diff options
| -rwxr-xr-x | ratspub.py | 44 | ||||
| -rw-r--r-- | ratspub_keywords.py | 33 |
2 files changed, 41 insertions, 36 deletions
diff --git a/ratspub.py b/ratspub.py index dbe1f1a..64e750a 100755 --- a/ratspub.py +++ b/ratspub.py @@ -2,8 +2,11 @@ from nltk.tokenize import sent_tokenize import os import re +import ratspub_keywords -global function_d, brain_d, drug_d, addiction_d, brain_query_term +global function_d, brain_d, drug_d, addiction_d, brain_query_term, pubmed_path + +pubmed_path="/media/hao/2d554499-6c5b-462d-85f3-5c49b25f4ac8/PubMed/Archive" ## turn dictionary (synonyms) to regular expression def undic(dic): @@ -13,7 +16,7 @@ def findWholeWord(w): return re.compile(r'\b({0})\b'.format(w), flags=re.IGNORECASE).search def getSentences(query, gene): - abstracts = os.popen("esearch -db pubmed -query " + query + " | efetch -format uid |fetch-pubmed -path /run/media/hao/PubMed/Archive/ | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read() + abstracts = os.popen("esearch -db pubmed -query " + query + " | efetch -format uid |fetch-pubmed -path "+ pubmed_path + " | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read() out=str() for row in abstracts.split("\n"): tiab=row.split("\t") @@ -63,44 +66,13 @@ def generate_edges(data, filename): json0+="{ data: { id: '" + edgeID + "', source: '" + source + "', target: '" + target + "', sentCnt: " + str(edgeCnts[edgeID]) + ", url:'/sentences?edgeID=" + edgeID + "' } },\n" return(json0) -nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7"} -addiction_d = {"reward":"reward|hedonic|incentive|intracranial self stimulation|ICSS|reinforcement|reinforcing|conditioned place preference|CPP|self administration|self administered|drug reinforced|operant|instrumental response", - "aversion":"aversion|aversive|CTA|conditioned taste aversion", - "withdrawal":"withdrawal", - "relapse":"relapse|reinstatement|craving|drug seeking|seeking", - "sensitization":"sensitization", - "addiction":"addiction|addictive|drug abuse|punishment|compulsive|escalation", - "dependence":"dependence", - "intoxication":"intoxication|binge" - } -addiction=undic(addiction_d) -drug_d = {"alcohol":"alcohol|alcoholism|alcoholic|alcoholics", - "nicotine":"smoking|nicotine|tobacco|smoker|smokers", - "cocaine":"cocaine", - "opioid":"opioid|opioids|fentanyl|oxycodone|oxycontin|heroin|morphine|methadone|buprenorphine|vicodin|hydrocodone|hycodan|kadian|percoset|hydromorphone|naloxone|codeine|suboxone|tramadol|kratom|ultram", - "amphetamine":"methamphetamine|amphetamine|METH|AMPH", - "cannabinoid":"endocannabinoid|cannabinoids|cannabis|endocannabinoids|marijuana|cannabidiol|cannabinoid|tetrahydrocannabinol|thc|thc 9|Oleoylethanolamide|palmitoylethanolamide|acylethanolamides" - } -drug=undic(drug_d) -brain_d ={"cortex":"cortex|prefrontal|pfc|mPFC|vmpfc|corticostriatal|cortico limbic|corticolimbic|prl|prelimbic|infralimbic|orbitofrontal|cingulate|cerebral|insular|insula", - "striatum":"striatum|STR|striatal|caudate|putamen|basal ganglia|globus pallidus|GPI", - "accumbens":"accumbens|accumbal|shell|core|Nacc|NacSh|acbs|acbc", - "hippocampus":"hippocampus|hippocampal|hipp|hip|ca1|ca3|dentate gyrus|subiculum|vhipp|dhpc|vhpc", - "amygdala":"amygdala|cea|bla|amy|cna", - "VTA":"ventral tegmental|vta|pvta|mesolimbic|limbic|midbrain|mesoaccumbens|mesoaccumbal", - "habenula":"habenula|lhb|mhb", - "hypothalamus":"hypothalamus|hypothalamic|PVN|paraventricular nucleus" - } # brain region has too many short acronyms to just use the undic function, so search PubMed using the following