From 6042a538e94bd4e7e34d9d3b1fccde6b02a81f43 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 26 Mar 2026 18:01:01 +0100 Subject: Remove unused statements [AI] --- more_functions.py | 3 --- old/ratspub_keywords.py | 50 +++++++++++++++++++++++++++++++++++++++++++++++++ ratspub_keywords.py | 50 ------------------------------------------------- 3 files changed, 50 insertions(+), 53 deletions(-) create mode 100644 old/ratspub_keywords.py delete mode 100644 ratspub_keywords.py diff --git a/more_functions.py b/more_functions.py index 7c21c2a..8162acc 100755 --- a/more_functions.py +++ b/more_functions.py @@ -3,11 +3,9 @@ from nltk.tokenize import sent_tokenize import os import re -from nltk.util import pr from addiction_keywords import * from gene_synonyms import * import ast -from flask import session global pubmed_path @@ -29,7 +27,6 @@ def getabstracts(gene,query): + " | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read() return(abstracts) -sentences_ls=[] def getSentences(gene, sentences_ls): out=str() # Keep the sentence only if it contains the gene diff --git a/old/ratspub_keywords.py b/old/ratspub_keywords.py new file mode 100644 index 0000000..d3836e0 --- /dev/null +++ b/old/ratspub_keywords.py @@ -0,0 +1,50 @@ +addiction_d={'addiction':'addiction|addictive|compulsive|drug abuse|escalation|punishment', +'aversion':'aversion|aversive|conditioned taste aversion|CTA', +'dependence':'dependence', +'intoxication':'binge|intoxication', +'relapse':'craving|drug seeking|reinstatement|relapse|seeking', +'reward':'conditioned place preference|CPP|drug reinforced|hedonic|ICSS|incentive|instrumental response|intracranial self stimulation|operant|reinforcement|reinforcing|reward|self administered|self administration', +'sensitization':'behavioral sensitization|locomotor sensitization|drug sensitization|incentive sensitization', +'social':'social', +'withdrawal':'withdrawal'} + +brain_d={'accumbens':'acbc|acbs|accumbal|accumbens|core|Nacc|NacSh|shell', +'amygdala':'amy|amygdala|bla|cea|cna', +'cortex':'cerebral|cingulate|cortex|cortico limbic|corticolimbic|corticostriatal|infralimbic|insular*|mPFC|orbitofrontal|pfc|prefrontal|prelimbic|prl|vmpfc', +'habenula':'habenula|lhb|mhb', +'hippocampus':'ca1|ca3|dentate gyrus|dhpc|hip|hipp|hippocampal|hippocampus|subiculum|vhipp|vhpc', +'hypothalamus':'hypothalamic|hypothalamus|LHA|paraventricular nucleus|PVN', +'striatum':'basal ganglia|caudate|globus pallidus|GPI|putamen|STR|striatal|striatum', +'VTA':'limbic|mesoaccumbal|mesoaccumbens|mesolimbic|midbrain|pvta|ventral tegmental|vta'} + +drug_d={'alcohol':'acamprosate|alcohol|alcoholics*|alcoholism|antabuse|campral|disulfiram|ethanol|naltrexone|revia|vivitrol', +'amphetamine':'AMPH|amphetamine|METH|methamphetamine', +'benzodiazepine':'adinazolam|alprazolam|benzodiazepine|benzos|brotizolam|chlordiazepoxide|climazolam|clobazam|clonazepam|clorazepate|diazepam|estazolam|flunitrazepam|flurazepam|halazepam|librium|loprazolam|lorazepam|lormetazepam|midazolam|nimetazepam|nitrazepam|normison|oxazepam|prazepam|temazepam|triazolam|valium|xanax', +'cannabinoid':'acylethanolamines|cannabichromene|cannabidiol|cannabigerol|cannabinoids*|cannabinol|cannabis|cannabivarin|cesamet|drobinal|dronabinol|endocannabinoids*|epidiolex|JWH 018|JWH 122|JWH 250|marijuana|marinol|nabilone|Oleoylethanolamide|palmitoylethanolamide|phytocannabinoid|rimonabant|SR141716|SR144528|syndros|tetrahydrocannabinol|tetrahydrocannabivarin|thc|thc 9', +'cocaine':'cocaine', +'nicotine':'nicotine|smokers*|smoking|tobacco', +'opioid':'buprenorphine|codeine|fentanyl|heroin|hycodan|hydrocodone|hydromorphone|kadian|kratom|methadone|morphine|naloxone|opioids*|oxycodone|oxycontin|percocet|suboxone|tramadol|ultram|vicodin', +'psychedelics':'ayahuasca|ecstasy|ibogaine|ketamine|LSD|lysergic