ArticlePloS one2015
Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed.
- The Role of Health Literacy in Cardiometabolic Disease among People with Serious Mental Illness.Community mental health journal · 2026Article
- Article
- Analysing and simulating energy-based models in biology using BondGraphTools.The European physical journal. E, Soft matter · 2021Article
- Modular assembly of dynamic models in systems biology.PLoS computational biology · 2021Article
- Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data.Journal of the Royal Society, Interface · 2021Article
- Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective.NPJ systems biology and applications · 2021Article
- Hierarchical semantic composition of biosimulation models using bond graphs.PLoS computational biology · 2021Article
- SemGen: a tool for semantics-based annotation and composition of biosimulation models.Bioinformatics (Oxford, England) · 2019Article
- Harmonizing semantic annotations for computational models in biology.Briefings in bioinformatics · 2019Review
- Recent advances in biomedical simulations: a manifesto for model engineering.F1000Research · 2019Review
- FindSim: A Framework for Integrating Neuronal Data and Signaling Models.Frontiers in neuroinformatics · 2018Article
- CropsFrontiers in plant science · 2017Article
- Modular modelling with Physiome standards.The Journal of physiology · 2016Article
- Qualitative causal analyses of biosimulation models.CEUR workshop proceedings · 2016Article
- Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models.F1000Research · 2015Article
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
Semantics-based model composition is an approach for generating complex biosimulation models from existing components that relies on capturing the biological meaning of model elements in a machine-readable fashion. This approach allows the user to work at the biological rather than computational level of abstraction and helps minimize the amount of manual effort required for model composition. To support this compositional approach, we have developed the SemGen software, and here report on SemGen's semantics-based merging capabilities using real-world modeling use cases. We successfully reproduced a large, manually-encoded, multi-model merge: the "Pandit-Hinch-Niederer" (PHN) cardiomyocyte excitation-contraction model, previously developed using CellML. We describe our approach for annotating the three component models used in the PHN composition and for merging them at the biological level of abstraction within SemGen. We demonstrate that we were able to reproduce the original PHN model results in a semi-automated, semantics-based fashion and also rapidly generate a second, novel cardiomyocyte model composed using an alternative, independently-developed tension generation component. We discuss the time-saving features of our compositional approach in the context of these merging exercises, the limitations we encountered, and potential solutions for enhancing the approach.
Indexed as
Identifiers
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.