Pubmed behaviour

SalishSea
First, apologies for multiple postings, but my postings to Site-translators has not received any responses. Here's a full description.

I wanted to document how Zotero behaves when I use PUBMED, and ask if it might behave in a slightly different manner. My concern is that Zotero only downloads PDFs rather later in the pubmed search game than I would like.

If I begin with a pretty standard VPN-ed connection to pubmed via my university. I search for a set of papers of interest. Zotero is of course aware of the papers in the pubmed results page, and by pressing the icon, I can select the paper(s) I am interested in and (of course!) Zotero downloads the citation.

However, when I explore the Zotero database for these papers or for a single paper, the citation information is there, but not the PDF.

So, if I want the PDF, I have to focus on a single article and not on a set of articles. I select a single article within pubmed, and bring up the pubmed details into the browser. Zotero is likewise aware of this page as well, and if I select the zotero icon from the browser navigation window, the citation downloads into Zotero
However, again, no PDF.

The only way I have found to get the PDF is to press on the “Full Text” icon from the article-specific PUBMED result, and be sent to the journal-specific web-page.

When I use the Zotero icon from this page, Zotero captures the PDF and the citation information.

What I wish would happen is that PDFs could be downloaded right off the initial pubmed result screen, and consequently that I could have PDFs and citations for multiple selected articles in one step.

Is this possible? Can you even guess at whether this is a quick fix or is it big and (I fear) site-specific problem.

Thanks for a great product.
  • mikowitz
    Sure, I'd be happy to look into this. Thanks for pointing it out.

    What would help a lot is if you could copy and paste here links to a couple of example sites: one for a search page that does not save PDFS, and one for a full text page that does save a PDF attachment. That should help us figure out where the problem is coming from. Thanks.
  • SalishSea
    Sending to your email. Many thanks.
  • SalishSea
    edited April 8, 2008
    As of today, it appears that the new pubmed interface works almost seemlessly with Zotero including the long-awaited ability to download multiple citations and their associated PDF files! Wow!

    Kudos to what I suspect was a joint NLM and Zotero effort!

    Small bug also filed in this forum re: diacritical handling in author names.
  • Con_Sole
    Hi! For me the problem still exists. From pubmed I1m not able to grab any PDF automatically. I have to go to the page of the journal. From there Zotero is automatically downloading the PDF file while adding it to my database.
    http://www.ncbi.nlm.nih.gov/sites/entrez here entering wrn as keyword and selecting reference 6 no PDF download
    reference 6
    http://www.ncbi.nlm.nih.gov/pubmed/18337721?ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
    still no PDF download while adding to database

    going directly to the journal:
    http://www.nature.com/nature/journal/v452/n7186/abs/nature06736.html;jsessionid=8E2C6CF0B0BC7C277224C702CF3D8F5C
    It is automatically downloading PDF while adding reference.
    Using: Firefox/2.0.0.13 on XP SP2 updated regulary

    So is it possible directly from pubmed? If yes, how?
  • SalishSea
    I think the issue may be two-fold. First, I suspect you need the development version of the plug-in which is described and available here:

    http://dev.zotero.org/svn_and_trac_access

    More importantly,when I posted this a couple of days back pubmed had a different interface, and each citation from a search had a PDF link (along with other text options). That interface is no longer up at pubmed.

    I will write NLM and see what they say.
  • SalishSea
    Ahh, try to search the PMC not pubmed databases... I don't think the content is different, but the display is, and Zotero is able to scrape the PDFs from PMC. Database is "set" in fill-in box in upper-left of pubmed/entrez search screen.
  • Con_Sole
    Thanx the PMC database is more or less the same like searching Pub-Med.... anyway it will do for me for some time.... Thank you very much...
  • SalishSea
    edited April 14, 2008
    This thread began as a request for Zotero to capture PDFs from multiple hits as returned from a pubmed search. Through a change to the PMC database (from the default PUBMED), or through improvements to Zotero, or some combination of things, this amazingly helpful feature is now functioning.

    Can someone close this thread? Thanks again Zotero!
  • SalishSea
    As for the differences between PUBMED and PMC see:

    http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppmc.section.pmchelp.PubMed_Central_Quick#pmchelp.Why_do_I_get_differe


    So, still big differences between PUBMED and PMC and PMC is no replacement for PUBMED.


    ------------------------

    Why do I get different search results in PubMed and PMC?

    PubMed is a database of citations and abstracts for millions of articles from thousands of journals. It includes links to full-text articles at several thousand journal web sites as well as to most of the articles in PMC.

    PMC is an electronic archive of full-text journal articles, offering free access to most of its contents. PMC contains over one million articles, most of which have a corresponding entry in PubMed.

