Best workflow for attaching PDFs to items

delenca
I've recently installed Zotero (beta rc5) on a new laptop (Mac Book Pro, 10.6.2, Firefox 3.6)) and I would like advice on the most efficient way to download the pdf of an article together with the reference entry to the item.

Right now what I do:
1) Pubmed search
2) Open Zotero and make sure I am in the correct folder
3) Click "Save to Zotero" on the address bar of browser -> item gets created in the library
4) Then I click on the Journal icon on the pubmed webpage and eventually download the pdf
5) Then I navigate in the Finder to the article in question and drag it to the item in the zotero library
6) Then I rightclick no the pdf in zotero and click "Rename per parent metadata" (or whatever it

One solution I don't like is directly downloading Ref + PDF from the journal website b/c I have found that the translators for the different journal website can be different enough to create heterogeneity in my library. By keeping all references from Pubmed I minimize that variability a bit.

In the past, on my PC, I could sometimes speed up the process by dragging the pdf link address on the address bar of the webpage directly to the item in zotero. However, on the Mac now when I click on a pdf link it never opens in the browser but rather in Preview outside the browser. There must be a way to change that behavior but I haven't found it.

Thanks for any advice,
-Alex
  • migugg
    you can shortcut 5)-6) with using zotfile
    http://www.columbia.edu/~jpl2136/zotfile.html

    I think to adress the problem
    "However, on the Mac now when I click on a pdf link it never opens in the browser but rather in Preview outside the browser. "
    you need to setup a pdf-viewer as firefox add-on, for example
    https://addons.mozilla.org/en-US/firefox/addon/7518
  • noksagt
    One solution I don't like is directly downloading Ref + PDF from the journal website b/c I have found that the translators for the different journal website can be different enough to create heterogeneity in my library.
    Heterogeneous in what way? Some sites provide mediocre data & some issues may be fairly cosmetic (i.e., citing them from Zotero may often produce identical citations, whether the data is from PubMed or the publisher). But there may be some issues with some translators that can and should be corrected.
  • delenca
    "you can shortcut 5)-6) with using zotfile
    http://www.columbia.edu/~jpl2136/zotfile.html"

    That's true - I had it installed on my PC before. I just thought that Zotero had made the automatic renaming a feature in later updates.

    (side question: how do I quote comments in this forum?)
  • delenca
    "heterogeneous in what way? Some sites provide mediocre data & some issues may be fairly cosmetic (i.e., citing them from Zotero may often produce identical citations, whether the data is from PubMed or the publisher). But there may be some issues with some translators that can and should be corrected. "

    I have noticed this for a while. For example, fields such as Journal Abbreviation and page numbers seem to be filled differently (or in some cases left empty) by the different translators. There might be others. And if I remember correctly this leads to non-uniform results in the end-product (i.e. citations), so from now on I have just decided to pick up data from Pubmed. At least this way the only variability comes from the evolution of Pubmed + Pubmed's Zotero translators.
  • ajlyon
    (side question: how do I quote comments in this forum?)
    Use the <blockquote>tags around the text you want to quote</blockquote>, then select "Format comments as Html".
  • maggiejmin
    I have the plugin but has anyone figured out how to make notes on the pdf? the toolbar that has all the highlighting and annotation tools does not come about when you are viewing one of these pdfs in your firefox browser.

    when i'm trying to organize my files, I first try and find the html version of the paper. Those aren't usually very pretty though so I open the pdf of it in my firefox browser then save the pdf as an attatchment to either the full article in HTML or just its abstract. This way the meta-data of the article can be automatically generated from the webpage, and i have an aesthetically pleasing pdf. But who can solve my problem of not being able to take notes on the pdf using zotero?
  • adamsmith
    http://www.zotero.org/support/kb/highlighting_and_annotating_pdfs
    http://forums.zotero.org/discussion/987/can-i-annotate-my-pdf-snapshots

    remember, forum search is your friend.
  • kithairon
    @maggiejmin: If you happen to be on a Mac I suggest you have a look at Skim, an excellent opensource PDF-Tool to view and annotate pdfs. Just configure FF to open pdfs with this app. There are similar tools for Windows and most likely Linux.
    http://skim-app.sourceforge.net/
  • delenca
    On the Mac I just use the built-in Preview. The latest version (comes with Snow Leopard) lets you annotate to your heart's content. On the Windows side I use(d) "pdf-xchange" (which I liked far better than Adobe's product).
  • delenca
    But back to the topic:
    I don't really mind steps 1-3. The real problem, annoyance comes with steps 4-5, when the journals website does NOT link directly to the pdf file. In those cases, dragging the pdf link to the Zotero item creates a link to the script that downloads the pdf rather than the pdf itself. Which forces me, as my only option (that I can see - correct me if I'm wrong) to click, download to desktop and then drag to the library. If I could get around this problem, I would be more than happy with the rest of the workflow. An example of a such a paper/journal, taken at random:
    http://mcb.asm.org/cgi/content/short/21/1/164

    On 2nd thought, there might be a workaround, because if you grab the article the journal website using "Save to Zotero" address bar gizmo and you have it set to automatically download the pdf, the Zotero translator knows how to resolve the pdf script/link to download the pdf itself.

