@article{Courtot2011a,
  author = {Courtot, M\'{e}lanie and Juty, Nick and Kn\"upfer, Christian and
	Waltemath, Dagmar and Zhukova, Anna and Dr\"ager, Andreas and Dumontier,
	Michel and Finney, Andrew and Golebiewski, Martin and Hastings, Janna
	and Hoops, Stefan and Keating, Sarah M. and Kell, Douglas B. and Kerrien,
	Samuel and Lawson, James and Lister, Allyson and Lu, James and Machne,
	Rainer and Mendes, Pedro and Pocock, Matthew and Rodriguez, Nicolas
	and Vill\'{e}ger, Alice and Wilkinson, Darren J. and Wimalaratne,
	Sarala and Laibe, Camille and Hucka, Michael and {Le Nov\`{e}re}, Nicolas},
  title = {Controlled vocabularies and semantics in systems biology},
  journal = {Molecular Systems Biology},
  year = {2011},
  volume = {7},
  pages = {543},
  number = {1},
  month = sep,
  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.},
  doi = {10.1038/msb.2011.77},
  keywords = {dynamics; kinetics; model; ontology; simulation},
  pdf = {https://www.embopress.org/doi/epdf/10.1038/msb.2011.77},
  url = {https://doi.org/10.1038/msb.2011.77}
}