All I want for Christmas is PMCID import

granto
NIH grants require PMCID's in the bibliography. But when you use zotero to import refs, this info is not imported unless you import directly from pubmed. So any ref I imported in the more convenient zoteroesque way (i.e. that pulls the pdf etc) does not have this info. Then I either have to go find out which refs need PMCIDs and import those again from pubmed, which would take about a day, or, more realistically, just give up on zotero end export my library to endnote, which despite being the most cumbersome reference software available is able to handle this basic capability.

I have requested this over the years (including linking to pubmed's API that enables one to import this metadata) and I assure you, I am not the only one who feels this pain. I want to love Zotero but it's not working out for us. Maybe 2017 will be different? How can I help? Cash money? If I were better at coding I would do it!!
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  • granto
    This guy is getting close. Anyone?

    https://groups.google.com/forum/#!topic/zotero-dev/Cqobqnzm6Xc
  • qdr
    the advice he got from @bwiernik was spot on. Using the google scholar citation code, this should be pretty straightforward.
  • adamsmith
    (that was me posting under an institutional account)
  • granto
    If it's straightforward, what's the barrier to implementation? If it can be done within the next few weeks I will seriously pay someone to do this because I can't spare the time to look all these hundreds of PMCID's up individually and I don't know java. I see several requests for this and other types of auto metadata updating (e.g., DOI) over the years, and a lot of talk from the mods about implementing this, but nothing.

    I think zotero is one of the few ref managers that can't do this.. I'm saying this not to ruffle feathers but to be constructive and talk about a real demand that exists.
  • adamsmith
    It's really just that someone has to do it and that there are way more things that'd be great (and for some people essential) to have than there's developer time at any given point in time.
    I'd see if you can follow up with the person on that thread. Within the next 3 months or so, someone hacking together an add-on is definitely your best bet.
  • granto
    OK thanks. So if he writes an FF plugin, can you answer this part of that thread?

    "is this a bad idea since zotero is moving away from xulrunner? How will electron plugins be managed?"

    thanks,
    Grant
  • adamsmith
    I don't think there's a clear answer on electron plugins beyond that add-ons will continue to play an important role. But Electron is also at least a year down the road.
  • darbyjack
    any updates on this?
  • granto
    Almost 4 Christmases later and I'm still manually importing PMCID into articles and/or dealing with dual entries from importing from both pubmed and the publisher page. So consider this my note to Santa-- any chance of doing this? This would immensely help everyone who is submitting a federal grant.
  • emilianoeheyns
    So the desired functionality would take an item with a DOI, see if it doesn't have a PMCID, grab it from the API, and put it in the extra field?
  • granto
    Yes, exactly! And since not everything has a PMCID, it could also scrape the PMID if possible.
  • emilianoeheyns
    https://github.com/retorquere/zotero-pmcid-fetcher
  • granto
    Wow, thank you for writing that! However I've been trying to troubleshoot this for a while but can't seem to find a workaround-- when I try to install I get the error that it cannot install and appears to be corrupt. When I try to install with temporary addons in debug mode, it says the .xpi does not contain a valid manifest. I've set xpinstall.signatures.required to false, and (I am pretty sure) I repackaged the files without compression and tried to load again. If you know a quick fix I'd really appreciate it, but you're unsure of the problem I will keep looking! Thanks again for your help!!
  • enozkan
    edited August 29, 2020
    @granto Did you try to install this in Firefox by double clicking? That's a common mistake.

    This is intended for Zotero. Go to Zotero -> Tools -> Addons and install it there. I just did, and it works beautifully. Thank you, @emilianoeheyns

    May I suggest one level of improvement? Can it add the PMID, even when the PMCID is present? I have no idea how I ended up with those, but I have a number of items in my library with DOIs and PMCIDs, but no PMIDs.
  • enozkan
    After working for a bit, the plugin stopped receiving PMCIDs. I tried it on a variety of items, and also tried it after manually deleting the PMCIDs from items retrieved from Pubmed before. Nothing shows up in the error console. Happy to help debug and/or open an issue in github.
  • emilianoeheyns
    @enozkan that's in 0.0.6 now. Earlier versions had a bug; you'll need to restart Zotero (cmd-Q if you're on a Mac) before the fix will take effect. Later versions should not need restarts after upgrade.

    Please do open an issue on GH. My debugging workflow is built around it.

  • enozkan
    It is working like a charm. Thank you! Until Zotero gets an update-item function that updates all bibliographic data, this will help those of us needing to write federal grants in the US.

    I will post the next issue on Github.
  • enozkan
    Plugin added to the "Plugins for Zotero" page under Item Metadata Import: https://www.zotero.org/support/plugins#new_features_and_enhancements
  • granto
    edited August 29, 2020
    Nice!! It works great! Yes I was foolishly trying to install with Firefox. Thanks so much for your contribution @emilianoeheyns !! Merry christmas!
  • emilianoeheyns
    The implementation is pretty rudimentary at this point. If it stops, the latest version has a menu item under Help that will allow you to send an debug log. No idea why it should stop -- there's very little code. Maybe the API is throttling? Anyhow, we'll know more when we see the logs.

    And a Happy New Year.
  • emilianoeheyns

    After working for a bit, the plugin stopped receiving PMCIDs.

    It looks like the API gives 429: too many requests occasionally, but there's no documentation on rate limits. The new version should tell you about it with a popup window when it happens, but I've changed the implementation to do bulk-requests of 200 items rather than the one-by-one requests I used to do. Does mean that if it still hits the limit, it will fail for potentially 200 items at once. On the other hand, it's safe to do this multiple times on the same items, because it won't replace existing PMCIDs/PMIDs.

  • emilianoeheyns
    You can also have them auto-fetched.
  • nguyenhd83
    I'm just trying out Zotero. I'm trying to insert bibliography with NLM to include PMCID. THe example on Zotero desktop shows PMCID # but when I insert in Word for bibliography, it shows up as PMID. Can't figure out how to change that.
  • bwiernik
    The NLM grant proposal style will include the PMCID with the appropriate label if one is present in your Zotero data. It will include the PMID with the appropriate label if no PMCID is in your Zotero data.

    PMCID should be entered in Extra like this:
    PMCID: 12345

    PMID should be entered in Extra like this:
    PMID: 12345
  • pnestadt
    Just here to say THANK YOU to Emiliano!
  • enozkan
    PMCID Fetcher is currently one of the plugins marked incompatible with Zotero 6 beta.
  • enozkan
    Funny, I downloaded and reinstalled version 0.0.11 (which is what was already installed and showed as up-to-date) and the incompatibility went away. And install.rdf does not appear to have been updated since 2020. Anyway, working now. Thanks!
  • dstillman
    edited February 17, 2022
    (Version compatibility can be set via the update manifest online. There's no need for a new version of the plugin as long as it's already functionally compatible.)
  • enozkan
    But it is it still showing up as incompatible in all my other computers running Zotero 6 beta. Restarting Zotero did not change that. Until I manually re-installed the same version from two years ago, Zotero kept the plugin disabled. Wouldn't a version update help with re-enabling, even if no change was made in the plugin?
  • dstillman
    If the change was just made Zotero would have to check for an update. That should happen automatically within a day, assuming auto-updates are working properly on your system. You can check manually from the gear icon in the Add-ons pane, which should force Zotero to notice the compatibility change.
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