Systems Biology Markup Language
In the following recommendations:
How to cite this record FAIRsharing.org: SBML; Systems Biology Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.9qv71f; Last edited: April 10, 2019, 10:49 a.m.; Last accessed: Apr 17 2021 12:02 p.m.
Record added: May 14, 2015, 11:14 a.m.
Record updated: April 10, 2019, 10:47 a.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.9qv71f' by 'The FAIRsharing Team' at 10:47, 10 Apr 2019 (approved): 'supportLinks' has been modified: Before: FAQ|http://sbml.org/Documents/FAQ online documentation|http://sbml.org/Documents rss|http://sbml.org/index.php?title=News&action=feed twitter|@sbmlnews After: FAQ|http://sbml.org/Documents/FAQ forum|https://sourceforge.net/p/sbml/sbml-org-website/ forum|http://sbml.org/Forums help|http://sbml.org/SBML_Software_Guide online documentation|http://sourceforge.net/projects/sbml online documentation|http://sbml.org/News online documentation|http://sbml.org/Basic_Introduction_to_SBML online documentation|http://sbml.org/About online documentation|http://sbml.org/Community online documentation|http://sbml.org/Documents rss|http://sbml.org/index.php?title=News&action=feed twitter|@sbmlnews Added: forum|https://sourceforge.net/p/sbml/sbml-org-website/ forum|http://sbml.org/Forums help|http://sbml.org/SBML_Software_Guide online documentation|http://sourceforge.net/projects/sbml online documentation|http://sbml.org/News online documentation|http://sbml.org/Basic_Introduction_to_SBML online documentation|http://sbml.org/About online documentation|http://sbml.org/Community Removed: 'dataProcesses' has been modified: Before: browse After: SBML Level 3 Version 2 Release 1 Core Specification SBML Level 3 Packages Specification SBML Level 1 Version 2 Specification SBML Level 2 Version 5 Specification Added: SBML Level 3 Version 2 Release 1 Core Specification SBML Level 3 Packages Specification SBML Level 1 Version 2 Specification SBML Level 2 Version 5 Specification Removed: browse
Edits to 'https://fairsharing.org/FAIRsharing.9qv71f' by 'The FAIRsharing Team' at 13:11, 17 Jul 2018 (approved): 'related_standards' has been modified: Before: bsg-s000050|CellML bsg-s000148|Simulation Experiment Description Markup Language bsg-s000092|Systems Biology Graphical Notation bsg-s000178|Minimal Information Required In the Annotation of Models bsg-s000730|Open Food Safety Model Ontology bsg-s000668|Open Modeling EXchange format bsg-s000637|Systems Biology Ontology bsg-s000636|Mathematical Modelling Ontology bsg-s001143|Extensible Markup Language After: bsg-s000050|CellML bsg-s000148|Simulation Experiment Description Markup Language bsg-s000092|Systems Biology Graphical Notation bsg-s000178|Minimal Information Required In the Annotation of Models bsg-s000730|Open Food Safety Model Ontology bsg-s000668|Open Modeling EXchange format bsg-s000637|Systems Biology Ontology bsg-s001143|Extensible Markup Language Added: Removed: bsg-s000636|Mathematical Modelling Ontology
Edits to 'https://fairsharing.org/FAIRsharing.9qv71f' by 'The FAIRsharing Team' at 11:21, 15 Mar 2018 (approved): 'miriam_url' has been modified: Before: None After:
|help||SBML Software Guide|
|online documentation||SBML on SourceForge|
|online documentation||SBML News|
|online documentation||Introduction to SBML|
|online documentation||About SBML|
|online documentation||SBML Community|
|SBML Test Suite||http://sbml.org/Software/SBML_Test_Suite||3.3.0|
|Online Services / Facilities||http://sbml.org/Facilities|
Conditions of Use
|SBML Level 3 Version 2 Release 1 Core Specification||http://sbml.org/Documents/Specifications#SBML_Level_3|
|SBML Level 3 Packages Specification||http://sbml.org/Documents/Specifications#SBML_Level_3_Packages|
|SBML Level 1 Version 2 Specification||http://sbml.org/Documents/Specifications#SBML_Level_1|
|SBML Level 2 Version 5 Specification||http://sbml.org/Documents/Specifications#SBML_Level_2|
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Hucka M,Finney A,Sauro HM,Bolouri H,Doyle JC,Kitano H,Arkin AP,Bornstein BJ,Bray D,Cornish-Bowden A,Cuellar AA,Dronov S,Gilles ED,Ginkel M,Gor V,Goryanin II,Hedley WJ,Hodgman TC,Hofmeyr JH,Hunter PJ,Juty NS,Kasberger JL,Kremling A,Kummer U,Le Novere N,Loew LM,Lucio D,Mendes P,Minch E,Mjolsness ED,Nakayama Y,Nelson MR,Nielsen PF,Sakurada T,Schaff JC,Shapiro BE,Shimizu TS,Spence HD,Stelling J,Takahashi K,Tomita M,Wagner J,Wang J
Models and Formats
No identifier schema standards defined
No metrics standards defined
The MetaCrop resource contains information on the major metabolic pathways mainly in crops of agricultural and economic importance. The database includes manually curated information on reactions and the kinetic data associated with these reactions. Ontology terms are used and publication identification available to ease mining the data.
