Import from zotero to endnote with pdf attachments

kieren
I'm stuck in a research group sharing a communal Endnote library. Until my university supports zotero officially I'm stuck putting the relevant bits of my Zotero collection into endnote periodically. Meanwhile I won't use Endnote because I have become dependent on Zotero's numerous, incredibly useful features which Endnote lacks.

This is fine except I want to be able to import pdfs into endnote as well.

In this case it would be great to have zotero's RIS export to provide a feature for this. Presumably it's simply a matter of finding the pdf attachment(s) for each record and adding a field like: 

L1  - file://path/to/file.pdf
For each article. A check box "include links to fulltext pdfs" could be included.

This would be great, and would presumably be easy to implement for someone familiar with the RIS export functionality.
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  • kmp
    Any method to transfer a bulk attachments to Zotero??
  • Peter100
    edited November 6, 2009
    Hi, I have the same issue. I am a new Zotero user but experienced Endnote user and want the flexibility to move between the two, at least for some time.

    I have searched the Zotero support forum and documentation for 'export pdf endnote' but can only find advice for how to import FROM Endnote TO Zotero (e.g. http://www.zotero.org/support/kb/importing_records_from_endnote and http://www.zotero.org/support/kb/exporting_from_endnote_with_pdfs). However I need help the other way: export TO Endnote FROM Zotero WITH pdfs. (Strangely this post ends with no resolution.)

    I've managed to find advice for how to export using the Zotero RDF option (including files and notes) but Endnote does not want to import the pdf(s) along with the item(s).

    My current Endnote X1 library is ca 1500 most with pdf attachments. I am considering importing them into Zotero but I want the option of exporting them out again for my colleagues who still use Endnote.
  • adamsmith
    Zotero can import the files - people have done this successfully - you can search around the forum a little more or wait if someone else remembers the thread and links you to it.
  • Peter100
    edited November 8, 2009
    As noted on the other post http://forums.zotero.org/discussion/9733/how-to-export-item-pdf-from-zotero-to-endnote/#Item_5, there are several good suggestions for going from Endnote (export) to Zotero (import) but NOT the other way around (Zotero export with pdf to Endnote import with pdf); at least I have been unable to find such advice. