Controlled vocabularies and semantics in systems biology

Melanie Courtot; Nick Juty; Christian Knuepfer; Dagmar Waltemath; Anna Zhukova; Andreas Draeger; Michel Dumontier; Andrew Finney; Martin Golebiewski; Janna Hastings; Stefan Hoops; Sarah Keating; Douglas B. Kell; Samuel Kerrien; James Lawson; Allyson Lister; James Lu; Rainer Machne; Pedro Mendes; Matthew Pocock; Nicolas Rodriguez; Alice Villeger; Darren J. Wilkinson; Sarala Wimalaratne; Camille Laibe; Michael Hucka; Nicolas Le Novere

doi:10.1038/msb.2011.77

Controlled vocabularies and semantics in systems biology

Melanie Courtot, Nick Juty, Christian Knuepfer, Dagmar Waltemath, Anna Zhukova, Andreas Draeger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B. Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew PocockNicolas Rodriguez, Alice Villeger, Darren J. Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novere^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Journal	Molecular Systems Biology
Volume	7
DOIs	https://doi.org/10.1038/msb.2011.77
Publication status	Published - Oct 2011
Externally published	Yes

Keywords

dynamics
kinetics
model
ontology
simulation

Access to Document

10.1038/msb.2011.77Licence: Unspecified

Cite this

Courtot, M., Juty, N., Knuepfer, C., Waltemath, D., Zhukova, A., Draeger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., Hoops, S., Keating, S., Kell, D. B., Kerrien, S., Lawson, J., Lister, A., Lu, J., Machne, R., Mendes, P., ... Le Novere, N. (2011). Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7. https://doi.org/10.1038/msb.2011.77

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title = "Controlled vocabularies and semantics in systems biology",

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.",

keywords = "dynamics, kinetics, model, ontology, simulation",

author = "Melanie Courtot and Nick Juty and Christian Knuepfer and Dagmar Waltemath and Anna Zhukova and Andreas Draeger and Michel Dumontier and Andrew Finney and Martin Golebiewski and Janna Hastings and Stefan Hoops and Sarah Keating and Kell, {Douglas B.} and Samuel Kerrien and James Lawson and Allyson Lister and James Lu and Rainer Machne and Pedro Mendes and Matthew Pocock and Nicolas Rodriguez and Alice Villeger and Wilkinson, {Darren J.} and Sarala Wimalaratne and Camille Laibe and Michael Hucka and {Le Novere}, Nicolas",

year = "2011",

month = oct,

doi = "10.1038/msb.2011.77",

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Courtot, M, Juty, N, Knuepfer, C, Waltemath, D, Zhukova, A, Draeger, A, Dumontier, M, Finney, A, Golebiewski, M, Hastings, J, Hoops, S, Keating, S, Kell, DB, Kerrien, S, Lawson, J, Lister, A, Lu, J, Machne, R, Mendes, P, Pocock, M, Rodriguez, N, Villeger, A, Wilkinson, DJ, Wimalaratne, S, Laibe, C, Hucka, M & Le Novere, N 2011, 'Controlled vocabularies and semantics in systems biology', Molecular Systems Biology, vol. 7. https://doi.org/10.1038/msb.2011.77

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AU - Courtot, Melanie

AU - Juty, Nick

AU - Knuepfer, Christian

AU - Waltemath, Dagmar

AU - Zhukova, Anna

AU - Draeger, Andreas

AU - Dumontier, Michel

AU - Finney, Andrew

AU - Golebiewski, Martin

AU - Hastings, Janna

AU - Hoops, Stefan

AU - Keating, Sarah

AU - Kell, Douglas B.

AU - Kerrien, Samuel

AU - Lawson, James

AU - Lister, Allyson

AU - Lu, James

AU - Machne, Rainer

AU - Mendes, Pedro

AU - Pocock, Matthew

AU - Rodriguez, Nicolas

AU - Villeger, Alice

AU - Wilkinson, Darren J.

AU - Wimalaratne, Sarala

AU - Laibe, Camille

AU - Hucka, Michael

AU - Le Novere, Nicolas

PY - 2011/10

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N2 - 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.

AB - 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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KW - kinetics

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KW - ontology

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DO - 10.1038/msb.2011.77

M3 - Article

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SN - 1744-4292

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JO - Molecular Systems Biology

JF - Molecular Systems Biology

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