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Protocols

SBO specifications

Information


Unique identifier OMICS_19739
Name SBO
Alternative name Systems Biology Ontology
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Nicolas Le Novère

Additional information


(Le Novère,Courtot,Laibe, 2007) Adding semantics in kinetics models of biochemical pathways. Proceedings of the 2nd International Symposium on Experimental Standard Conditions of Enzyme Characterizations. http://europepmc.org/abstract/CTX/C7516

Publications for Systems Biology Ontology

SBO citations

 (9)
call_split

An integrated text mining framework for metabolic interaction network reconstruction

2016
PeerJ
PMCID: 4806637
PMID: 27019783
DOI: 10.7717/peerj.1811
call_split See protocol

[…] s well as metabolite entities according to our annotation guideline (www.sbi.kmutt.ac.th/ preecha/metrecon). presents annotated entity types along with reference databases i.e., EcoCyc and ChEBI and Systems Biology Ontology (SBO) ID. Afterwards, manual correction using BRAT () by individual domain experts was performed. The metabolic events in the abstracts and titles were annotated according to […]

library_books

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

2015
J Integr Bioinform
PMCID: 5451324
PMID: 26528564
DOI: 10.2390/biecoll-jib-2015-266

[…] arefully curated controlled vocabularies (CVs). This is the purpose of the optional sboTerm attribute provided on the SBML class SBase. The sboTerm attribute always refers to terms belonging to the Systems Biology Ontology (SBO, http://biomodels.net/SBO/). In this section, we discuss the sboTerm attribute, SBO, the motivations and theory behind their introduction, and guidelines for their use.S […]

library_books

Correlating Information Contents of Gene Ontology Terms to Infer Semantic Similarity of Gene Products

2014
PMCID: 4054916
PMID: 24963342
DOI: 10.1155/2014/891842

[…] gy (GO) [–], the inference of phenotype similarity between human diseases based on the human phenotype ontology (HPO) [, ], the modeling of general computational tasks in systems biology based on the systems biology ontology (SBO) [], and many others [–]. With an ontology to provide controlled and structured vocabularies in a specific biological domain and annotations to characterize entities in t […]

library_books

Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)

2011
Stand Genomic Sci
PMCID: 3235518
PMID: 22180826
DOI: 10.4056/sigs.2034671

[…] cond day was devoted to the topic of semantics in computational models. It began with a session on the resources available to annotate models. Nick Juty, from the EMBL-EBI, presented an update on the Systems Biology Ontology [], describing the new links between mathematical expressions and quantitative parameters []. Camille Laibe, from the same group, described the planned evolution of MIRIAM Res […]

library_books

PathCase SB architecture and database design

2011
BMC Syst Biol
PMCID: 3229461
PMID: 22070889
DOI: 10.1186/1752-0509-5-188

[…] ems biology data source.Sbase entity serves as a base object for the actual entities. Each entity (except DataSource) in the database extends Sbase entity. Sbase contains a sboTerm attribute for SBO (Systems Biology Ontology) annotations. Most SBML elements have SBO annotations which define the semantics of the corresponding term. For instance, for a modifier in a reaction, its SBO term (if availa […]

library_books

Parameter Balancing in Kinetic Models of Cell Metabolism†

2010
PMCID: 2999964
PMID: 21038890
DOI: 10.1021/jp108764b

[…] e, see Figure and Table ). In the model, enzymes and allosteric activators and inhibitors need to be listed as reaction modifiers and specified by SBO terms. The quantity types are defined as in the Systems Biology Ontology,() and the names of the reactions and species refer to IDs in the SBML model. All this helps the process to run in an almost fully automated manner. For further details, see t […]

Citations

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SBO institution(s)
Terry Fox Laboratory, Vancouver, CB, Canada; Department of Computational Neurobiology, EMBL European Bioinformatics Institute, Wellcome-Trust Genome Campus, Hinxton, UK; Institute of Computer Science, Friedrich-Schiller University, Jena, Germany; Bioinformatics and Systems Biology, Rostock University, Rostock, Germany; Center for Bioinformatics Tuebingen, University of Tuebingen, Tubingen, Germany; Department of Biology, Carleton University, Ottawa, ON, Canada; Ansys, Abingdon, UK; HITS gGmbH, Heidelberg, Germany; Virginia Bioinformatics Institute, Blacksburg, VA, USA; Manchester Interdisciplinary Biocentre, Manchester, UK; School of Chemistry, University of Manchester, Manchester, UK; Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand; Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle upon Tyne, UK; School of Computing Science, Newcastle University, Newcastle upon Tyne, UK; Biomolecular Signaling and Control Group, Automatic Control Laboratory, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland; Theoretical Biochemistry Group, University of Vienna, Vienna, Austria; School of Computer Science, University of Manchester, Manchester, UK; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA
SBO funding source(s)
Supported by the National Institute of General Medical Sciences, European Commission (FP7 SP4 Capacities Preparatory Phase 211601, ELIXIR) and Marie-Curie BioStar.

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