DrugBank Drug Interaction Sentences Seem to Be of a Standard Type #383
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Here are the most common phrases in the drug interaction sentences: |
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The risk/severity items can be decoded with this code. This maps 1,209,578 of the 2,839,486 drug interaction sentences (roughly 43%): def risk_or_severity_matches(sentence):
start = "The risk or severity of "
increased = " can be increased when "
decreased = " can be decreased when "
middle2 = " is combined with "
if sentence.startswith(start):
sentence_cut1 = sentence.replace(start, '')
dir_flag = ""
middle1 = ""
if increased in sentence_cut1:
dir_flag = "increased"
middle1 = increased
elif decreased in sentence_cut1:
dir_flag = "decreased"
middle1 = decreased
else:
return None, None
sentence_div1 = sentence_cut1.split(middle1)
risk_item = sentence_div1[0]
sentence_cut2 = sentence_cut1.replace(risk_item + middle1, "")
sentence_div2 = sentence_cut2.split(middle2)
comb_item1 = sentence_div2[0]
comb_item2 = sentence_div2[1].strip('.')
return risk_item, (risk_item, dir_flag, comb_item1, comb_item2)
return None, NoneThese are the different risk/severity items, which we will need to map: |
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The increase/decrease activity items were extracted with this code. These sentences account for about 310,627 of the total 2,839,486 (about 10%). def may_impact_activities(sentence):
increased = " may increase the "
decreased = " may decrease the "
dir_flag = ""
middle1 = ""
middle2 = " activities of "
if increased in sentence and middle2 in sentence:
dir_flag = "increased"
middle1 = increased
elif decreased in sentence and middle2 in sentence:
dir_flag = "decreased"
middle1 = decreased
else:
return None, None
sentence_div1 = sentence.split(middle1)
item1 = sentence_div1[0]
sentence_cut1 = sentence.replace(item1 + middle1, "")
sentence_div2 = sentence_cut1.split(middle2)
activity = sentence_div2[0]
item2 = sentence_div2[1]
return activity, (item1, dir_flag, activity, item2)These are the different increase/decrease activity of items that will need to be mapped: |
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This map covers all of the sentence types in the DrugBank drug interaction field: (the keys are placeholders for the fields that change with each entry) "risk_or_severity_increase": ["The risk or severity of ", DISEASE_KEY, " can be increased when ", MAIN_DRUG_KEY " is combined with ", INTERACTION_DRUG_KEY]
"risk_or_severity_decrease": ["The risk or severity of ", DISEASE_KEY, " can be decreased when ", MAIN_DRUG_KEY " is combined with ", INTERACTION_DRUG_KEY]
"may_impact_activity_increase": [MAIN_DRUG_KEY, " may increase the ", ACTIVITY_KEY, " activities of ", INTERACTION_DRUG_KEY]
"may_impact_activity_decrease": [MAIN_DRUG_KEY, " may decrease the ", ACTIVITY_KEY, " activities of ", INTERACTION_DRUG_KEY]
"therapeutic_efficacy_increase": ["The therapeutic efficacy of ", INTERACTION_DRUG_KEY, " can be increased when used in combination with ", MAIN_DRUG_KEY]
"therapeutic_efficacy_decrease": ["The therapeutic efficacy of ", INTERACTION_DRUG_KEY, " can be decreased when used in combination with ", MAIN_DRUG_KEY]
"higher_serum_level": [MAIN_DRUG_KEY, " may decrease the excretion rate of ", INTERACTION_DRUG_KEY, " which could result in a higher serum level"]
"metabolism_increase": ["The metabolism of ", MAIN_DRUG_KEY, " can be increased when combined with ", INTERACTION_DRUG_KEY]
"metabolism_decrease": ["The metabolism of ", MAIN_DRUG_KEY, " can be decreased when combined with ", INTERACTION_DRUG_KEY]
"serum_concentration_increase": ["The serum concentration of ", MAIN_DRUG_KEY, " can be increased when it is combined with ", INTERACTION_DRUG_KEY]
"serum_concentration_decrease": ["The serum concentration of ", MAIN_DRUG_KEY, " can be decreased when it is combined with ", INTERACTION_DRUG_KEY]
"excretion_rate_increase": [INTERACTION_DRUG_KEY, " may increase the excretion rate of ", MAIN_DRUG_KEY, " which could result in a lower serum level and potentially a reduction in efficacy"]
"absorption_decrease": [INTERACTION_DRUG_KEY, " can cause a decrease in the absorption of ", MAIN_DRUG_KEY, " resulting in a reduced serum concentration and potentially a decrease in efficacy"]
