Export PubMed Citations

BioMedQuery has functions to search PubMed for PMIDs and save the xml data as either a BibTex or EndNote citation.

Here we export EndNote/BibTex citations from a PMID or a list of PMIDs. If you need to search Entrez/PubMed and save the results as citations, refer to Examples / PubMed Search and Save.

Set Up



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using BioMedQuery.Processes

The functions require a directory to save the citation files to



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results_dir = ".";

if !isdir(results_dir)
     mkdir(results_dir)
end

For this example, the below PMIDs are searched and saved as citations



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pmid = 11748933;
pmid_list = [24008025, 24170597];

Export as an EndNote library file

Saving one PMID's citaiton as an EndNote file



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enw_file = results_dir * "/11748933.enw";
export_citation(pmid, "endnote", enw_file);

Saving two PMIDs' citations as an EndNote file



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enw_file = results_dir * "/pmid_list.enw";
export_citation(pmid_list, "endnote", enw_file);

Explore one of the output files



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println(read(enw_file, String))

Export as a Bibtex file

Saving one PMID's citation as a BibTex file



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bib_file = results_dir * "/11748933.bib";
export_citation(pmid, "bibtex", bib_file);

Saving two PMIDs' citations as a BibTex file



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bib_file = results_dir * "/pmid_list.bib";
export_citation(pmid_list, "bibtex", bib_file);

Explore one of the output files



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println(read(bib_file, String))

This notebook was generated using Literate.jl.