318:. SBML is now largely accepted and used in the field. However, as important as the definition of a common syntax is, it is also necessary to make clear the semantics of models. SBO tries to give us a way to label models with words that describe how they should be used in a large group of models that are commonly used in computational systems biology. The development of SBO was first discussed at the 9th SBML Forum Meeting in Heidelberg on October 14–15, 2004. During the forum,
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interpret SBO terms to augment the mathematics in the SBML file. Simulation tools can check the consistency of a rate law, convert reaction from one modelling framework to another (e.g., continuous to discrete), or distinguish between identical mathematical expressions based on different assumptions
386:, therefore supporting a large set of characters in the definitions of terms. Distributed curation is made possible by using a custom-tailored locking system allowing concurrent access. This system allows a continuous update of the ontology with immediate availability and suppress merging problems.
309:
The rise of systems biology, seeking to comprehend biological processes as a whole, highlighted the need to not only develop corresponding quantitative models but also to create standards allowing their exchange and integration. This concern drove the community to design common data formats, such as
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proposed to create a controlled vocabulary to store the content of Pedro Mendes' mind before he wandered out of the community. The development of the ontology was announced more officially in a message from Le Novère to
Michael Hucka and Andrew Finney on October 19.
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Le Novère N., Courtot M., Laibe C. Adding semantics in kinetics models of biochemical pathways. Proceedings of the 2nd
International Symposium on experimental standard conditions of enzyme characterizations (2007), 137-153.
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Le Novère N. BioModels.net, tools and resources to support
Computational Systems Biology. Proceedings of the 4th Workshop on Computation of Biochemical Pathways and Genetic Networks (2005), Logos, Berlin, pp.
442:
provides a mechanism to annotate model components with SBO terms, therefore increasing the semantics of the model beyond the sole topology of interaction and mathematical expression. Modelling tools such as
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can use the SBO annotation to integrate individual models into a larger one. The use of SBO is not restricted to the development of models. Resources providing quantitative experimental information such as
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mentioned that modellers possessed a lot of knowledge that was necessary to understand the model and, more importantly, to simulate it, but this knowledge was not encoded in SBML.
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Krause F, Uhlendorf J., Lubitz T., Schulz M., Klipp E., Liebermeister W. (2010), Annotation and merging of SBML models with semanticSBML, Bioinformatics 26 (3), 421-422
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will be able to annotate the parameters (what do they mean exactly, how were they calculated) and determine relationships between them.
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To curate and maintain SBO, a dedicated resource has been developed and the public interface of the SBO browser can be accessed at
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771:"The systems biology markup language (SBML): A medium for representation and exchange of Biochemical Network Models"
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for the validation. The libraries, full documentation, samples and tutorial are available
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occurring entity representation (biochemical process, molecular or genetic interaction...)
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languages are associated with an SBO term. This permits, for instance, to help generate
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Lloyd CM, Halstead MD, Nielsen PF (2004). "CellML: its future, present and past".
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physical entity representation (transporter, physical compartment, observable...)
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systems description parameter (catalytic constant, thermodynamic temperature...)
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The
Systems Biology Pathway Exchange (SBPAX) allows SBO terms to be added to
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mathematical expression (mass-action rate law, Hill-type rate law...)
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SBO is currently made up of seven different vocabularies:
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Hucka M, Finney A, Sauro HM, et al. (March 2003).
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Li C, Courtot M, Le Novère N, Laibe C (November 2009).
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696:Leonidou, Nantia; Fritze, Elisabeth; Renz, Alina;
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535:National Institute of General Medical Sciences
404:To allow programmatic access to the resource,
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345:modelling framework (discrete, continuous...)
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423:The SourceForge project can be accessed at
370:. A relational database management system (
50:Learn how and when to remove these messages
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1341:Timeline of biology and organic chemistry
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576:Nicolas Le Novère, personal communication
274:Learn how and when to remove this message
256:Learn how and when to remove this message
111:Learn how and when to remove this message
1387:Science and technology in Cambridgeshire
529:SBO has benefited from the funds of the
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469:All the graphical symbols used in the
192:Please improve this article by adding
72:contains content that is written like
1336:Nobel Prize in Physiology or Medicine
531:European Molecular Biology Laboratory
501:SBO is built in collaboration by the
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491:Biological Pathway Exchange (BioPAX)
425:http://sourceforge.net/projects/sbo/
357:metadata representation (annotation)
452:can be used. Other tools such as
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503:Computational Neurobiology Group
412:for the communication layer and
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39:or discuss these issues on the
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382:. Its content is encoded in
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664:10.1186/s12918-015-0212-9
389:Several exports formats (
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642:; Zell, Andreas (2015).
368:http://www.ebi.ac.uk/sbo
295:Systems Biology Ontology
459:SABIO Reaction Kinetics
950:Biological engineering
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181:relies excessively on
1035:Developmental biology
1010:Computational biology
990:Cellular microbiology
592:Brief. Bioinformatics
517:Team (Michael Hucka,
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93:neutral point of view
1255:Reproductive biology
1140:Mathematical biology
1065:Evolutionary biology
1015:Conservation biology
640:Palsson, Bernhard O.
505:(Nicolas Le Novère,
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884:Branches of biology
651:BMC Systems Biology
85:promotional content
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1265:Structural biology
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1200:Pharmacology
1190:Parasitology
1185:Paleontology
1165:Neuroscience
1145:Microbiology
1055:Epidemiology
1025:Cytogenetics
985:Cell biology
965:Biosemiotics
955:Biomechanics
935:Biogeography
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598:(3): 270–7.
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465:SBO and SBGN
454:semanticSBML
450:SBOannotator
445:SBMLsqueezer
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431:SBO and SBML
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83:by removing
79:Please help
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33:Please help
30:
1310:Xenobiology
1305:Virophysics
1275:Systematics
1230:Primatology
1175:Ornithology
1115:Ichthyology
1100:Herpetology
1095:Gerontology
1060:Epigenetics
1020:Cryobiology
910:Agrostology
900:Aerobiology
895:Abiogenesis
410:Apache Axis
393:flat file,
1356:Categories
1295:Toxicology
1290:Teratology
1235:Proteomics
1220:Physiology
1160:Neontology
1125:Lipidology
1120:Immunology
1090:Geobiology
1050:Embryology
1030:Dendrology
960:Biophysics
940:Biogeology
541:References
477:maps from
378:(JSP) and
305:Motivation
216:newspapers
183:references
81:improve it
36:improve it
1210:Phycology
1195:Pathology
1180:Osteology
1170:Nutrition
1130:Mammalogy
1105:Histology
824:CiteSeerX
783:CiteSeerX
657:(1): 68.
380:JavaBeans
362:Resources
331:Structure
246:July 2023
155:July 2023
101:July 2023
42:talk page
1382:Proteins
1372:Genetics
1324:See also
1300:Virology
1285:Taxonomy
1225:Pomology
1155:Mycology
1085:Genomics
1080:Genetics
905:Agronomy
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729:10371491
700:(2023).
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533:and the
521:, USA).
481:models.
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1045:Ecology
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613:2913671
519:Caltech
395:SBO-XML
230:scholar
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712:(7).
647:(PDF)
384:UTF-8
372:MySQL
237:JSTOR
223:books
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679:PMID
618:PMID
515:SBML
507:EMBL
479:SBML
475:SBGN
471:SBGN
440:SBML
397:and
314:and
312:SBML
293:The
209:news
834:doi
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399:OWL
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