Full text literature mining on PubMed for keyword combinations

A Python package for literature mining on PubMed

EXAMPLE USAGE 1 - Toxins of Cyanobacteria

Cyanobacteria - conservative search¹

python3 01_litMiningPubmed_conductMining.py \
-q "(Cyanobacteria[tiab] OR Cyanobacteria[mh]) \
AND (cyanotox*[tiab] OR cyanotox*[mh]) \
AND (*synthesis[tiab] OR *synthesis[mh]) \
AND (gene[tiab] OR gene[mh]) \
AND 2000:2022[dp] \
AND free full text[sb]" \
-m your_email@address_here.at

Cyanobacteria - liberal search -- NOT RECOMMENDED

python3 01_litMiningPubmed_conductMining.py \
-q "Cyanobacteria[all]\
AND cyanotox*[all] \
AND *synthesis[all] \
AND gene[all] \
AND 2000:2022[dp] \
AND free full text[sb]" \
-m your_email@address_here.at

• "cyanotox*" is necessary b/c possible terms include "cyanotoxin(s)", "cyanotoxicity", etc.
• "2000:2022[dp]" selects only those publications that have been published in the genomic era (2000 ff.)
• "free full text[sb]" is necessary to ensure that full text of article can be retrieved
• "AND open access[filter]" would find all PMC Open Access subset articles with this filter but is too restrictive in practice

EXAMPLE USAGE 2 - Mycotoxins of Trichoderma

Trichoderma - conservative search¹

python3 01_litMiningPubmed_conductMining.py \
-q "(Trichoderma[tiab] OR Trichoderma[mh]) \
AND (mycotox*[tiab] OR mycotox*[mh]) \
AND (*synthesis[tiab] OR *synthesis[mh]) \
AND (gene[tiab] OR gene[mh]) \
AND 2000:2022[dp] \
AND free full text[sb]" \
-m your_email@address_here.at

Trichoderma - liberal search -- NOT RECOMMENDED

python3 01_litMiningPubmed_conductMining.py \
-q "Trichoderma[all]\
AND mycotox*[all] \
AND *synthesis[all] \
AND gene[all] \
AND 2000:2022[dp] \
AND free full text[sb]" \
-m your_email@address_here.at

Footnotes

1. Notes regarding query string: ↩ ↩²