Ruchira S. Datta
BioPathways SIG: Nicolas Le Novére "The Systems Biology Graphical Notation"
supposedly biologist-friendly pathway maps are completely unintelligible - Ruchira S. Datta
by contrast, electric circuit diagrams, even very complex ones, can be understood by high school students - Ruchira S. Datta
Systems Biology Graphical Notation a limited number of well-defined symbols for biochemical and cellular events - Ruchira S. Datta
3 languages: process diagrams, entity relationships, and activity flow - Ruchira S. Datta
Thanks for updating us - I'm reading with interest from the DAM SIG room in between talks! - Allyson Lister
process diagrams: biochemistry; entity relationships: molecular biology; activity flow: physiology/genetics - Ruchira S. Datta
we're "projecting" the biological process onto different dimensions (the different languages) - Ruchira S. Datta
process diagrams: entity pool nodes (things that can be counted): containers, and process nodes: pipes - Ruchira S. Datta
also connecting arcs, which connect the various nodes w/ logical operators - Ruchira S. Datta
syntactic rules define what can connect with what, and diagram rules show how to render well-formed expressions - Ruchira S. Datta
can contract large diagrams into small ones - Ruchira S. Datta
color is strictly insignificant, so can photocopy diagrams - Ruchira S. Datta
entity relationships can be viewed as rules - Ruchira S. Datta
a process diagram representation of the same process would result in combinatorial explosion; the rule expresses this much more compactly - Ruchira S. Datta
activity flow never represents molecules, only the activities of those molecules - Ruchira S. Datta
have also annotations (not strictly part of SBGN), e.g., GO annotations - Ruchira S. Datta
SBGN is supported by many tools - Ruchira S. Datta
new version is about to be released - Ruchira S. Datta
have upcoming fora and hackathons - Ruchira S. Datta
it is compatible with BioPAX - Ruchira S. Datta
SBGN is more concerned about the graphic representation, so you can import BioPax pathways and visualize them with SBGN - Michael Kuhn
Science Daily summary of the August 8 Nature Biotechnology article: reshared from Jenny Morman - Ruchira S. Datta