    I suppose a really, really cool thing is IF we could change the NCBI Pubmed translator so that we could have it follow the journal links on the right (if they exist) to automatically download the pdf from the journal website. THat would be super cool. That would reduce my workflow above to steps 1-3 and allow me to use Pubmed for all my referencing (thus avoiding the worries about the heterogeneity of data from different translators, etc).

    Thanks for your attention.
    -Alex
  • adamsmith
    Alex - people have mentioned this as a desirable feature of pubmed, but I don't think this is something that is likely to happen any time soon - the fact that different articles on pubmed are stored in different databases makes this more than just a little tricky.

    Going back to your first post - you should be able to get FF to display pdfs in your browser -
    I don't know a lot about Macs, but this seems like an option:
    https://addons.mozilla.org/en-US/firefox/addon/7518
    there might be other ways - in general that's where I would look for a solution.
  • delenca
    Hi Adam,

    Yeah, I forgot to respond to that option (display pdfs in browser). Even doing that, those sites end up with pdfs in the browser that I can't drag to Zotero (i.e. the link in the address bar is not the link to the pdf but still to the script, or something like that).

    Thanks,
    -Alex
  • adamsmith
    but you should be able to attach the pdf to an item by clicking on the paper clip and select "attach snapshot of current page".
    If not - could you give me an example of such a page?
  • delenca
    I tried that and it doesn't download the pdf. It creates a browser link instead.

    For example you can try the one I mentioned before:
    http://mcb.asm.org/cgi/content/short/21/1/164

    Thanks,
    -Alex
  • adamsmith
    ah yes, I thought so - the pages that work like that (including the one you link to and all Sage journals) usually have a small link to "View article in full window" on the bottom of the right frame. That should work for you.
  • delenca
    Ah, ok. That works!

    Now I have 2 minor Feature Requests vis-a-vis PDF downloads. I'll give them their own threads but in a nutshell:

    1) Allow us to right-click on link to pdf to "save pdf to selected zotero entry"
    2) Feedback in zotero window that pdf is being downloaded

    Thanks, ALex
  • aaronchall
    I would like to suggest adding to the knowledge-base article a little bit more detail about this. "Begin by dragging your existing PDFs into your Zotero library. Once they appear in the middle column, select the ones for which you wish to retrieve metadata." This instruction is not very clear. I attempted to drag the file there from my desktop, and this did not work for me. I attempted this in various ways, dragging to different sections/columns in Zotero. Wasted time and got frustrated.

    I then attempted to drag the link, and this worked. The rest was intuitive: right click to collect metadata, be informed that a plugin needs to be installed, be offered the chance to install it, accept, right click it again to collect metadata, it disappears and reappears as a child document of an almost perfect Bib entry. Then right click and select rename based on the parent item, and I have my entry just the way I wanted it.

    Is there a way for me to drop a PDF from my desktop into Zotero? I have more I would like to do this with.

    Aaron
  • adamsmith
    dragging the file from the desktop should work, actually. And I think that's what's meant here. Not sure why it didn't for you. File drag&drop is broken on Linux if that's relevant.
  • aaronchall
    I use Ubuntu, so that's relevant! It would be nice if that were noted in the knowledge base! (When might it be fixed?)
  • adamsmith
    added this to the instructions - you can use the "store copy of file" function in the add new item menu (green plus) instead. Note that this takes a while and freezes FF - that's not a crash.
  • aaronchall
    Thanks for that tidbit. I may have known that before, but I had completely forgot it...
  • lqvang79
    Delenca and Others:
    I have done with many journals this way:
    Do one time: Open Zotero preferences: On "General" Tab, Miscellaneous section, tick this option: "Automatically attach associated PDFs ..."

    With that done, you only have to do steps 1-3 as you mentioned.

    FYI, I am using Snow Leopard, Firefox 3.6, Zotero 2.0
  • Matthew HudgensHaney
    (side question: how do I quote comments in this forum?)


    Use the /block quote/ tags around the text you want to quote //block quote/, then select "Format comments as Html".
    Back to the side question briefly: Is there somewhere on the site where information like this is gathered? It took a lot of searching for me to find out (here) how to quote.
  • adamsmith
    not on this site, no, but you can look up simple html code all over the internet and I think it's pretty clear that it's html code that you need from the fact that is says "Html" next to the box that you have to check.
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