acid diethylamide|MDMA|mescaline|methylenedioxymethamphetamine|N methoxybenzyl|NBOMes*|peyote|psilocybin|psychedelic|psychedelics'} + +function_d={'neuroplasticity':'boutons*|epsc|epsp|IPSC|IPSP|long term depression|long term potentiation|LTD|LTP|mIPSC|neurite|neurogenesis|neuroplasticity|plasticity|synaptic', +'neurotransmission':'5 ht|acetylcholine|cholinergic|DAergic|dopamine|dopaminergic|GABA|GABAergic|glutamate|glutamatergic|muscarinic|neuropeptides*|neurotransmission|nicotinic|serotonergic|serotonin', +'signalling':'glycosylation|phosphorylation|signaling|signalling|kinase|binding|signal transduction|second messengers|cGMP|cAMP', +'transcription':'histone|hypermethylation|hypomethylation|methylation|ribosome|transcription'} + +psychiatric_d={'anxiety':'anxiety|anxious', +'autism':'autism|autistic', +'bipolar':'bipolar disorder', +'compulsive':'compulsive|obsessive', +'depression':'depression|depressive|major depressive disorder|MDD', +'impulsivity':'5 CSRTT|5 choice task|delay discounting|delay exposure|delay intolerance|delayed reward|delay task|five choice serial reaction time task|impulsive|impulsivity|premature responding', +'schizophrenia':'schizophrenia'} + +cell_d={'neuron':'adrenergic neurons*|cholinergic neurons*|dopaminergic neurons*|gabaergic neurons*|glutamatergic neurons*|GnRH neurons*|interneurons*|monoaminergic neurons*|medium spiny neurons*|motor neurons*|neuronal cells*|nitrergic neurons*|noradrenergic neurons*|projection neurons*|pyramidal neurons*|sensory neurons*|serotonergic neurons*|somatostatin neurons*|neurons*|excitatory neurons*|inhibitory neurons*|corticospinal neurons*|dopamine neurons*|D1 neurons*|D2 neurons*|afferent neurons*|efferent neurons*|serotonin neurons*|cortical neurons*|hippocampal neurons*|DA neurons*|CNS neurons*|cortex neurons*|mesencephalic neurons*|orexin neurons*|catecholaminergic neurons*|striatal neurons*|bipolar neurons*|ganglion cells*|RGC|horizontal cells*|amacrine cells*', +'astrocyte':'astrocytic|astrocytes*|astroglia|astroglial', +'microglia':'microglia|microglial', +'endothelium':'endothelium|endothelial cells*', +'oligodendrocyte':'oligodendrocytes*'} + +stress_d={'PTSD':'PTSD|post traumatic stress|post traumatic stress symptoms*|post traumatic stress disorder', +'stress':'distress|psychological trauma|stress'} + diff --git a/ratspub_keywords.py b/ratspub_keywords.py deleted file mode 100644 index d3836e0..0000000 --- a/ratspub_keywords.py +++ /dev/null @@ -1,50 +0,0 @@ -addiction_d={'addiction':'addiction|addictive|compulsive|drug abuse|escalation|punishment', -'aversion':'aversion|aversive|conditioned taste aversion|CTA', -'dependence':'dependence', -'intoxication':'binge|intoxication', -'relapse':'craving|drug seeking|reinstatement|relapse|seeking', -'reward':'conditioned place preference|CPP|drug reinforced|hedonic|ICSS|incentive|instrumental response|intracranial self stimulation|operant|reinforcement|reinforcing|reward|self administered|self administration', -'sensitization':'behavioral sensitization|locomotor sensitization|drug sensitization|incentive sensitization', -'social':'social', -'withdrawal':'withdrawal'} - -brain_d={'accumbens':'acbc|acbs|accumbal|accumbens|core|Nacc|NacSh|shell', -'amygdala':'amy|amygdala|bla|cea|cna', -'cortex':'cerebral|cingulate|cortex|cortico limbic|corticolimbic|corticostriatal|infralimbic|insular*|mPFC|orbitofrontal|pfc|prefrontal|prelimbic|prl|vmpfc', -'habenula':'habenula|lhb|mhb', -'hippocampus':'ca1|ca3|dentate gyrus|dhpc|hip|hipp|hippocampal|hippocampus|subiculum|vhipp|vhpc', -'hypothalamus':'hypothalamic|hypothalamus|LHA|paraventricular nucleus|PVN', -'striatum':'basal