Systems Biology Graphical Notation
Abbreviation: SBGN
Homepage https://sbgn.github.io/
Countries that developed this resource Canada , European Union , Japan , United Kingdom , United States
Created in 2005
Taxonomic range
Knowledge Domains
Subjects
How to cite this record FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Nov 29 2021 2:41 p.m.
Record updated: June 23, 2021, 11:58 a.m. by The FAIRsharing Team.
| FAQ | FAQ |
| contact form | Contact Information |
| help | Examples |
| help | Learning SBGN |
Additional Information
| Contact | SBGN Editors |
TeSS training resources
Pathway visualization in the Reactome pathway database
Graphical & Computational Modelling of Biological Pathways
| SBGN Tools and Libraries | https://sbgn.github.io/software |
No XSD schemas defined
Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.
Sorokin A,Le Novere N,Luna A,Czauderna T,Demir E,Haw R,Mi H,Moodie S,Schreiber F,Villeger A
J Integr Bioinform 2015
The Systems Biology Graphical Notation.
Le Novere N et al.
Nat Biotechnol 2009
Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.
Mi H,Schreiber F,Moodie S,Czauderna T,Demir E,Haw R,Luna A,Le Novere N,Sorokin A,Villeger A
J Integr Bioinform 2015
gammaCaMKII shuttles Ca(2)(+)/CaM to the nucleus to trigger CREB phosphorylation and gene expression.
Ma H,Groth RD,Cohen SM,Emery JF,Li B,Hoedt E,Zhang G,Neubert TA,Tsien RW
Cell 2014
Reporting Guidelines
No guidelines defined
Terminology Artifacts
Models and Formats
Identifier Schemas
No identifier schema standards defined
Metrics
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.
SubtiWiki
Collaborative resource for the Bacillus community.
Termini-Oriented Protein Function INferred Database
The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases.
BioModels
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.
Pathway Commons
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely available under the license terms of each contributing database.
Protein ANalysis THrough Evolutionary Relationships: Classification of Genes and Proteins
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
PathBank
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.
Atlas of Cancer Signalling Network
ACSN is a web-based multi-scale resource of biological maps depicting molecular processes in cancer cell and tumor microenvironment. The Atlas represents interconnected cancer-related signalling and metabolic network maps. Molecular mechanisms are depicted on the maps at the level of biochemical interactions, forming a large seamless network. The Atlas is a "geographic-like" interactive "world map" of molecular interactions leading the hallmarks of cancer as described by Hanahan and Weinberg.
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Record Maintainer
This record is maintained by matthiaskoenig ORCID
Funds
Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
Biological Network Modelling Center (BNMC), Beckman Institute, California Institute of Technology (Caltech), Pasadena, CA, USA (Government body)
New Energy and Industrial Technology Development Organization (Company)
Okinawa Institute of Science and Technology Graduate University, OIST
National Science Foundation (NSF), USA (Government body)
Maintains
COmputational Modeling in BIology NEtwork (COMBINE) (Consortium)
