AutoFill and missing PMIDs? Or a "Get PMID" Command

[iandol]

Hi Jon, is there any way if a ref has no PMID but a DOI to use "Autofill from Internet" to get the PMID? If not, you have a "Get DOI" command, it would be great to have a "Get PMID" command (use title and authors for a pubmed search?) too.

[Jon]

If you have the DOI and the reference is on PubMed, Refs -> Autofill From Internet OR right-click on the PMID field and select Autofill This Field From Internet should fetch the PMID for you. Didn't you try this -- and it failed?

Jon
Sonny Software

[iandol]

Yes, I've tried both and they failed for me, here is an example ref with a working DOI that fails (exported as BibTeX, it is present in pubmed as PMID: 21151887 / PMCID: PMC2998442):

Code: Select all

@Article{Brown2010,
author = {Brown, Timothy and Gias, Carlos and Hatori, Megumi and Keding, Sheena and Semo, Ma’ayan and Coffey, Peter and Gigg, John and Piggins, Hugh and Panda, Satchidananda and Lucas, Robert}, 
title = {Melanopsin Contributions to Irradiance Coding in the Thalamo-Cortical Visual System}, 
journal = {PLoS Biol.}, 
volume = {8}, 
number = {12}, 
pages = {e1000558}, 
year = {2010}, 
abstract = {}, 
doi = {10.1371/journal.pbio.1000558}, 
pmid = {}, 
url = {}, 
location = {}, 
keywords = {}}

[Jon]

It works fine for me. I make a new reference and paste 10.1371/journal.pbio.1000558 into the DOI field. Then I right-click on it and Autofill from Internet. The whole Brown ref is imported, along with the PMID and PMCID (which are the ones you list below).

Jon
Sonny Software

[iandol]

Even if I delete my application support folder, create a new library still not working for me. I'll contact support.

The second request still kind of stands, if there is no DOI and PMID but an article is on Pubmed having a "Get PMID" command would be great. Endnote has a "Find Reference Updates..." which can do this (not automatic as it brings up a merge window to select fields to update).

[Jon]

I'll look for your tech support request.

As for the request, you can do this now, sequentially. Get DOI and then Autofill From Internet, as described above.

Jon
Sonny Software

[iandol]

That doesn't seem to work for me (apart from taking two actions, each of which blocks the GUI until it completes). For example:

Code: Select all

@Article{Alexander2015,
author = {Alexander, David and Trengove, Chris and van Leeuwen, Cees}, 
title = {Donders is dead: cortical traveling waves and the limits of mental chronometry in cognitive neuroscience.}, 
journal = {Cognitive processing}, 
volume = {}, 
number = {}, 
pages = {}, 
year = {2015}, 
abstract = {}, 
doi = {}, 
pmid = {}, 
url = {}, 
location = {}, 
keywords = {}}

I have a title, authors and journal but no DOI or PMID. Get DOI doesn't retrieve anything, so then I can't get a PMID. I can manually copy the title to BE's pubmed search (it succesfully does an esearch.fcgi and an efetch.fcgi using the EUtils interface, getting the full record back), then manually copy and paste the bits back into the database. It would be great to have a single command that simplifies this. For a user, what are the use cases of having a "Get DOI" (but no "Get PMID") and separate "Autofill" commands? I'd assume most users just want to update their reference, and at least for most sciences, the PMID and DOI are both equally important.

[Jon]

It doesn't work for you, personally, because of other problems you're having with your slow Internet connection and perhaps other issues, as you know. Get DOI and then Get PMID works just fine (I just tested, again), so don't mislead others reading this thread. We're dealing with your other problem in tech support, let's keep it there.

Jon
Sonny Software

[iandol]

Sorry Jon, I thought the main point of the issue we're working through tech support was when we had a DOI then tried to "Autofill" the rest, but yes it probably must be that my "autofill" not working and my "Get DOI" not working are part of the same problem.