ArticleBioinformatics (Oxford, England)2019
SemGen: a tool for semantics-based annotation and composition of biosimulation models.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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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.
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.
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Who cites it
14 citing papers in PubMed.
- Neuro-psycho MMSig: multimodal mechanism enrichment platform for neuropsychiatric disorders.Frontiers in bioinformatics · 2026Article
- 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 scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.Nature communications · 2022Article
- Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility.Frontiers in systems biology · 2022Article
- NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories.Frontiers in physiology · 2022Article
- Article
- Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data.Journal of the Royal Society, Interface · 2021Article
- Publishing reproducible dynamic kinetic models.Briefings in bioinformatics · 2021Article
- Hierarchical semantic composition of biosimulation models using bond graphs.PLoS computational biology · 2021Article
- The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).Journal of integrative bioinformatics · 2020Article
- BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks.Genome biology · 2020Article
- BioModels-15 years of sharing computational models in life science.Nucleic acids research · 2020Article
- Model annotation and discovery with the Physiome Model Repository.BMC bioinformatics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
summaryAs the number and complexity of biosimulation models grows, so do demands for tools that can help users understand models and compose more comprehensive and accurate systems from existing models. SemGen is a tool for semantics-based annotation and composition of biosimulation models designed to address this demand. A key SemGen capability is to decompose and then integrate models across existing model exchange formats including SBML and CellML. To support this capability, we use semantic annotations to explicitly capture the underlying biological and physical meanings of the entities and processes that are modeled. SemGen leverages annotations to expose a model's biological and computational architecture and to help automate model composition. AVAILABILITY AND IMPLEMENTATION: SemGen is freely available at https://github.com/SemBioProcess/SemGen. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.