standards > model/format > DOI:10.25504/FAIRsharing.z9kvry


ready Systems Biology Graphical Notation

Abbreviation:SBGN


General Information
The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in maps of biological processes. The mission of SBGN project is to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers.



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.


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Record updated: March 28, 2017, 10:25 a.m. by lenov.

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Publications

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

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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

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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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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

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Integrated Pathway Analysis and Visualization System
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SubtiWiki
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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.

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Reactome - a curated knowledgebase of biological pathways
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