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Update interpretation of DrugBank actions #1265

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@cthoyt cthoyt commented Apr 1, 2021

This PR closes #1263 by updating some of the interpretations made in DrugBank's action field.

It's most likely the case that all curated interactions in DrugBank imply binding between an active molecule and the target. For example, some actions like agonist, partial agonist, antagonist, partial antagonist, and inverse agonist do not give enough information to infer activates or inhibits, because they are with respect to the native ligand. Therefore, the best we can do is say that these chemicals bind to their targets (in the absence a more generic INDRA Statement for apolar regulates activity).

This PR also does the following:

  • adds several interpretations that were missing
  • reorganizes the order of priority of mapping to statement types
  • small style updates in the DrugBank processor code

Statistics

Before

Action Count
Inhibition 16,026
Activation 2,569
DecreaseAmount 69
IncreaseAmount 8

After

Statement Type Count
Inhibition 5,012
Activation 2,088
Complex 1,325
DecreaseAmount 73
IncreaseAmount 27

@cthoyt cthoyt marked this pull request as ready for review April 1, 2021 10:04
@bgyori bgyori self-requested a review April 2, 2021 03:32
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There are a few questionable cases still, for instance, we now map agonist and antagonist somewhat conservatively to Complex, but binder, binding, and antibody are still mapped to Inhibition. Do those interpretations make sense?

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cthoyt commented Apr 2, 2021

Binder and binding both are neutral, but most antibodies that I know of exert their action by binding to a protein, which either tags it for degradation or inhibits it. I think leaving as inhibits is fine.

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bgyori commented Apr 2, 2021

It turns out that there is a large number of entries that neither specify an action, nor declare that there is a direct interaction between the drug and the target. Since it's not clear what statement type these can be mapped to if we want to be precise, we skip them now. The statement count drops significantly, with the overall statement stats before this PR:

('Inhibition', 16026),
('Activation', 2569),
('DecreaseAmount', 69),
('IncreaseAmount', 8)

and after this PR

('Complex', 4320),
('Inhibition', 3121),
('Activation', 724),
('DecreaseAmount', 60),
('IncreaseAmount', 28)

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Review DrugBank statement polarities
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