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import logging
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from xml .etree import ElementTree
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- from indra .databases .identifiers import ensure_chebi_prefix , ensure_chembl_prefix
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+ from indra .databases .identifiers import ensure_chebi_prefix ,\
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+ ensure_chembl_prefix
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from indra .ontology .standardize import get_standard_agent
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- from indra .statements import Activation , Complex , DecreaseAmount , Evidence , IncreaseAmount , Inhibition
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+ from indra .statements import Activation , Complex , DecreaseAmount , Evidence ,\
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+ IncreaseAmount , Inhibition
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from indra .statements .validate import assert_valid_db_refs
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logger = logging .getLogger (__name__ )
@@ -178,8 +180,8 @@ def _complex(a, b, evidence):
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'inactivator' , 'binding' , 'blocker' , 'negative modulator' ,
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'neutralizer' , 'weak inhibitor' ,
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'suppressor' , 'disruptor' , 'chelator' ,
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- 'inhibitory allosteric modulator' , 'translocation inhibitor' ,
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- 'nucleotide exchange blocker' ,
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+ 'inhibitory allosteric modulator' ,
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+ 'translocation inhibitor' , ' nucleotide exchange blocker' ,
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}
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decrease_amount_actions = {
@@ -200,9 +202,11 @@ def _complex(a, b, evidence):
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'substrate' ,
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'agonist' ,
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'ligand' ,
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- 'intercalation' , # e.g., Doxorubicin intercalates DNA to prevent transcription
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+ # e.g., Doxorubicin intercalates DNA to prevent transcription
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+ 'intercalation' ,
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'inverse agonist' ,
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- 'aggregation inhibitor' , # e.g., inhibits process on a protein's aggregation (like APP or LRRK)
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+ # e.g., inhibits process on a protein's aggregation (like APP or LRRK)
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+ 'aggregation inhibitor' ,
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'partial agonist' ,
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'partial antagonist' ,
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'antisense oligonucleotide' ,
@@ -211,7 +215,9 @@ def _complex(a, b, evidence):
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'product of' ,
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'reducer' ,
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'oxidizer' ,
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- 'acetylation' , # map to Ac INDRA statement?, but I'm not convinced by the idea of splitting up actions
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+ # map to Ac INDRA statement?, but I'm not convinced by the idea of
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+ # splitting up actions
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+ 'acetylation' ,
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'allosteric modulator' ,
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'deoxidizer' ,
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'cross-linking/alkylation' , # e.g. Busulfan (DB01008) alkalytes DNA
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