ganglia|caudate|globus pallidus|GPI|putamen|STR|striatal|striatum', -'VTA':'limbic|mesoaccumbal|mesoaccumbens|mesolimbic|midbrain|pvta|ventral tegmental|vta'} - -drug_d={'alcohol':'acamprosate|alcohol|alcoholics*|alcoholism|antabuse|campral|disulfiram|ethanol|naltrexone|revia|vivitrol', -'amphetamine':'AMPH|amphetamine|METH|methamphetamine', -'benzodiazepine':'adinazolam|alprazolam|benzodiazepine|benzos|brotizolam|chlordiazepoxide|climazolam|clobazam|clonazepam|clorazepate|diazepam|estazolam|flunitrazepam|flurazepam|halazepam|librium|loprazolam|lorazepam|lormetazepam|midazolam|nimetazepam|nitrazepam|normison|oxazepam|prazepam|temazepam|triazolam|valium|xanax', -'cannabinoid':'acylethanolamines|cannabichromene|cannabidiol|cannabigerol|cannabinoids*|cannabinol|cannabis|cannabivarin|cesamet|drobinal|dronabinol|endocannabinoids*|epidiolex|JWH 018|JWH 122|JWH 250|marijuana|marinol|nabilone|Oleoylethanolamide|palmitoylethanolamide|phytocannabinoid|rimonabant|SR141716|SR144528|syndros|tetrahydrocannabinol|tetrahydrocannabivarin|thc|thc 9', -'cocaine':'cocaine', -'nicotine':'nicotine|smokers*|smoking|tobacco', -'opioid':'buprenorphine|codeine|fentanyl|heroin|hycodan|hydrocodone|hydromorphone|kadian|kratom|methadone|morphine|naloxone|opioids*|oxycodone|oxycontin|percocet|suboxone|tramadol|ultram|vicodin', -'psychedelics':'ayahuasca|ecstasy|ibogaine|ketamine|LSD|lysergic acid diethylamide|MDMA|mescaline|methylenedioxymethamphetamine|N methoxybenzyl|NBOMes*|peyote|psilocybin|psychedelic|psychedelics'} - -function_d={'neuroplasticity':'boutons*|epsc|epsp|IPSC|IPSP|long term depression|long term potentiation|LTD|LTP|mIPSC|neurite|neurogenesis|neuroplasticity|plasticity|synaptic', -'neurotransmission':'5 ht|acetylcholine|cholinergic|DAergic|dopamine|dopaminergic|GABA|GABAergic|glutamate|glutamatergic|muscarinic|neuropeptides*|neurotransmission|nicotinic|serotonergic|serotonin', -'signalling':'glycosylation|phosphorylation|signaling|signalling|kinase|binding|signal transduction|second messengers|cGMP|cAMP', -'transcription':'histone|hypermethylation|hypomethylation|methylation|ribosome|transcription'} - -psychiatric_d={'anxiety':'anxiety|anxious', -'autism':'autism|autistic', -'bipolar':'bipolar disorder', -'compulsive':'compulsive|obsessive', -'depression':'depression|depressive|major depressive disorder|MDD', -'impulsivity':'5 CSRTT|5 choice task|delay discounting|delay exposure|delay intolerance|delayed reward|delay task|five choice serial reaction time task|impulsive|impulsivity|premature responding', -'schizophrenia':'schizophrenia'} - -cell_d={'neuron':'adrenergic neurons*|cholinergic neurons*|dopaminergic neurons*|gabaergic neurons*|glutamatergic neurons*|GnRH neurons*|interneurons*|monoaminergic neurons*|medium spiny neurons*|motor neurons*|neuronal cells*|nitrergic neurons*|noradrenergic neurons*|projection neurons*|pyramidal neurons*|sensory neurons*|serotonergic neurons*|somatostatin neurons*|neurons*|excitatory neurons*|inhibitory neurons*|corticospinal neurons*|dopamine neurons*|D1 neurons*|D2 neurons*|afferent neurons*|efferent neurons*|serotonin neurons*|cortical neurons*|hippocampal neurons*|DA neurons*|CNS neurons*|cortex neurons*|mesencephalic neurons*|orexin neurons*|catecholaminergic neurons*|striatal neurons*|bipolar neurons*|ganglion cells*|RGC|horizontal cells*|amacrine cells*', -'astrocyte':'astrocytic|astrocytes*|astroglia|astroglial', -'microglia':'microglia|microglial', -'endothelium':'endothelium|endothelial cells*', -'oligodendrocyte':'oligodendrocytes*'} - -stress_d={'PTSD':'PTSD|post traumatic stress|post traumatic stress symptoms*|post traumatic stress disorder', -'stress':'distress|psychological trauma|stress'} - -- cgit 1.4.1