Biological and Medical Ontologies: Systems Biology Ontology (SBO)

The Systems Biology Ontology (SBO) comprises a number of controlled vocabularies containing terms commonly used in Systems Biology, in particular in computational modelling. It is applied, among other ontologies, within the Systems Biology Markup Language (SBML) to restrict and better characterize the components of models. It has been created within the BioModels.net effort to be used in an integrated fashion with the MIRIAM standard to curate and annotate models, and the BioModels Database, which stores published mathematical models of biological interests.

[1]  Hugh D. Spence,et al.  Minimum information requested in the annotation of biochemical models (MIRIAM) , 2005, Nature Biotechnology.

[2]  Kevin Donnelly,et al.  SNOMED-CT: The advanced terminology and coding system for eHealth. , 2006, Studies in health technology and informatics.

[3]  James M. Bower,et al.  The book of GENESIS - exploring realistic neural models with the GEneral NEural SImulation System (2. ed.) , 1994 .

[4]  Mark A. Musen,et al.  BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF , 2013, Semantic Web.

[5]  Hiroaki Kitano,et al.  CellDesigner: a process diagram editor for gene-regulatory and biochemical networks , 2003 .

[6]  Catherine M Lloyd,et al.  CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.

[7]  C E Lipscomb,et al.  Medical Subject Headings (MeSH). , 2000, Bulletin of the Medical Library Association.

[8]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[9]  Nicolas Le Novère,et al.  Beyond Structure: KiSAO and TEDDY—Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology , 2009 .

[10]  Michael Hucka,et al.  Systems Biology Markup Language (SBML) , 2014, Encyclopedia of Computational Neuroscience.

[11]  Melanie I. Stefan,et al.  BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models , 2010, BMC Systems Biology.

[12]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[13]  Sherri de Coronado,et al.  NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information , 2007, J. Biomed. Informatics.

[14]  Nicolas Le Novère,et al.  Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY , 2010 .

[15]  Attila Csikász-Nagy,et al.  Minimum Criteria for DNA Damage-Induced Phase Advances in Circadian Rhythms , 2009, PLoS Comput. Biol..

[16]  María Martín,et al.  UniProt: A hub for protein information , 2015 .

[17]  Lei Shi,et al.  SABIO-RK—database for biochemical reaction kinetics , 2011, Nucleic Acids Res..

[18]  F. Dhombres,et al.  Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users , 2012, Human mutation.

[19]  Michel Dumontier,et al.  Controlled vocabularies and semantics in systems biology , 2011, Molecular systems biology.

[20]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[21]  Michel Dumontier,et al.  Integrating systems biology models and biomedical ontologies , 2011, BMC Systems Biology.

[22]  Cynthia L. Smith,et al.  The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information , 2004, Genome Biology.

[23]  Jessica A. Turner,et al.  The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience , 2008, Neuroinformatics.

[24]  Ron Henkel,et al.  MaSyMoS: Finding Hidden Treasures in Model Repositories , 2014, SWAT4LS.

[25]  Andrew P Davison,et al.  Computational Neuroscience Ontology: a new tool to provide semantic meaning to your models , 2012, BMC Neuroscience.

[26]  Edmund J. Crampin,et al.  Minimum Information About a Simulation Experiment (MIASE) , 2011, PLoS Comput. Biol..

[27]  Christopher G. Chute,et al.  BioPortal: ontologies and integrated data resources at the click of a mouse , 2009, Nucleic Acids Res..

[28]  Nicolas Le Novère,et al.  BioModels.net Web Services, a free and integrated toolkit for computational modelling software , 2010, Briefings Bioinform..

[29]  Andreas Zell,et al.  SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks , 2008, BMC Systems Biology.

[30]  Edda Klipp,et al.  Annotation and merging of SBML models with semanticSBML , 2010, Bioinform..

[31]  Nicolas Le Novère,et al.  Model storage, exchange and integration , 2006, BMC Neuroscience.