Trouble with NCBI Pubmed translator

zekeb
I had no problem importing pubmed references until earlier today. Books from amazon.com still import normally.

When I try to import a pubmed reference e.g.:
http://www.ncbi.nlm.nih.gov/pubmed/9566477
the grey box pops up in the lower right corner, but remains blank. When I import a book from amazon.com it reports status "Saving..."

I have updated my translators and restarted firefox, but still the same result.
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  • anders_royce
    Same here. I can save from search results, but not articles. The icon on article pages does say (NCBI PubMed), but nothing happens when I click it.
  • lcdrcjnes
    Same problem here. Tried resetting and updating translators as well as manually deleting and then updating them. PubMed Central still works but not PubMed itself.

    Has happened for several papers including:
    http://www.ncbi.nlm.nih.gov/pubmed/19303854
  • vijumoses
    edited April 7, 2010
    Me too. Would like to add some more information here.
    It worked fine yesterday.
    The problem is: Cannot import individual journal articles from pubmed, ie when you are having a single article in pubmed in the browser window. Same description as opening poster. But I am able to import articles from lists in pubmed ie search for some term (that brings up more than 1 result), click on the folder icon in address bar, select 1 or 2 articles and save. That's interesting.

    What about other sites? Google scholar: am able to use it normally (importing from listings), including importing the same articles that could not be imported in pubmed.

    So importing from lists in pubmed and (from lists in) google scholar are temporary (though inconvenient) solutions while zotero developers find the fix.

    Zotero or Pubmed must have updated their software, causing the incompatibility (probably pubmed as I haven't recently seen zotero updates).

    Restarting the browser, Windows Vista, etc doesn't work.
  • zaduplum
    Same for me.
    Since just a few hours ago.

    Interesting thing is that the translator imports well from listings in PubMed.
    Hope to fix this problem soon.
  • LFM
    Same thing happening here. What is going on? It is not only a pubmed problem, I also have problems capturing references from some journals, when that happened my backup plan was to use pubmed, now even that is not working! I need something reliable. I do own endnote and ref manager, I could use those, but that is not the point, Zotero you are breaking my heart!
    First you didn't warn me of the issues with abbreviated journal names (e.g. Journal of Forgotten Research: J Forg Res vs. J. Forg. Res.) and I had to manually fix over 100 references (on a deadline), noticing also that some journal names weren't even captured right. Now this?

    I vote for the addition of a page with known issues, it is very time consuming to sift through the forums to find an answer to common issues.
  • MainMan_pl
    edited April 7, 2010
    Exact behavior for me - empty box showing - no references added to database.
    Here's the link : http://www.ncbi.nlm.nih.gov/pubmed/8570736
  • Wittgenstein
    Same problem here...
  • lakky
    The same for me. Here's the error code: 595311821.
    And here's the link.
    http://www.ncbi.nlm.nih.gov/pubmed/12668594
  • rflight79
    Same problem. Initially thought it might be a general problem, but I can still import refs from other journal sites. This is certainly odd to say the least.
  • GR
    Same problem: D430765296
    I really need to import citations from pubmed.
    GR
  • jussia
    Same issue here. I really wish the developers can sort this one out quickly..
  • catia
    Same problem. At first, I thought maybe it was because I hadn't upgraded to 2.0 yet. The problem remained even after I performed the upgrade.
  • vircasti
    You can still add references with the PID
  • mboivin
    Everyone can get around the issue if you are working on a project.

    Copy the PMID on the Pub MED page and click the magic wand in zotero (4th icon over when you pull zotero up) and enter in the PMID. It will import the citation. But this takes a few more steps then just clicking once.

    I hope this helps.
  • anders_royce
    Add by PMID is a good workaround. You can also still use the PubMed translator from search result lists. Finally, unless you are particularly attached to the NCBI interface, there are many alternative ways to search PubMed. Pubget, for example, is a nice one, and has a (working) translator.
  • notan
    Clicking the magic wand in zotero and pasting the PMID from the PubMed page (PMID: 6129117) gives me the error message "Zotero could not find a record for the specified identifier."

    Am I not formatting it correctly or is that broke too?
  • anders_royce
    That works fine for me. Make sure you are just entering the number, not the "PMID" part.
  • ajlyon
    Is anyone currently working on a fix for this? I could look into fixing it, but I don't want to be duplicating someone else's work.
  • notan
    Using the magic wand seems to put the item in "My Library" but I was trying to get it into a collection in a group library which is what was open and displayed on the right in Zotero. I was expecting it to go into the collection of the group library.
  • zekeb
    I am using the list import suggestion by vijumoses is working for me.

    NCBI translation is important as this is the link I have to use within my institution to easily access fee-based articles. (There are other alternatives, but this is the most straightforward).

    Hope this is resolved soon!

    thanks for all the replies - thought it was just me!
  • dstillman
    ajlyon: All yours if you want it.
  • Sadie Richards
    I am having the same problem, but when I try to enter the PMID with the wand nothing happens (dialog box closes, but no empty red square or any sign that Zotero has added the reference). Then when I try to click on my libraries (personal and group) I am told an error has occurred and that I must restart firefox. Doing so does not help. Thank you to those of you working on a fix!
  • jasonnpitt
    broken. the wand thing works though...and pubget is cool! thanks for the tip!
  • ajlyon
    The updated translator at http://groups.google.com/group/zotero-dev/web/NCBI PubMed.js should now work. This or a similar version will likely hit clients some time soon. In the meantime, you can place the file in the translators folder of your Zotero data directory and NCBI Pubmed should work again. Please post if this doesn't do the trick for you-- I'm not a Pubmed user myself, so I may have missed something in my quick testing.
  • lacaputo
    Works for me, thanks very much for the quick fix!
  • Wittgenstein
    Works perfectly! Thank you!
  • nicrobertson
    Hi - I just wanted to say thanks to mboivin for the workaround and the developers who made the new translator, it was a very frustrating problem for about an hour until I found this thread! Cheers guys.

    Nic
  • andiratih
    i don't understand, please give a step by step tutorial for dummy to add this translator file to zotero.
    thanks a lot
  • GR
    Copy the file with a file manager to the directory called "translators" in your zotero directory (I renamed the existing ".broken", just in case). You can find zoteros directory in zoteros preferences: it is either somewhere in the firefox home directory (default) or you specified anonther location.

    Thanks a lot, ajlyon!

    GR
  • dstillman
    The updated translator is now available. Your copy of Zotero should auto-update within 24 hours, or you can update manually by clicking Update Now in the General pane of the Zotero prefs.

    Thanks to ajlyon for the quick fix.
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