Relationships for transporters/transport; inference of transporters

[deustp01]

We need to remember to update the relationships for transporters/transport. We will replace transports_or_maintains_localization_of with has_primary_input, but we should also review the causal relationship between catalytic reactions and transporter activities. Right now they are causally_upstream_of, but should be replaced with directly_provides_input_for.
We need to review the inference of transporters. In some cases we are actually referring to the process of transport, R-HSA-2022911.
PD comment: The physical entity being transported here is any member of a set of chondroitin sulfate proteoglycans, proteins covalently modified with chondroitin sulfate. We assert that transport involves movement form the Golgi lumen to the extracellular space via the transgolgi network the blackBoxEvent R-HSA-2022911 probably mixes both of our editorial resons for not annotating regular reactions: we don't want to re-annotate a specific instance of a secretory process that has already been annotated for a generic substrate AND not all the details of how this collection of molecules gets recognized and targeted for secretion are know. (A known current limitation of Reactome is that we don't have a way to link a specific choose-not-to-annotate blackBox instance of a process to the generic pathway it is an instance of.)
Beyond the scope of this ticket, PMID: 25951880 looks like a useful starting point for sorting out the steps of the golgi-to-extracellular transport process, should we ever want to annotate it.

[ukemi]

I think I was in error about the relationship between the transporter activities and the downstream functions. THere are some that I have seen that are directoy_provides_input_for ans some that are causally upstream. It seems to depend on whether the trasporter activity is part of the pathway. Another whole discussion in and of itself.