Integrated Pathway Analysis and Visualization System
iPAVS provides a collection of highly-structured manually curated human pathway data, it also integrates biological pathway information from several public databases and provides several tools to manipulate, filter, browse, search, analyze, visualize and compare the integrated pathway resources.
BRENDA is the main collection of enzyme functional data available to the scientific community.
Gramene: A curated, open-source, integrated data resource for comparative functional genomics in plants
Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other plant species. It represents a broad spectrum of species ranging from unicellular photo-autotrophs, algae, monocots, dicots and other important taxonomic clades. Within Plant Reactome, a database portal of Gramene, there are over 60 plant genomes as well as pathways for more than 80 species.
BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-linked to publicly available reference information.
Reactome - a curated knowledgebase of biological pathways
The cornerstone of Reactome is a freely available, open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in Reactome include classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. Inferred orthologous reactions are available for 15 non-human species including mouse, rat, chicken, zebrafish, worm, fly, and yeast.
SABIO-RK Biochemical Reaction Kinetics Database
SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
YEASTNET: A consensus reconstruction of yeast metabolism
This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from various research groups.
Experimental data repository for KInetic MOdels of biological SYStems
KiMoSys is a user-friendly platform that includes a public data repository of relevant published measurements, including metabolite concentrations (time-series and steady-state), flux data, and enzyme measurements in order to build ODE-based kinetic model. It is designed to search, exchange and disseminate experimental data (and associated kinetic models) for the systems modeling community.
SIGnaling Network Open Resource
SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.
Physiome Model Repository
The Physiome Model Repository (PMR) is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. PMR also provides a mechanism to create persistent access to specific revisions of a workspace, termed exposures. Exposure plugins are available for specific types of data (e.g., CellML or FieldML documents) which enable customizable views of the data when browsing the repository via a web browser, or an application accessing the repository’s content via web services.
The FAIRDOMHub is a publicly available resource build using the SEEK software, which enables collaborations within the scientific community. FAIRDOM will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.
JWS Online is a Systems Biology tool for the construction, modification and simulation of kinetic models and for the storage of curated models.
BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.
MetaNetX/MNXref is a database for reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. The tools developed at MetaNetX are useful for accessing, analysing and manipulating metabolic networks. MetaNetX goal is to automate model construction and genome annotation for large-scale metabolic networks.
Virtual Parts Repository
A repository of reusable, modular and composable models of biological parts.
PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other pathway database. PathBank is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics, and systems biology. All PathBank pathways include information on the relevant organelles, subcellular compartments, protein complex cofactors, protein complex locations, metabolite locations, chemical structures, and protein complex quaternary structures. The database is easily browsed and supports full text, sequence, and chemical structure searching.
Scroll for more...
COmputational Modeling in BIology NEtwork (COMBINE) (Consortium)
SBML Community (Consortium)
California Institute of Technology (University)
R01 GM070923 (National Institute of General Medical Sciences (NIGMS), Bethesda, MD, USA)