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Download PubMed OA figures

Titipat Achakulvisut edited this page Jan 21, 2020 · 1 revision

Here, we explain how to download PubMed OA figures corresponded to the parsed information

  • In pubmed_parser, you can use parse_pubmed_caption to parse figures (to be specific figure_id) and captions corresponding to a manuscript.
  • To download the images corresponding to a given PMC or PMID, you can download a CSV file from ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_file_list.csv first. - The file will have columns PMID, Accession ID (PMC), and File where it looks something like oa_package/08/e0/PMC13900.tar.gz.
  • You can then download a tar file for a given PMID or PMC from ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/08/e0/PMC13900.tar.gz. You can check out ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/ to get all the access for tar files.