The Systems Biology Graphical Notation

By N. Novère, Michael Hucka, Huaiyu Mi, Stuart L. Moodie, Falk Schreiber, Anatoly A. Sorokin, Emek Demir, Katja Wegner, M. Aladjem, Sarala M. Wimalaratne and 29 more. Nature Biotechnology, 2009

975 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0a6b6a5ba7ca77252f02dcf960456770abf83e6e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees (2012, methodology): “To support other pathway analysis and modeling tools, PANTHER Pathways can now be downloaded in three major pathway exchange formats: Systems Biology Market Language (SBML) (22), Systems Biology Graphical Notation (SBGN-ML) (23,24) and BioPAX (25).”
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis (2020, neutral): “…inferred, manually annotated, complexes etc so that the user can filter with respect to quality. e.g. CellPhoneDB is much more accurate than the other resources, as it was manually curated and so provides better insight since it doesn't cloud the cell-cell networks with as much noise.”
Pathway Commons, a web resource for biological pathway data (2010, methodology): “Left: The full BioPAX model of the AKT pathway, shown as an SBGN process diagram (19).”
The Reactome Pathway Knowledgebase 2024 (2023, methodology): “Processes are systematically described in molecular detail to generate an ordered network of molecular transformations, resulting in an extended version of a classic metabolic map ( 4 ) generally compliant with the SBGN process description standard ( 5 ).”
The Reactome Pathway Knowledgebase (2017, methodology): “Our SBGN-based (7) scheme for representing pathways, implemented eight years ago, yields pathway diagrams that become cluttered and difficult for biologist users to navigate as we achieve more nearly complete annotations of the participants in a process and their functions, and our approximately…”
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models (2010, methodology): “A utility to convert graphs into the Systems Biology Graphical Notation (SBGN) [60] is currently being developed.”
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium (2009, methodology): “PANTHER 7 has adopted the Systems Biology Graphical Notation (SBGN) standard (26) for the 165 pathway diagrams currently available on the PANTHER website.”
An Efficient Method for Structural Identifiability Analysis of Large Dynamic Systems (2012, methodology): “In the original algorithm presented by Sedoglavic [2002], parameters are treated as state variables with zero timederivatives.”
Potential unsatisfiability of cyclic constraints on stochastic biological networks biases selection towards hierarchical architectures (2015, background): “(row 1) The systems biology graphical notation (SBGN) is capable of representing arbitrary biological networks including processes that involve metabolites, signaling molecules, genes, and enzymes [11].”
Quantitative and logic modelling of gene and molecular networks (2015, methodology): “Entity relationships have been standardized using the SBGN entity relationship language (40), and such maps have been constructed to represent molecular events underlying, for instance, the cell cycle (41,42) and apoptosis (43).”
PANTHER: Making genome‐scale phylogenetics accessible to all (2021, methodology): “Graphical representations that are compliant with the Systems Biology Graphical Notation standards 16 are also available for all pathways.”