Pipeline for identifying papers with drugs

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Revision as of 19:39, 6 August 2012 by Rkishore (talk | contribs)
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  • Initial plan was to use the 'molecules' list to identify papers with drugs, output was overloaded with papers with biomolecules, does not work for drugs.
  • Building the drug lexicon: The following sources were used:
  • Antifungal agents: http://en.wikipedia.org/wiki/Antifungal_medication
  • Antibiotics--antimicrobial, anti-fungal, anti-viral, anti-parasitic and anti-tumor agents:


  • Antiparasitic drugs--Aldicarb, Ivermectin, Levamisole
  • Anti-depressants, anti-depressants, anticonvulsants, anti-psychotic and psycho-active drugs:



http://en.wikipedia.org/wiki/Psychoactive_drug (Table under the heading Affected neurotransmitter systems, capture columns 'Classification' and 'Examples')


Exceptions: --Skip pure numbers



  • Need to add Resveratrol, Gingko biloba and the anticonvulsants--Ethosuximide, Arimethadione, if not present in lists
  • Will drop the above nutritional supplement list, this list is huge, thousands of terms, too big to clean and the Textpresso run output is really bad.
  • After dropping the supplement list, script re-run, still having problems with the following terms:
AGa  ATP  alanine  acetate  aspartic acid  Ca2  bovine serum albumin
biotin  chloroform  choline  date  deoxyribonucleic acid  DRAKE  ethanol
EDTA  fluoride  histidine  glycine  hydroxyapatite  same  soma  ROS
NADH  sodium dodecyl sulfate  violet  nucleotides  nucleic  tetramisole
tyrosine  tryptophan
pears  potassium  protease  PEPE  sodium phosphate  GABA  glycerol  phenylalanine
pyruvic acid  alanine  glutamate  glutathione  baker's yeast  protamine  lysine
fatty acid  fluoride  methionine  nitrogen  succinic acid  sulphate  oatmeal
cholinergic  acetic acid  amber  serine  steroid  calcium  AMP  constancy
liver extract  bovine serum albumin  rabbits  valine Saccharomyces cerevisiae