Pubmed Batch Import

mobio20
I am new to Zotero and I have what may be a simple problem. I would like to import the entries from a Pubmed search that returns around 300 entries. My Firefox browser bar has the Zotero folder icon displayed. However, when I click on the folder, I am only given the option to import a few of the original 300 entries. By changing the Pubmed "display" settings to "abstract" I can usually gain access to a few more entries. Regardless of which "display" I choose I can never import more than 25-50% of the entries.

Currently, the only way to batch import the entire search is to search with RefWorks and then export the search as a bibliography which allows me to import the search into Zotero.

What am I doing wrong? Thanks for your time.
  • aurimas
    Zotero imports the entries that are displayed on the page. If you have PubMed display 20 search results, Zotero will give you a choice of 20 items. You can have PubMed display up to 200 items.
  • mobio20
    Thank you for your reply, but that is not the issue.

    My search returns 257 entries and I have "display" set to 200 items.

    With the "summary" view I cannot import anything and I receive an error about the translator.

    With the "abstract" view I can import 6 of the 200.

    With the "medline" view I can import 141 of the 200.

    With the "xml" view I cannot import anything and I receive an error about the translator.

    With the "pmid" view I do not have the option to batch import.

    I am using Firefox 16 on a Windows 8 machine. I appreciate any suggestions. Thanks
  • aurimas
    Make sure your Zotero and translators are up to date: http://www.zotero.org/support/troubleshooting_translator_issues (steps 3, 5, 6, 11) If you're still experiencing issues, please post the information from steps 6 and 11 here.
  • mobio20
    website with issue: www.pubmed.com
    search that produces issue (257 results):
    Neuron AND (BDNF[Title] AND (Cortex OR Hippocampus)) NOT (Arc OR Arg3.1 OR "Gene Therapy" OR Cancer OR Fibroblast OR Serum OR Plasma OR Synapse OR Dendrite OR Motor OR Amphib OR Arcuate OR Reflex)
    Zotero: 3.0.8- translators updated 1 hour ago.
    Firefox: 16.02.
    Folder icon in address bar produces the following translators:
    1. NCBI Pubmed - IF "summary" view is enabled.
    2. DOI - IF "medline" view is enabled.


    The report ID is:879747418

    In medline view, out of 200 possible results on the first page, after checking "select all", only 141 entries show up in my zotero folder.

    Thanks
  • adamsmith
    edited November 15, 2012
    With the "summary" view I cannot import anything and I receive an error about the translator.
    I just did that - it locks the browse down for a while, but imports all 200 items for me. You still get an error? How about if you only display 20 items?


    Your results for the Medline view are what we'd expect.

    As the fastest batch import of a larger number of items, I'd recommend a different route alltogether, though:
    After searching, click on
    "Send to" in pubmed, select "File" and "XML".
    Pubmed will create a .xml file you can download.
    In Zotero, in the gears menu, click "Import" and then open the downloaded file (by default named pubmed_results.xml ). The import will include all 257 items.
  • aurimas
    In medline view, out of 200 possible results on the first page, after checking "select all", only 141 entries show up in my zotero folder.
    Your results for the Medline view are what we'd expect.
    To help you better understand how/why this works, Zotero is not designed to work with the Medline view of PubMed search results at all. However, Medline view does list DOIs, which Zotero looks for on all pages (hence the DOI label for the icon in Medline view). For your query and 200 search results per page, the Medline view lists 147 DOIs (since not all articles have a DOI). It seems that Zotero fails to import 6 out of the 147 DOIs (the remaining DOIs may be registered with something other than CrossRef or maybe my quick and dirty scan miscounted).

    Are you still having problems importing articles from "summary" view? Otherwise, you can either follow what adamsmith is suggesting, or you can import 200 items at a time.
  • mobio20
    So I just repeated the search in the summary view and I did not gen an error and it imported all 200 entries. I performed this search at least 20 times today and I always received an error.

    Oh well. Maybe I am insane. Regardless, your XML batch import is much faster and allows imports greater than 200 files. Thanks for the help and for creating a product that is much easier to use than RefWorks.
  • DWL-SDCA
    Maybe this is useful:: Several publishers provide their metadata to NLM-PubMed and other literature databases several days before the DOIs are registered with CrossRef. Emerald Group, and Lippincott Williams &Wilkins, and at least one other major publisher (that I cannot remember right now) almost always ship metadata well before the DOI links work and sometimes even before the articles are on their websites. By the time the records have been edited and assigned MeSH terms the DOIs are usually active.

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