Known BioPAX representation issues

BioPAX Level 1
Polymerization reactions from BioCyc DBs can't be represented. The BioCyc DBs represent some reactions with coefficients of N, N+1, etc. These are typically polymerization-type reactions. An example is EC# 2.3.1.85: acetyl-CoA + N malonyl-CoA + 2N NADPH + 2N H+ = a long-chain fatty acid + (N+1) CoA + N CO2 + 2N NADP+. Currently, these must be omitted from the biopax file (fortunately none of them are in pathways, so far). BioPAX STOICHIOMETRIC-COEFFICIENT is currently limited to type 'double'.

This issue belongs to a larger set, commonly referred as "Generic Reactions". For other examples see GenericParticipants

BioPAX all levels
Direct/Indirect Interaction