11import logging
22from xml .etree import ElementTree
33
4- from indra .databases .identifiers import ensure_chebi_prefix , ensure_chembl_prefix
4+ from indra .databases .identifiers import ensure_chebi_prefix ,\
5+ ensure_chembl_prefix
56from indra .ontology .standardize import get_standard_agent
6- from indra .statements import Activation , Complex , DecreaseAmount , Evidence , IncreaseAmount , Inhibition
7+ from indra .statements import Activation , Complex , DecreaseAmount , Evidence ,\
8+ IncreaseAmount , Inhibition
79from indra .statements .validate import assert_valid_db_refs
810
911logger = logging .getLogger (__name__ )
@@ -178,8 +180,8 @@ def _complex(a, b, evidence):
178180 'inactivator' , 'binding' , 'blocker' , 'negative modulator' ,
179181 'neutralizer' , 'weak inhibitor' ,
180182 'suppressor' , 'disruptor' , 'chelator' ,
181- 'inhibitory allosteric modulator' , 'translocation inhibitor' ,
182- 'nucleotide exchange blocker' ,
183+ 'inhibitory allosteric modulator' ,
184+ 'translocation inhibitor' , ' nucleotide exchange blocker' ,
183185 }
184186
185187decrease_amount_actions = {
@@ -200,9 +202,11 @@ def _complex(a, b, evidence):
200202 'substrate' ,
201203 'agonist' ,
202204 'ligand' ,
203- 'intercalation' , # e.g., Doxorubicin intercalates DNA to prevent transcription
205+ # e.g., Doxorubicin intercalates DNA to prevent transcription
206+ 'intercalation' ,
204207 'inverse agonist' ,
205- 'aggregation inhibitor' , # e.g., inhibits process on a protein's aggregation (like APP or LRRK)
208+ # e.g., inhibits process on a protein's aggregation (like APP or LRRK)
209+ 'aggregation inhibitor' ,
206210 'partial agonist' ,
207211 'partial antagonist' ,
208212 'antisense oligonucleotide' ,
@@ -211,7 +215,9 @@ def _complex(a, b, evidence):
211215 'product of' ,
212216 'reducer' ,
213217 'oxidizer' ,
214- 'acetylation' , # map to Ac INDRA statement?, but I'm not convinced by the idea of splitting up actions
218+ # map to Ac INDRA statement?, but I'm not convinced by the idea of
219+ # splitting up actions
220+ 'acetylation' ,
215221 'allosteric modulator' ,
216222 'deoxidizer' ,
217223 'cross-linking/alkylation' , # e.g. Busulfan (DB01008) alkalytes DNA
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