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Review DrugBank statement polarities

Open bgyori opened this issue 3 years ago • 1 comments

@cthoyt brought up an interesting point in https://github.com/sorgerlab/indra/pull/1262#issue-603695782 about assumptions of polarity for statements derived from agonist and antagonist relations. We should review the extracted statements to see if the current assumptions result in any incorrect polarities.

bgyori avatar Mar 30 '21 13:03 bgyori

This also includes partial agonists, partial antagonists, and inverse agonists.

Here are some more of my concerns:

  • chelators are more about decreasing activity than amount, since they bind to the protein in a way that stops it from doing its job.
  • being a ligand of a protein does not necessarily say if it's an activator or a deactivator. It also doesn't say if it's in the normal site or an allosteric site, so if there's some hierarchy hiding behind all of these, ligand is probably on the top. I'd say the same about binding - I don't think it belongs in the inhibition action.
  • the chaperone should be in increase amounts, since I assume it's something that helps with stabilization

cthoyt avatar Mar 30 '21 14:03 cthoyt