ArticleMolecular systems biology2011
Controlled vocabularies and semantics in systems biology.
Article in Molecular systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers, 2 of them syntheses that pooled it.
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Who cites it
134 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
- Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.Journal of integrative bioinformatics · 2015Guideline
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- Nutrient control enables metabolic reconstruction ofbioRxiv : the preprint server for biology · 2026Article
- From FAIR to CURE: guidelines for computational models of biological systems.NPJ systems biology and applications · 2026Review
- MCC: automated mass and charge curation at the genome scale applied toMicrobiology spectrum · 2026Article
- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- The Virtual Brain Ontology: A Digital Knowledge Framework for Reproducible Brain Network Modeling.bioRxiv : the preprint server for biology · 2025Article
- FAIRification of computational models in biology.bioRxiv : the preprint server for biology · 2025Article
- SIMPROV: Provenance capturing for simulation studies.PloS one · 2025Article
- Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling.PLoS pathogens · 2024Article
- Simulation studies of social systems: telling the story based on provenance patterns.Royal Society open science · 2024Article
- Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems.BMC bioinformatics · 2024Article
- Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024.Journal of integrative bioinformatics · 2024Article
- Standardizing Extracted Data Using Automated Application of Controlled Vocabularies.Environmental health perspectives · 2024Article
- An automated model annotation system (AMAS) for SBML models.Bioinformatics (Oxford, England) · 2023Article
- Adapting modeling and simulation credibility standards to computational systems biology.Journal of translational medicine · 2023Review
- SBOannotator: a Python tool for the automated assignment of systems biology ontology terms.Bioinformatics (Oxford, England) · 2023Article
- A High-Quality Genome-Scale Model forACS synthetic biology · 2023Article
- SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models.BMC bioinformatics · 2023Article
74 more citing papers are in PubMed but not listed here.
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Authors and funding
27 authors.
Funding
Abstract
The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments.
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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.