Controlled vocabularies and semantics in systems biology

被引：185

作者：

Courtot, Melanie ^{[2
]}

Juty, Nick ^{[1
]}

Knuepfer, Christian ^{[3
]}

Waltemath, Dagmar ^{[4
]}

Zhukova, Anna ^{[1
]}

Draeger, Andreas ^{[5
]}

Dumontier, Michel ^{[6
]}

Finney, Andrew ^{[7
]}

Golebiewski, Martin ^{[8
]}

Hastings, Janna ^{[1
]}

Hoops, Stefan ^{[9
]}

Keating, Sarah ^{[1
]}

Kell, Douglas B. ^{[10
,11
]}

Kerrien, Samuel ^{[1
]}

Lawson, James ^{[12
]}

Lister, Allyson ^{[13
,14
]}

Lu, James ^{[15
]}

Machne, Rainer ^{[16
]}

Mendes, Pedro ^{[10
,17
]}

Pocock, Matthew ^{[14
]}

Rodriguez, Nicolas ^{[1
]}

Villeger, Alice ^{[10
,17
]}

Wilkinson, Darren J. ^{[13
]}

Wimalaratne, Sarala ^{[1
]}

Laibe, Camille ^{[1
]}

Hucka, Michael ^{[18
]}

Le Novere, Nicolas ^{[1
]}

机构：

[1] EMBL European Bioinformat Inst, Dept Computat Neurobiol, Hinxton, England

[2] Terry Fox Lab, Vancouver, BC, Canada

[3] Univ Jena, Inst Comp Sci, Jena, Germany

[4] Univ Rostock, Rostock, Germany

[5] Univ Tubingen, Ctr Bioinformat Tuebingen, Tubingen, Germany

[6] Carleton Univ, Dept Biol, Ottawa, ON K1S 5B6, Canada

[7] Ansys, Abingdon, Oxon, England

[8] HITS gGmbH, Heidelberg, Germany

[9] Virginia Bioinformat Inst, Blacksburg, VA USA

[10] Manchester Interdisciplinary Bioctr, Manchester, Lancs, England

[11] Univ Manchester, Sch Chem, Manchester, Lancs, England

[12] Univ Auckland, Auckland Bioengn Inst, Auckland 1, New Zealand

[13] Inst Ageing & Hlth, Ctr Integrated Syst Biol Ageing & Nutr, Newcastle Upon Tyne, Tyne & Wear, England

[14] Newcastle Univ, Sch Comp Sci, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England

[15] Swiss Fed Inst Technol, Automat Control Lab, Biomol Signaling & Control Grp, Zurich, Switzerland

[16] Univ Vienna, Theoret Biochem Grp, Vienna, Austria

[17] Univ Manchester, Sch Comp Sci, Manchester, Lancs, England

[18] CALTECH, Div Engn & Appl Sci, Pasadena, CA 91125 USA

来源：

MOLECULAR SYSTEMS BIOLOGY | 2011年 / 7卷

基金：

英国生物技术与生命科学研究理事会;

关键词：

dynamics; kinetics; model; ontology; simulation; MINIMUM INFORMATION; BIOMODELS DATABASE; MARKUP LANGUAGE; MODELS; SBML; INTEGRATION; ONTOLOGIES; LIBRARY; REPRESENTATION; MATHEMATICS;

D O I：

10.1038/msb.2011.77

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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. Molecular Systems Biology 7: 543; published online 25 October 2011; doi:10.1038/msb.2011.77

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