Command line application to search Pubmed. This tool utilizes the API provided by https://biopython.org/docs/latest/api/Bio.Entrez.html to communicate with PubMed.
You can install this package either from source or directly from GitHub. This package was developed using python==3.9.
Via GitHub:
pip install git+https://github.com/RDoerfel/pubmed-search
From Source:
git clone https://github.com/RDoerfel/pubmed-search.git
cd pubmed-search
pip install .
I recommend using the package in its own conda environment to make sure that everything works.
The search parameters are defined using a json file, like it is provided in data/search.json.
"terms":"(PubMed) AND (Search)" - The PubMed search query to execute.
"settings":{"db":"pubmed"} - The database to use (pubmed is recommended)
"result_dir":"<path_to_result_dir>" - Path to store the results.
"settings":
{
"db":"pubmed",
"sort":"relevance",
"mindate":"2010/01/01",
"maxdate":"2022/05/20",
"retmax":1000,
"retmode":"xml"}
Settings as specified in https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch.
"exclude_file":"<path_to_exclude_file>" - The path to the file containing Journal Types to exclude from search
"include":"PMID1,PMID2" - list of PMIDs to check if they are included in results.
Run pubmed search using:
pmsearch -f <path_to_search.json>