It seems that some KEGG reactions are present in certain organism-specific pathways, but not in others (e.g. not marked as present in the organism). For example, reaction 'R00341' is not marked as human in glycolysis (hsa00010) pathway, but it is marked as human in the overview pathway (hsa01100), here being marked as a part of the glycolysis.
I want to find organism specific pathways for each reaction. Would it be better to:
a.) Map reactions to pathways (reference, not organism specific) and then retain pathways present in the organism. In the case of the example above the reaction would be associated with glycolysis in human, thus potentially removing false negatives. However, it could also create false positives by associating reactions with pathways in which the reactions in fact do not occur in the organism.
b.) Map reactions to organism-specific pathways.