<p>If you can use R, consider using web scraping.</p>

<p>See here : <a href="http://bradleyboehmke.github.io/2015/12/scraping-html-tables.html" rel="nofollow noreferrer">http://bradleyboehmke.github.io/2015/12/scraping-html-tables.html</a></p>

CC BY-SA 4.0
2019-02-04T10:06:38.830Z
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 - (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970438/) that extracts tables from xml and restructures them into MySQL tables using text-mining algorithm.
PinkBanter
CC BY-SA 4.0
2019-02-03T07:55:12.913Z
2019-02-03T07:55:12.913Z
Alexandre georges
<p>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 <a href="https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&amp;identifier=oai:pubmedcentral.nih.gov:6148705&amp;metadataPrefix=pmc" rel="noreferrer">here</a> (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?</p>

CC BY-SA 4.0
2018-12-19T16:21:25.023Z
Is connecting to a remote database an option? Also what data do you need? All of it? Only the paper? Only the abstract?
terdon
CC BY-SA 4.0
2018-12-19T16:44:33.733Z
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.
PinkBanter
<public-databases><text-processing>
Is there a way to import tables in PubMed Central to MySQL or other Relational databases?
# Is there a way to import tables in PubMed Central to MySQL or other Relational databases?

(Asked by: username_0 on 2018-12-19)

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](https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&identifier=oai:pubmedcentral.nih.gov:6148705&metadataPrefix=pmc) (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?

**Tags:** public-databases, text-processing
> **Comments:**
> **username_1**: Is connecting to a remote database an option? Also what data do you need? All of it? Only the paper? Only the abstract?  
> **username_0**: 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.  

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## 1 answers

### Answer by username_2 on 2019-02-03. Score: 1

If you can use R, consider using web scraping.

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

> **Comments:**
> **username_0**: 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 - (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970438/) that extracts tables from xml and restructures them into MySQL tables using text-mining algorithm.  

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