[TIP] Simplify Stored Pubmed URLs

[iandol]

All of my URLs back to Pubmed looked like this in my Bookends database:

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https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=3385477

If you follow this link it actually resolves to the much cleaner:

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https://www.ncbi.nlm.nih.gov/pubmed/3385477

For some of my formats I do print the URL in the bibliography and so this simplified format makes much nicer final bibliographies. In Bookends it is easy to find and replace.

First, for safety I add only those refs with a PMID to the Hits list:

Screen Shot 2017-08-06 at 11.35.51.png (10.78 KiB) Viewed 2615 times

Then you can Find and Replace only URL field only in the hits list:

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You have to do this Find and Replace twice, because older URLs use http:// and newer ones use https://. So here is the find text:

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https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=

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http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=

The replace text is the same:

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https://www.ncbi.nlm.nih.gov/pubmed/

This updates all the Pubmed URLs stored in Bookends to the simpler format.

[Jon]

Another tip: the URL prefix is applied by the PubMed filter, so you can change it yourself.

Open File -> Import Filter Manager -> PubMed and click on the Misc tab.

In the text box after "Insert Text", replace the old prefix with

https://www.ncbi.nlm.nih.gov/pubmed/

And leave the field to be inserted into as "URL".

This will be the setting in the upcoming Bookends 12.8.3, but you can do it yourself now if you want.

Jon
Sonny Software

[iandol]

Ah, I was curious why PMID- was assigned to the URL field in the import filter, but I missed the misc tab to see that it is configurable, cool!