Update loadDrugMechDB.py to include treats edges for indication paths

[beasleyjonm]

Each indication path in drugmechdb describes the COP for a drug-disease indication pair, but the "treats" edge is not explicitly included. I edited the parser to introduce these as "biolink:treats" edges.

[eKathleenCarter]

Looks like this needs a refactor.

[eKathleenCarter]

Given the "treats"/"ameliorates" edge refactor, I hesitate to approve this PR. I suggest we look at it more before merging it into main.

[beasleyjonm]

From the DrugMechDB paper: "DrugMechDB was constructed considering drug-disease indications from the DrugCentral
database, using the version downloaded on September 18, 2020"

So each drug-disease pair in each path in the source file could be considered an indication, at least as of 2020.

[eKathleenCarter]

@beasleyjonm, how about we use the biolink:treats_or_applied_or_studied_to_treat for now until we can dig in to this some more?

[beasleyjonm]

@beasleyjonm, how about we use the biolink:treats_or_applied_or_studied_to_treat for now until we can dig in to this some more?

Let's do that, since it's not clear that they update this regularly with latest indications on drug central and they state they used the 2020 version. It's possible some of the indications could have changed since then, so "treats_or_applied_or_studied_to_treat" seems the safest option.

[eKathleenCarter]

Looks good to me!

[cbizon]

Given that we are independently ingesting drugcentral, my opinion is that we would not want to also add those same edges from here.