FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2088901672> ?p ?o ?g. }

• W2088901672 abstract "Abstract Background In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system. Results For purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm. Conclusions Hierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models, such as the BioNetGen language (BNGL). Thus, the proposed use of hierarchical graphs should promote clarity and better understanding of rule-based models." @default.
• W2088901672 created "2016-06-24" @default.
• W2088901672 creator A5010255615 @default.
• W2088901672 creator A5016126519 @default.
• W2088901672 creator A5043402436 @default.
• W2088901672 date "2011-02-02" @default.
• W2088901672 modified "2023-10-07" @default.
• W2088901672 title "Hierarchical graphs for rule-based modeling of biochemical systems" @default.
• W2088901672 cites W1586735752 @default.
• W2088901672 cites W1607824205 @default.
• W2088901672 cites W1618519163 @default.
• W2088901672 cites W1660272337 @default.
• W2088901672 cites W1859573897 @default.
• W2088901672 cites W1964538907 @default.
• W2088901672 cites W1974974415 @default.
• W2088901672 cites W1975507400 @default.
• W2088901672 cites W1977290213 @default.
• W2088901672 cites W1977306646 @default.
• W2088901672 cites W1980843814 @default.
• W2088901672 cites W1986397618 @default.
• W2088901672 cites W1986649132 @default.
• W2088901672 cites W1989305528 @default.
• W2088901672 cites W2010152893 @default.
• W2088901672 cites W2013245328 @default.
• W2088901672 cites W2013817486 @default.
• W2088901672 cites W2016291752 @default.
• W2088901672 cites W2016493782 @default.
• W2088901672 cites W2028161249 @default.
• W2088901672 cites W2030205108 @default.
• W2088901672 cites W2034492556 @default.
• W2088901672 cites W2035562653 @default.
• W2088901672 cites W2040860090 @default.
• W2088901672 cites W2042629507 @default.
• W2088901672 cites W2053799953 @default.
• W2088901672 cites W2054047789 @default.
• W2088901672 cites W2069941324 @default.
• W2088901672 cites W2072499270 @default.
• W2088901672 cites W2081098704 @default.
• W2088901672 cites W2082620735 @default.
• W2088901672 cites W2082874501 @default.
• W2088901672 cites W2094358340 @default.
• W2088901672 cites W2099015579 @default.
• W2088901672 cites W2099693848 @default.
• W2088901672 cites W2104655345 @default.
• W2088901672 cites W2105038431 @default.
• W2088901672 cites W2117633759 @default.
• W2088901672 cites W2120824302 @default.
• W2088901672 cites W2121811364 @default.
• W2088901672 cites W2123121534 @default.
• W2088901672 cites W2126359798 @default.
• W2088901672 cites W2135354983 @default.
• W2088901672 cites W2137561154 @default.
• W2088901672 cites W2144114582 @default.
• W2088901672 cites W2145006655 @default.
• W2088901672 cites W2145080853 @default.
• W2088901672 cites W2152529416 @default.
• W2088901672 cites W2157989234 @default.
• W2088901672 cites W2159629828 @default.
• W2088901672 cites W2163493106 @default.
• W2088901672 cites W2165700291 @default.
• W2088901672 cites W2165714871 @default.
• W2088901672 cites W2166987747 @default.
• W2088901672 cites W2169193349 @default.
• W2088901672 cites W2412770081 @default.
• W2088901672 cites W2611943439 @default.
• W2088901672 cites W3102875255 @default.
• W2088901672 cites W4251538155 @default.
• W2088901672 doi "https://doi.org/10.1186/1471-2105-12-45" @default.
• W2088901672 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/3152790" @default.
• W2088901672 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/21288338" @default.
• W2088901672 hasPublicationYear "2011" @default.
• W2088901672 type Work @default.
• W2088901672 sameAs 2088901672 @default.
• W2088901672 citedByCount "18" @default.
• W2088901672 countsByYear W20889016722013 @default.
• W2088901672 countsByYear W20889016722014 @default.
• W2088901672 countsByYear W20889016722015 @default.
• W2088901672 countsByYear W20889016722016 @default.
• W2088901672 countsByYear W20889016722017 @default.
• W2088901672 countsByYear W20889016722018 @default.
• W2088901672 countsByYear W20889016722019 @default.
• W2088901672 countsByYear W20889016722020 @default.
• W2088901672 countsByYear W20889016722021 @default.
• W2088901672 crossrefType "journal-article" @default.
• W2088901672 hasAuthorship W2088901672A5010255615 @default.
• W2088901672 hasAuthorship W2088901672A5016126519 @default.
• W2088901672 hasAuthorship W2088901672A5043402436 @default.
• W2088901672 hasBestOaLocation W20889016721 @default.
• W2088901672 hasConcept C132525143 @default.
• W2088901672 hasConcept C41008148 @default.
• W2088901672 hasConcept C80444323 @default.
• W2088901672 hasConcept C80899671 @default.
• W2088901672 hasConceptScore W2088901672C132525143 @default.
• W2088901672 hasConceptScore W2088901672C41008148 @default.
• W2088901672 hasConceptScore W2088901672C80444323 @default.
• W2088901672 hasConceptScore W2088901672C80899671 @default.
• W2088901672 hasIssue "1" @default.
• W2088901672 hasLocation W20889016721 @default.
• W2088901672 hasLocation W20889016722 @default.
• W2088901672 hasLocation W20889016723 @default.

• next