"excretion_increase": ["The excretion of ", MAIN_DRUG_KEY, " can be increased when combined with ", INTERACTION_DRUG_KEY]
"excretion_decrease": ["The excretion of ", MAIN_DRUG_KEY, " can be decreased when combined with ", INTERACTION_DRUG_KEY]
"active_metabolites_increase": ["The serum concentration of the active metabolites of ", INTERACTION_DRUG_KEY, " can be increased when ", INTERACTION_DRUG_KEY, " is used in combination with ", MAIN_DRUG_KEY]
"active_metabolites_decrease": ["The serum concentration of the active metabolites of ", INTERACTION_DRUG_KEY, " can be decreased when ", INTERACTION_DRUG_KEY, " is used in combination with ", MAIN_DRUG_KEY]
"bioavailibility_decrease": ["The bioavailability of ", MAIN_DRUG_KEY, " can be decreased when combined with ", INTERACTION_DRUG_KEY]
"bioavailibility_increase": ["The bioavailability of ", MAIN_DRUG_KEY, " can be increased when combined with ", INTERACTION_DRUG_KEY]
"diagnostic_agent_effectiveness_decrease": [INTERACTION_DRUG_KEY, " may decrease effectiveness of ", MAIN_DRUG_KEY, " as a diagnostic agent"]
"absorption_increase": [MAIN_DRUG_KEY, " can cause an increase in the absorption of ", INTERACTION_DRUG_KEY, " resulting in an increased serum concentration and potentially a worsening of adverse effects"]
"diagnostic_agent_effectiveness_increase": [INTERACTION_DRUG_KEY, " may increase effectiveness of ", MAIN_DRUG_KEY, " as a diagnostic agent"]
"absorption_of_decreased": ["The absorption of ", INTERACTION_DRUG_KEY, " can be decreased when combined with ", MAIN_DRUG_KEY]
"protein_binding_decrease": ["The protein binding of ", INTERACTION_DRUG_KEY, " can be decreased when combined with ", MAIN_DRUG_KEY]
"hypersensitivity_reaction_increase": ["The risk of a hypersensitivity reaction to ", INTERACTION_DRUG_KEY, " is increased when it is combined with ", MAIN_DRUG_KEY]
"serum_concentration_of_active_metabolites": ["The serum concentration of the active metabolites of ", MAIN_DRUG_KEY, " can be reduced when ", MAIN_DRUG_KEY, " is used in combination with ", INTERACTION_DRUG_KEY, " resulting in a loss in efficacy"]
"serum_concentration_increased_in_combination": ["The serum concentration of ", INTERACTION_DRUG_KEY, ", an active metabolite of ", MAIN_DRUG_KEY, ", can be increased when used in combination with ", MAIN_DRUG_KEY]
"serum_concentration_decreased_in_combination": ["The serum concentration of ", INTERACTION_DRUG_KEY, ", an active metabolite of ", MAIN_DRUG_KEY, ", can be decreased when used in combination with ", MAIN_DRUG_KEY]Here are the counts for each sentence type: {
"absorption_decrease": 22367,
"absorption_increase": 555,
"absorption_of_decreased": 648,
"active_metabolites_decrease": 154,
"active_metabolites_increase": 578,
"bioavailibility_decrease": 1844,
"bioavailibility_increase": 170,
"diagnostic_agent_effectiveness_decrease": 1505,
"diagnostic_agent_effectiveness_increase": 20,
"excretion_decrease": 19972,
"excretion_increase": 570,
"excretion_rate_increase": 60388,
"higher_serum_level": 352172,
"hypersensitivity_reaction_increase": 2101,
"may_impact_activity_decrease": 89722,
"may_impact_activity_increase": 220905,
"metabolism_decrease": 295535,
"metabolism_increase": 109532,
"protein_binding_decrease": 2820,
"risk_or_severity_decrease": 986,
"risk_or_severity_increase": 1208592,
"serum_concentration_decrease": 40104,
"serum_concentration_decreased_in_combination": 44,
"serum_concentration_increase": 129870,
"serum_concentration_increased_in_combination": 436,
"serum_concentration_of_active_metabolites": 206,
"therapeutic_efficacy_decrease": 232445,
"therapeutic_efficacy_increase": 45245
} |
ecwood
added a commit
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Jun 27, 2024
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02f1cbb contains the code for identifying and extracting information from the different sentence types. A few disclaimers:
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This should hopefully be a good stepping stone towards #369 (to include other free text information from DrugBank in KG2). |
ecwood
added a commit
that referenced
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Jul 9, 2024
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We might be able to get more precise information from the DrugBank drug-interactions by mapping the standard sentence forms onto edge types.
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