    For a comprehensive search, it is advisable to search PubMed and PMC separately for the following reasons:

    * PubMed does not have citations for certain types of PMC material, such as book reviews, that are considered out of scope for PubMed. Currently, there are no plans to include them in PubMed.
    * PMC includes research articles that are outside of the scope of PubMed subject indexing. These include research articles whose subject matter is primarily non-biomedical (e.g., physics, mathematics). Currently some but not all of these PMC articles are indexed in PubMed, although eventually all of these articles will be indexed in PubMed and will have corresponding PubMed citations.
    * In addition, articles published prior to 1966 (and added to PMC via the Back Issue Digitization project) generally will be in PMC for several months before appearing in PubMed. Citations and links for these pre-1966 articles are added to PubMed one journal at a time, after all of the back issues for that journal have been added to PMC.

    Also note that searches in PMC and in PubMed will generate separate search histories. (A separate search History is kept for each of the Entrez databases, although the search statement numbers will be assigned sequentially for all databases.) The History tab is located on the PMC Search page.
  • sagearbor
    I appear to be having this problem in chrome, 5 years after this resolved post (I am new to zotero though and have never downloaded pdfs in bluk so maybe I am doing it wrong). In either pubmed or PMC if I click the folder in the address bar and choose to download all, the references are downloaded but not the pdfs. I have selected only opensource articles so the pdfs are available. I have not switched to a development version of zotero, thinking that was needed after 5 years. I have the standalone version of zotero
  • adamsmith
    in pubmed that's expected - pubmed isn't a full text database and while we may one day be able to follow the link to the publisher on the pubmed page, that has never been possible and likely won't be for some time to come. SalishSea above when reporting getting PDFs from Pubmed had used PMC.

    PMC should import PDFs, though, and I haven't seen any reports to the contrary. Please post a URL for a _single_ article (I want to keep this as simple as possible for troubleshooting, so don't use the folder icon, but click through to the item view and use the article icon) that doesn't come with an attached PDF.

    Are you getting PDFs attached on any other database? E.g. here? http://www.energsustainsoc.com/content/2/1/6 (open access)
  • sagearbor
    Click through for a single article as you suggested works, the pdf is downloaded. However trying to do in bulk with the folder does not (sorry we will have to look at a more complicated scenario since that the only place its failing). Below is an example link:

    http://www.ncbi.nlm.nih.gov/pmc/?term=butte+stanford+2012+patel
  • adamsmith
    OK, I can confirm that. Should be fixable, I'll let you know when this works.
  • adamsmith
    The translator fix is now up. Your version of Zotero will automatically update within 24hs, or you can update manually using the "Update Now" button in the "General" tab of the Zotero preferences.

    Any problems let us know.
  • sagearbor
    Its fixed (I verified in PMC). Amazing turn around time, thanks so much. Better than a company in support time. One more question, I couldn't find the right site for. Can you paste a link to a list of the sites that support this bulk download of pdf's by zotero, such as PMC. I'm not sure what you mean by "pubmed isn't a full text database", but I assume that means PMC does keep the pdf's locally so you can easily pull there.
  • adamsmith
    I assume that means PMC does keep the pdf's locally so you can easily pull there.
    that exactly. We don't have a list of sites that support PDF download, though generally we try to support it whenever the PDF is available on the site, which means it's supported on major databases (JSTOR, EBSCO, PMC, Proquest...) and major publishers (Elsevier/Sciencedirect, Springerlink, Taylor&Francis, Wiley, PLOS etc.).
    If you find one that you think should work and doesn't start a new thread and we'll see if it's possible. Always provide a sample URL.
  • chrislux
    Hi AdamSmith: I too am trying to add multiple citations WITH PDFs and don't seem to have the 'fix' working for me. If I go to http://www.ncbi.nlm.nih.gov/pubmed/?term=lux+ct and click Save to Zotero, I get no PDFs. If I go article by article I do. Can you help me?
  • adamsmith
    you're looking on pubmed. As I say, PDF download only works from PMC.
  • chrislux
    I see. I tried this link: http://www.ncbi.nlm.nih.gov/pmc/?term=lux+ct and only 1 of 3 works (one doesn't try, one tries and fails, one works). Thoughts?
  • chrislux
    Looks like most of the articles not working are from Blood. PMC seems to be linking only ePub and you have to link out to the Blood site directly then the PDF is housed there. Can Zotero 'link out' automatically to find the PDF?
  • aurimas
    Not currently, but in theory, yes.
  • chrislux
    Playing with things further, it appears that several journals in PMC are being moved to ePub and require linking out to get to a PDF. I'm sure it's no easy task keeping up with all of the constant changes on so many site. (I'm not complaining, you guys rock!)
  • adamsmith
    While linking out requires changes in Zotero that are still a bit out, we should be able to get the PDF for the 3rd item on that page by adjusting the translator. Will try to take a look.
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