáš ;  University of Nebraska-Lincoln
König, Matthias ;  Humboldt-Universitat zu Berlin, Faculty of Life Science, Institute of Biology, Philippstrasse 13, 10115 Berlin, Germany, University Hospital Schleswig-Holstein, Campus Lubeck, First Department of Medicine, 23538 Lubeck, Germany
Maia Ladeira, Luiz Carlos  ;  Université de Liège - ULiège > Département d'aérospatiale et mécanique > Génie biomécanique ; Université de Liège - ULiège > GIGA > GIGA Molecular & Computational Biology - Biomechanics Research Unit
Monteiro, Pedro T ;  INESC-ID, Lisbon, Portugal, IST - University of Lisbon, Portugal
Noël, Vincent ;  Institut Curie, Universite PSL, Paris, France, INSERM, U1331, Paris, France
Pastva, Samuel ;  Faculty of Informatics, Masaryk University Botanicka 68a 602 00 Brno Czech Republic
Salazar, Albin;  Centre for the Advanced Study of Collective Behaviour and University of Konstanz
Šafránek, David ;  Faculty of Informatics, Masaryk University Botanicka 68a 602 00 Brno Czech Republic
Thieffry, Denis ;  Departement de Biologie, Ecole Normale Superieure, PSL Universite, Paris, France, Institut Curie, Universite PSL, F-75005, Paris, France
Tsirvouli, Eirini ;  Department of Clinical and Molecular Medicine, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
Niarakis, Anna ;  Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, UPS, CNRS, Toulouse, France, Lifeware Group, Inria, Saclay-Ile-de-France, Palaiseau, France
Gennari, John ;  Department of Medical Education and Biomedical Informatics, University of Washington, Seattle, United States
More authors (7 more) Less
Language :
English
Title :
TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual.
Publication date :
03 June 2026
Funders :
European Union
Available on ORBi :
since 09 October 2026

Statistics


Number of views
4 (1 by ULiège)
Number of downloads
2 (0 by ULiège)

OpenAlex citations
 
0

Bibliography


Similar publications



Contact ORBi