three types of searches

1 files changed, 60 insertions, 32 deletions

diff --git a/get_addiction_sentences.py b/get_addiction_sentences.py
index 30a8e50..e24f122 100644..100755
--- a/get_addiction_sentences.py
+++ b/get_addiction_sentences.py
@@ -7,29 +7,9 @@ import sys
 
 gene=sys.argv[1]
 
-addiction_terms="sensitization|intake|addiction|drug abuse|relapse|self-administered|self-administration|voluntary|reinstatement|binge|intoxication|withdrawal|chronic"
-
-drugs="alcohol|alcoholism|smoking|nicotine|tobacco|methamphetamine|amphetamine|cocaine|opioid|fentanyl|oxycodone|oxycontin|heroin|morphine|marijuana|cannabinoid|tetrahydrocannabinol|thc"
-
-brain_regions="cortex|accumbens|striatum|amygadala|hippocampus|tegmental|mesolimbic|infralimbic|prelimbic"
-
-brain_d ={"cortex":"cortex|pfc|vmpfc|il|pl|prelimbic|infralimbic",
-          "striatum":"striatum|STR",
-          "accumbens":"shell|core|NAcc|acbs|acbc",
-          "hippocampus":"hippocampus|hipp|hip|ca1|ca3|dentate|gyrus",
-          "amygadala":"amygadala|cea|bla|amy",
-          "ventral tegmental":"ventral tegmental|vta"
-          }
-
-function="LTP|LTD|plasticity|regulate|glutamate|GABA|cholinergic|serotoninergic|synaptic|methylation|transcription|phosphorylation"
-
-drugs_d = {"alcohol":"alcohol|alcoholism",
-        "nicotine":"smoking|nicotine|tobacco",
-        "amphetamine":"methamphetamine|amphetamine",
-        "cocaine":"cocaine",
-        "opioid":"opioid|fentanyl|oxycodone|oxycontin|heroin|morphine",
-        "cannabinoid":"marijuana|cannabinoid|Tetrahydrocannabinol|thc"
-        }
+## turn dictionary (synonyms) to regular expression
+def undic(dic):
+    return "|".join(dic.keys())+"|"+"|".join(dic.values())
 
 def findWholeWord(w):
     return re.compile(r'\b({0})\b'.format(w), flags=re.IGNORECASE).search
@@ -42,6 +22,7 @@ def getSentences(query):
         pmid = tiab.pop(0)
         tiab= " ".join(tiab)
         sentences = sent_tokenize(tiab)
+        ## keep the sentence only if it contains the gene 
         for sent in sentences:
             if findWholeWord(gene)(sent):
                 sent=re.sub(r'\b(%s)\b' % gene, r'<b>\1</b>', sent, flags=re.I)
@@ -49,32 +30,79 @@ def getSentences(query):
     return(out)
 
 def gene_addiction(gene):
-    q="\"(" + addiction_terms.replace("|", " OR ")  + ") AND (" + drugs.replace("|", " OR ", ) + ") AND " + gene + "\""
+    # search gene name & drug name  in the context of addiction terms (i.e., exclude etoh affects cancer, or methods to extract cocaine) 
+    q="\"(" + addiction.replace("|", " OR ")  + ") AND (" + drugs.replace("|", " OR ", ) + ") AND " + gene + "\""
     sents=getSentences(q)
     out=str()
     for sent in sents.split("\n"):
         for drug0 in drugs_d:
             if findWholeWord(drugs_d[drug0])(sent) :
                 sent=re.sub(r'\b(%s)\b' % drugs_d[drug0], r'<b>\1</b>', sent, flags=re.I)
-                out+=gene+"\t"+drug0+"\t"+sent+"\n"
+                out+=gene+"\t"+"drug\t" + drug0+"\t"+sent+"\n"
+        for add0 in addiction.split("|"):
+            if findWholeWord(add0)(sent) :
+                sent=re.sub(r'\b(%s)\b' % add0, r'<b>\1</b>', sent, flags=re.I)
+                out+=gene+"\t"+"addiction\t"+add0+"\t"+sent+"\n"
     return(out)
 
-def gene_brainRegion(gene):
-    q="\"(" + brain_regions.replace("|", " OR ")  + ") AND " + gene + "\""
+def gene_anatomical(gene):
+    q="\"(" + brain.replace("|", " OR ")  + ") AND " + gene + "\""
     sents=getSentences(q)
     out=str()
     for sent in sents.split("\n"):
         for brain0 in brain_d:
             if findWholeWord(brain_d[brain0])(sent) :
                 sent=re.sub(r'\b(%s)\b' % brain_d[brain0], r'<b>\1</b>', sent, flags=re.I)
-                out+=gene+"\t"+brain0+"\t"+sent+"\n"
+                out+=gene+"\t"+"brain\t"+brain0+"\t"+sent+"\n"
+    return(out)
+
+def gene_biological(gene):
+    q="\"(" + biological.replace("|", " OR ")  + ") AND " + gene + "\""
+    sents=getSentences(q)
+    out=str()
+    for sent in sents.split("\n"):
+        for bio0 in biological_d:
+            if findWholeWord(biological_d[bio0])(sent) :
+                sent=re.sub(r'\b(%s)\b' % biological_d[bio0], r'<b>\1</b>', sent, flags=re.I)
+                out+=gene+"\t"+"function\t"+bio0+"\t"+sent+"\n"
     return(out)
 
+addiction="reward|reinforcement|sensitization|intake|addiction|drug abuse|relapse|self-administered|self-administration|reinstatement|binge|intoxication|withdrawal|conditioned place preference|aversion|aversive|CPP"
+
+drugs_d = {"alcohol":"alcohol|alcoholism",
+        "nicotine":"smoking|nicotine|tobacco",
+        "amphetamine":"methamphetamine|amphetamine",
+        "cocaine":"cocaine",
+        "opioid":"opioid|fentanyl|oxycodone|oxycontin|heroin|morphine",
+        "cannabinoid":"marijuana|cannabinoid|Tetrahydrocannabinol|thc"
+        }
+drugs=undic(drugs_d)
+
+brain_d ={"cortex":"cortex|pfc|vmpfc|il|pl|prelimbic|infralimbic",
+          "striatum":"striatum|STR",
+          "accumbens":"shell|core|NAcc|acbs|acbc",
+          "hippocampus":"hippocampus|hipp|hip|ca1|ca3|dentate|gyrus",
+          "amygadala":"amygadala|cea|bla|amy",
+          "vta":"ventral tegmental|vta|pvta"
+          }
+# brain region has too many short acronyms to just use the undic function, so search PubMed using the following 
+brain="cortex|accumbens|striatum|amygadala|hippocampus|tegmental|mesolimbic|infralimbic|prelimbic"
+
+biological_d={"plasticity":"LTP|LTD|plasticity|synaptic|epsp|epsc",
+            "neurotransmission": "neurotransmission|glutamate|GABA|cholinergic|serotoninergic",
+            "signalling":"signalling|phosphorylation|glycosylation",
+#            "regulation":"increased|decreased|regulated|inhibited|stimulated",
+            "transcription":"transcription|methylation|histone|ribosome",
+            }
+biological=undic(biological_d)
+
 report=str()
-out=gene_addiction(gene)
-report+=out
-out=gene_brainRegion(gene)
-report+=out
+out0=gene_addiction(gene)
+report+=out0
+out1=gene_anatomical(gene)
+report+=out1
+out2=gene_biological(gene)
+report+=out2
 with codecs.open(gene+"_addiction_sentences.tab", "w", encoding='utf8') as writer:
    writer.write(report)
    writer.close()