I need to use these PMC tables from the medical journals for the purpose of integrating the data with a decision-making software. Though, I can see that one can access full-text for an article from PMC here (which includes the article table), but is there a way to extract the table from this XML document and export it to a local MySQL database or any other relational database?

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    $\begingroup$ Is connecting to a remote database an option? Also what data do you need? All of it? Only the paper? Only the abstract? $\endgroup$
    – terdon
    Dec 19 '18 at 16:21
  • $\begingroup$ I need only the tables from the Published articles (mainly to access individual patient characteristics like Age, Gender, Marital Status, Disease History, etc.) Connecting to a remote database is surely an option. $\endgroup$ Dec 19 '18 at 16:44

If you can use R, consider using web scraping.

See here : http://bradleyboehmke.github.io/2015/12/scraping-html-tables.html

  • $\begingroup$ The tables are already present in the xml files that PubMed allows to download, but there is no way to restructure those xml components into the tables. For example, this study - (ncbi.nlm.nih.gov/pmc/articles/PMC5970438) that extracts tables from xml and restructures them into MySQL tables using text-mining algorithm. $\endgroup$ Feb 4 '19 at 10:06

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