GuidelineJournal of integrative bioinformatics2015
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.
Guideline in Journal of integrative bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 2 of them syntheses that pooled it.
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
41 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.Journal of integrative bioinformatics · 2015Guideline
- The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.Journal of integrative bioinformatics · 2015Guideline
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.PLoS computational biology · 2026Article
- Optotransduction Pathway, Exploring Connections with Inflammation.Biomolecules · 2026Article
- Antimony 3: Extending human-readable model definitions for SBML Level 3 Core and Packages.bioRxiv : the preprint server for biology · 2026Article
- VIOLIN: A modular framework for scalable reconciliation of heterogeneous interaction graphs.bioRxiv : the preprint server for biology · 2026Article
- BioPAX in 2024: Where we are and where we are heading.Computational and structural biotechnology journal · 2024Review
- Modulation of colonic immunometabolic responses during Clostridioides difficile infection ameliorates disease severity and inflammation.Scientific reports · 2023Article
- Adapting modeling and simulation credibility standards to computational systems biology.Journal of translational medicine · 2023Review
- SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models.BMC bioinformatics · 2023Article
- Article
- An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism.NPJ systems biology and applications · 2021Article
- Enforcing ATP hydrolysis enhanced anaerobic glycolysis and promoted solvent production in Clostridium acetobutylicum.Microbial cell factories · 2021Article
- FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2.Bioinformatics (Oxford, England) · 2020Article
- Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model OrganismFrontiers in molecular biosciences · 2018Article
- SBML Level 3 package: Groups, Version 1 Release 1.Journal of integrative bioinformatics · 2016Article
- COMODI: an ontology to characterise differences in versions of computational models in biology.Journal of biomedical semantics · 2016Article
- Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases.Briefings in bioinformatics · 2016Article
- Top 10 metrics for life science software good practices.F1000Research · 2016Article
- SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.BMC systems biology · 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
13 authors.
Funding
Abstract
Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org.
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.