ReviewBriefings in bioinformatics2021
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
Review in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed.
- TabularQual: A spreadsheet-based format for annotating and curating logical models in SBML-qual.bioRxiv : the preprint server for biology · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- KGBN: Augmenting and optimizing logical gene regulatory networks using knowledge graphs.bioRxiv : the preprint server for biology · 2026Article
- LM-Merger: a workflow for merging logical models with an application to gene regulatory network models.BMC bioinformatics · 2025Article
- A large-scale Boolean model of the rheumatoid arthritis fibroblast-like synoviocytes predicts drug synergies in the arthritic joint.NPJ systems biology and applications · 2023Article
- A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.Frontiers in bioinformatics · 2023Article
- Hybrid computational modeling highlights reverse warburg effect in breast cancer-associated fibroblasts.Computational and structural biotechnology journal · 2023Article
- Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.Frontiers in immunology · 2023Article
- Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.Briefings in bioinformatics · 2022Article
- Building digital twins of the human immune system: toward a roadmap.NPJ digital medicine · 2022Review
- Boolean modelling as a logic-based dynamic approach in systems medicine.Computational and structural biotechnology journal · 2022Review
- SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.Bioinformatics (Oxford, England) · 2021Article
- COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.Molecular systems biology · 2021Article
- A practical guide to mechanistic systems modeling in biology using a logic-based approach.Briefings in bioinformatics · 2021Review
- The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling.Briefings in bioinformatics · 2021Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
The fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses from this enormous quantity of data remains challenging. Logical models have long been used to answer a variety of questions regarding the dynamical behaviours of regulatory networks. As the number of published logical models increases, there is a pressing need for systematic model annotation, referencing and curation in community-supported and standardised formats. This article summarises the key topics and future directions of a meeting entitled 'Annotation and curation of computational models in biology', organised as part of the 2019 [BC]2 conference. The purpose of the meeting was to develop and drive forward a plan towards the standardised annotation of logical models, review and connect various ongoing projects of experts from different communities involved in the modelling and annotation of molecular biological entities, interactions, pathways and models. This article defines a roadmap towards the annotation and curation of logical models, including milestones for best practices and minimum standard requirements.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.