Automatically retrieve PDFs from pubmed search entries

DEVONthink
1

Hi,

I am new to DevonThink and I am still trying to figure out how I can do certain jobs better. I often use DevonAgent to retrieve Pubmed entries to a certain topic (e.g. MET receptor). I get like up to 100 hits and import them to DT as resource. Most of the entries have available pdfs of the articles. Is there a way to retrieve the pdfs for all the 100 entries in DT automatically. I know how to do it manually but it takes a long time. Is it better to do this in Bookends and then bring them into DT?

Thanks,
Marco

1 Like
2

How do you download it manually? The URL of a result having PDFs would be useful.

3

It’s a multi step process. After I imported the journal resource page to DT:

I have to click on full text links after that and choose the source e.g.

Then I have to click on the pdf format source:

When you use Bookends or Endnote they can scrape the pdf directly from the citation in pubmed. I don’t know how they do it but would be great if DT could do the same.

Thanks,
Marco

4

This can be scripted, e.g. the following script checks whether one of the selected items in DEVONthink is a PubMed result and then tries to add the download to the download manager:

-- Download PDFs from PubMed

tell application id "DNtp"
	repeat with theRecord in selected records
		set theURL to URL of theRecord
		if theURL begins with "https://pubmed.ncbi.nlm.nih.gov/" then
			set theSource to download markup from theURL
			repeat with theLink in (get links of theSource base URL theURL)
				if theLink begins with "https://www.mdpi.com/resolver?pii=" then
					set theSource to download markup from theLink
					repeat with theDownload in (get links of theSource base URL theLink)
						if theDownload ends with "/pdf" then add download theDownload
					end repeat
					exit repeat
				end if
			end repeat
		end if
	end repeat
end tell

A revision of this script could be also used in smart rules so that this could be automatically performed after adding results to DEVONthink.

4 Likes
5

Thank you so much. I will test it later. One more question: The part in the script that is directing to a special journal in this case mdpi. Would there be a way to keep it as general as possible so that it can get the pdf file from any journal that is catalogued in pubmed. I am new to DT and still try to figure out what can be done by scripts and what not.

6

The script and its conditions could of course be extended. But it needs a way to figure out which links should be used.

7

Thanks Christian. I think I have to become first more experienced in DT 3 before I am able to change the script but working on it :slight_smile:

Marco