Difference between revisions of "Pipeline for identifying papers with drugs"
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*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. | *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: | *After dropping the supplement list, script re-run, still having problems with the following terms: | ||
− | AGa ATP | + | AGa, ATP, alanine, acetate, aspartic acid, Ca2, bovine serum albumin, |
− | biotin chloroform choline date deoxyribonucleic acid DRAKE ethanol | + | biotin, chloroform, choline, date, deoxyribonucleic acid, DRAKE, ethanol, |
− | EDTA fluoride histidine glycine hydroxyapatite same soma ROS | + | EDTA, fluoride, histidine, glycine, hydroxyapatite, same, soma, ROS, |
− | NADH sodium dodecyl sulfate violet nucleotides nucleic tetramisole | + | NADH, sodium dodecyl sulfate, violet, nucleotides, nucleic, tetramisole, |
− | tyrosine tryptophan | + | tyrosine, tryptophan, |
− | pears potassium protease PEPE sodium phosphate GABA glycerol | + | pears, potassium, protease, PEPE, sodium phosphate, GABA, glycerol, phenylalanine, |
− | pyruvic acid alanine glutamate glutathione baker's yeast protamine lysine | + | pyruvic acid, alanine, glutamate, glutathione, baker's yeast, protamine, lysine, |
− | fatty acid fluoride methionine nitrogen succinic acid sulphate oatmeal | + | fatty acid, fluoride, methionine, nitrogen, succinic acid, sulphate, oatmeal, |
− | cholinergic acetic acid amber serine steroid calcium AMP constancy | + | cholinergic, acetic acid, amber, serine, steroid, calcium, AMP, constancy |
− | liver extract bovine serum albumin rabbits valine Saccharomyces cerevisiae | + | liver extract, bovine serum albumin, rabbits, valine, Saccharomyces cerevisiae |
'''Ideas worth trying:''' | '''Ideas worth trying:''' | ||
− | *Skip the sections: 'Materials and Methods', 'Materials', 'Methods' | + | *Skip the sections: 'Materials and Methods', 'Materials', 'Methods' and 'References' |
− | * | + | *Once we get the out-put we will filter with the word 'drug' at document level. |
Revision as of 21:12, 6 August 2012
- 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:
http://antibiotics.toku-e.com/antimicrobial
- Antiparasitic drugs--Aldicarb, Ivermectin, Levamisole
- Anti-depressants, anti-depressants, anticonvulsants, anti-psychotic and psycho-active drugs:
http://en.wikipedia.org/wiki/List_of_antidepressants
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
http://www.surgeryencyclopedia.com/Fi-La/Immunosuppressant-Drugs.html
- 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
All output files are at:
http://textpresso-dev.caltech.edu/disease/drug_disease/output/
08/06/12:
Notes:
- 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
Ideas worth trying:
- Skip the sections: 'Materials and Methods', 'Materials', 'Methods' and 'References'
- Once we get the out-put we will filter with the word 'drug' at document level.