ArticleBMC bioinformatics2019
Model annotation and discovery with the Physiome Model Repository.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- A thermodynamically consistent approach to modeling epithelial solute and water transport in the proximal convoluted tubule.Journal of biological physics · 2026Article
- An automated model annotation system (AMAS) for SBML models.Bioinformatics (Oxford, England) · 2023Article
- CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities.Frontiers in bioinformatics · 2023Article
- Building a search tool for compositely annotated entities using Transformer-based approach: Case study in Biosimulation Model Search Engine (BMSE).F1000Research · 2023Article
- Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.Briefings in bioinformatics · 2022Article
- A modular and reusable model of epithelial transport in the proximal convoluted tubule.PloS one · 2022Review
- NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories.Frontiers in physiology · 2022Article
- SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks.Briefings in bioinformatics · 2021Article
- Hierarchical semantic composition of biosimulation models using bond graphs.PLoS computational biology · 2021Article
- Knowledge Representation for Multi-Scale Physiology Route Modeling.Frontiers in neuroinformatics · 2021Article
- History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications.Frontiers in physiology · 2021Review
- cellmlmanip and chaste_codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians.Wellcome open research · 2021Article
- The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).Journal of integrative bioinformatics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
backgroundMathematics and Phy sics-based simulation models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such models help to ensure that such models are accessible, discoverable, and reusable. To this end, researchers have developed tools and standards to encode mathematical models of biological systems enabling reproducibility and reuse, tools and guidelines to facilitate semantic description of mathematical models, and repositories in which to archive, share, and discover models. Scientists can leverage these resources to investigate specific questions and hypotheses in a more efficient manner.
resultsWe have comprehensively annotated a cohort of models with biological semantics. These annotated models are freely available in the Physiome Model Repository (PMR). To demonstrate the benefits of this approach, we have developed a web-based tool which enables users to discover models relevant to their work, with a particular focus on epithelial transport. Based on a semantic query, this tool will help users discover relevant models, suggesting similar or alternative models that the user may wish to explore or use.
conclusionThe semantic annotation and the web tool we have developed is a new contribution enabling scientists to discover relevant models in the PMR as candidates for reuse in their own scientific endeavours. This approach demonstrates how semantic web technologies and methodologies can contribute to biomedical and clinical research. The source code and links to the web tool are available at https://github.com/dewancse/model-discovery-tool.
Indexed as
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What OpenQuestion holds
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.