brain_query_term="cortex|accumbens|striatum|amygadala|hippocampus|tegmental|mesolimbic|infralimbic|prelimbic|habenula" -function_d={"signalling":"signalling|signaling|phosphorylation|glycosylation", - "transcription":"transcription|methylation|hypomethylation|hypermethylation|histone|ribosome", - "neuroplasticity":"neuroplasticity|plasticity|long term potentiation|LTP|long term depression|LTD|synaptic|epsp|epsc|neurite|neurogenesis|boutons|mIPSC|IPSC|IPSP", - "neurotransmission": "neurotransmission|neuropeptides|neuropeptide|glutamate|glutamatergic|GABA|GABAergic|dopamine|dopaminergic|DAergic|cholinergic|nicotinic|muscarinic|serotonergic|serotonin|5 ht|acetylcholine", -# "regulation":"increased|decreased|regulated|inhibited|stimulated", - } function=undic(function_d) +addiction=undic(addiction_d) +drug=undic(drug_d) +nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7"} #https://htmlcolorcodes.com/ n0=generate_nodes(function_d, 'function') n1=generate_nodes(addiction_d, 'addiction') diff --git a/ratspub_keywords.py b/ratspub_keywords.py new file mode 100644 index 0000000..6d63174 --- /dev/null +++ b/ratspub_keywords.py @@ -0,0 +1,33 @@ +addiction_d = {"reward":"reward|hedonic|incentive|intracranial self stimulation|ICSS|reinforcement|reinforcing|conditioned place preference|CPP|self administration|self administered|drug reinforced|operant|instrumental response", + "aversion":"aversion|aversive|CTA|conditioned taste aversion", + "withdrawal":"withdrawal", + "relapse":"relapse|reinstatement|craving|drug seeking|seeking", + "sensitization":"sensitization", + "addiction":"addiction|addictive|drug abuse|punishment|compulsive|escalation", + "dependence":"dependence", + "intoxication":"intoxication|binge" + } +drug_d = {"alcohol":"alcohol|alcoholism|alcoholic|alcoholics", + "nicotine":"smoking|nicotine|tobacco|smoker|smokers", + "cocaine":"cocaine", + "opioid":"opioid|opioids|fentanyl|oxycodone|oxycontin|heroin|morphine|methadone|buprenorphine|vicodin|hydrocodone|hycodan|kadian|percoset|hydromorphone|naloxone|codeine|suboxone|tramadol|kratom|ultram", + "amphetamine":"methamphetamine|amphetamine|METH|AMPH", + "cannabinoid":"endocannabinoid|cannabinoids|cannabis|endocannabinoids|marijuana|cannabidiol|cannabinoid|tetrahydrocannabinol|thc|thc 9|Oleoylethanolamide|palmitoylethanolamide|acylethanolamides" + } +brain_d ={"cortex":"cortex|prefrontal|pfc|mPFC|vmpfc|corticostriatal|cortico limbic|corticolimbic|prl|prelimbic|infralimbic|orbitofrontal|cingulate|cerebral|insular|insula", + "striatum":"striatum|STR|striatal|caudate|putamen|basal ganglia|globus pallidus|GPI", + "accumbens":"accumbens|accumbal|shell|core|Nacc|NacSh|acbs|acbc", + "hippocampus":"hippocampus|hippocampal|hipp|hip|ca1|ca3|dentate gyrus|subiculum|vhipp|dhpc|vhpc", + "amygdala":"amygdala|cea|bla|amy|cna", + "VTA":"ventral tegmental|vta|pvta|mesolimbic|limbic|midbrain|mesoaccumbens|mesoaccumbal", + "habenula":"habenula|lhb|mhb", + "hypothalamus":"hypothalamus|hypothalamic|PVN|paraventricular nucleus" + } +# brain region has too many short acronyms to just use the undic function, so search PubMed using the following +brain_query_term="cortex|accumbens|striatum|amygadala|hippocampus|tegmental|mesolimbic|infralimbic|prelimbic|habenula" +function_d={"signalling":"signalling|signaling|phosphorylation|glycosylation", + "transcription":"transcription|methylation|hypomethylation|hypermethylation|histone|ribosome", + "neuroplasticity":"neuroplasticity|plasticity|long term potentiation|LTP|long term depression|LTD|synaptic|epsp|epsc|neurite|neurogenesis|boutons|mIPSC|IPSC|IPSP", + "neurotransmission": "neurotransmission|neuropeptides|neuropeptide|glutamate|glutamatergic|GABA|GABAergic|dopamine|dopaminergic|DAergic|cholinergic|nicotinic|muscarinic|serotonergic|serotonin|5 ht|acetylcholine", + } +#"regulation":"increased|decreased|regulated|inhibited|stimulated", |