Pipeline for identifying papers with drugs
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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')
- Anaesthics: http://en.wikipedia.org/wiki/Anesthetic
- Anticonvulsants--Ethosuximide, Arimethadione
- Alkaloid drugs: http://en.wikipedia.org/wiki/Alkaloid
- Immunosuppressants: http://en.wikipedia.org/wiki/Immunosuppressive_drug
- Nutritional supplements: http://www.rxlist.com/supplements/alpha_a.htm
- For the purpose of the lexicon:Use generic name for drug name, trade name will be used as synonymn.
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