Currently, when a reaction is either directly upstream of, downstream of or within a pathway with an xref to a BP the reaction is included in a GO-CAM for the pathway. As curators move forward and use imported pathways for model organism pathways, they would effectively prune these reactions from their pathway representations. To save work for curators, we would like to not include these reactions in the GO-CAMs. The disadvantage to this is that it doesn't allow 'linking' of pathways but on the 'weeds' call we decided that losing the connection was ok for now. So in the new import test, only Reactions that would be part_of the core pathway/BP would be retained.
Here are a few examples from model R-HSA-70171:
Reaction R-HSA-6798335 is xref'd to a different process.
Reaction R-HSA-5696021 is xref'd to a different process.
Reaction R-HSA-6799604 is xref'd to a different process.
Reaction R-HSA-211346 is upstream of a reaction, R-HSA-70420, that is part of the process, but is not part of the process itself.
Reaction R-HSA-8955760 is downstream of a reaction, R-HSA-70420, that is part of the process, but is not part of the process itself.
Currently, when a reaction is either directly upstream of, downstream of or within a pathway with an xref to a BP the reaction is included in a GO-CAM for the pathway. As curators move forward and use imported pathways for model organism pathways, they would effectively prune these reactions from their pathway representations. To save work for curators, we would like to not include these reactions in the GO-CAMs. The disadvantage to this is that it doesn't allow 'linking' of pathways but on the 'weeds' call we decided that losing the connection was ok for now. So in the new import test, only Reactions that would be part_of the core pathway/BP would be retained.
Here are a few examples from model R-HSA-70171: Reaction R-HSA-6798335 is xref'd to a different process. Reaction R-HSA-5696021 is xref'd to a different process. Reaction R-HSA-6799604 is xref'd to a different process. Reaction R-HSA-211346 is upstream of a reaction, R-HSA-70420, that is part of the process, but is not part of the process itself. Reaction R-HSA-8955760 is downstream of a reaction, R-HSA-70420, that is part of the process, but is not part of the process itself.