{
  "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.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 17,
  "authors": [
    {
      "name": "Luna Xingyu Li"
    },
    {
      "name": "Carissa Bleker"
    },
    {
      "name": "Sylvain Soliman"
    },
    {
      "name": "Laurence Calzone"
    },
    {
      "name": "Noriko Hiroi"
    },
    {
      "name": "Tomáš Helikar"
    },
    {
      "name": "Matthias König"
    },
    {
      "name": "Luiz Ladeira"
    },
    {
      "name": "Pedro T Monteiro"
    },
    {
      "name": "Vincent Noël"
    },
    {
      "name": "Samuel Pastva"
    },
    {
      "name": "Albin Salazar"
    },
    {
      "name": "David Šafránek"
    },
    {
      "name": "Denis Thieffry"
    },
    {
      "name": "Eirini Tsirvouli"
    },
    {
      "name": "Anna Niarakis"
    },
    {
      "name": "John H Gennari"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/dqgpxj9t2zgfq.bib",
  "cited_by": 0,
  "doi": "10.1038/s41540-026-00841-w",
  "fulltext_url": null,
  "id": "dqgpxj9t2zgfq",
  "issns": [
    "2056-7189"
  ],
  "landing_url": "https://inria.hal.science/hal-05837659v1",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "openalex",
      "1312|Gene Regulatory Network Analysis"
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  "openalex": "W7223347565",
  "pdf_url": "https://inria.hal.science/hal-05837659/document",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-23",
  "publisher": "Nature Research",
  "ris": "https://research.draconitic.com/paper/dqgpxj9t2zgfq.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:01Z",
      "native_id": "hal-05837659",
      "source": "hal",
      "url": "https://inria.hal.science/hal-05837659v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "hal:1.sdv.bbm",
      "subfield": "general"
    },
    {
      "field": "biology",
      "origin": "hal:2.sdv.bbm.mn",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "TabularQual: a spreadsheet-based format for annotating and curating logical models in SBML-qual",
  "title_text": "TabularQual: a spreadsheet-based format for annotating and curating logical models in SBML-qual",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:01Z",
  "url": "https://research.draconitic.com/paper/dqgpxj9t2zgfq",
  "venue": "npj Systems Biology and Applications",
  "versions": []
}