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BiNOM #6

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
https://binom.curie.fr/
Investigate their support for BioPAX level3. Can they read biopax level 3 and 
write to level 3 fully?

Original issue reported on code.google.com by ugurdogr...@gmail.com on 30 Apr 2012 at 12:38

GoogleCodeExporter commented 8 years ago 
Importing from BioPAX L3 looks OK. When I try to export the imported network to 
BioPAX L3, it creates an empty L3 file.

Their reaction network displays reactions and entities associated (input, 
output, and effectors). Complex - Member relation is not shown. Generic - 
Member relation is not shown. Cellular locations are displayed as text in the 
name of the molecules.

Original comment by ozgunba...@gmail.com on 5 May 2012 at 1:33

GoogleCodeExporter commented 8 years ago 
When you import a BioPAX owl to BiNOM, it gives option to create 3 different 
views: Reaction network, pathway hierarchy, protein-protein interactions. I was 
writing about the reaction network in my previous comment. Pathway hierarchy 
shows pathways, contained pathway steps, and member interactions. We don't 
create such a view but we display a forest of pathways for the user to select. 
When I test pathway hierarchy view on a model, I see that this view does not 
show nesting relations between pathways.

Original comment by ozgunba...@gmail.com on 29 May 2012 at 6:55

GoogleCodeExporter commented 8 years ago

Original comment by ugurdogr...@gmail.com on 5 Jun 2012 at 6:14