Systems Biology Graphical Notation
How to cite this record FAIRsharing.org: SBGN; Systems Biology Graphical Notation; DOI: https://doi.org/10.25504/FAIRsharing.z9kvry; Last edited: Jan. 8, 2019, 1:38 p.m.; Last accessed: Apr 07 2020 8:35 p.m.
Record updated: March 28, 2017, 10:25 a.m. by lenov.
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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,Hucka M,Mi H,Moodie S,Schreiber F,Sorokin A,Demir E,Wegner K,Aladjem MI,Wimalaratne SM,Bergman FT,Gauges R,Ghazal P,Kawaji H,Li L,Matsuoka Y,Villeger A,Boyd SE,Calzone L,Courtot M,Dogrusoz U,Freeman TC,Funahashi A,Ghosh S,Jouraku A,Kim S,Kolpakov F,Luna A,Sahle S,Schmidt E,Watterson S,Wu G,Goryanin I,Kell DB,Sander C,Sauro H,Snoep JL,Kohn K,Kitano H
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
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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.
Collaborative resource for the Bacillus community.
Termini-Oriented Protein Function INferred Database
TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alternative splicing and alternative translation initiation or post-translational protein processing by proteases that cleave proteases as part of protein maturation or as a regulatory modification. Accordingly, protein termini evidence in TopFIND is inferred from other databases such as ENSEMBL transcripts, TISdb for alternative translation initiation, MEROPS for protein cleavage by proteases, and UniProt for canonical and protein isoform start sites. Additionally, termini are annotated from user submitted lists of termini and inferred from user submitted lists of cleavage sites. As a protein-centric database, TopFIND presents a website for each protein isoform (organized around UniProt accession codes). These websites contain general protein information, such as organism, chromosome location, and proteins sequence. They then list position information such as specific termini evidences, known cleavage sites, sequence features and domains for each protein. In addition, TopFIND shows each protein in the context of the protease web, a network of proteases and their inhibitors, where a protease can cleave of other proteases and their inhibitors thus influencing their activity. All information in TopFIND can be filtered by a powerful filter engine that relies on rich annotation as to the origin of data in TopFIND. TopFIND can also be programmatically queried using the PSICQUIC or XML API. Recently, software tools were developed to enable quick access to TopFIND data for lists of termini obtained by, for example, proteomic termini screens (terminomics). TopFIND Explorer “TopFINDer” reports position specific protein information for protein termini, such as terminus evidences, prime and non-prime sequences, and protein domains affected by cleavage. TopFINDer further reports summary statistics for protein cleavage by known proteases. PathFINDer is a second tool that reports proteolytic paths from a query protease to identified protein substrates thus enabling the differentiation between direct and indirect protease substrates and yielding mechanistic insights into pathways based on existing information.
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 17 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, rice, and Arabidopsis.
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.
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Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
National Science Foundation (NSF), USA (Government body)
COmputational Modeling in BIology NEtwork (COMBINE) (Consortium)