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: Feb. 22, 2018, 2:18 p.m.; Last accessed: Sep 22 2018 5:53 a.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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Models and Formats
No identifier schema 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.
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.
A repository of mathematical models of biological and biomedical systems
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 Reactome project is a collaboration to develop a curated resource of core pathways and reactions in human biology.
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Biotechnology and Biological Sciences Research Council (BBSRC), UK (Government body)
US National Science Foundation (NSF) (Government body)
COmputational Modeling in BIology NEtwork (COMBINE) (Consortium)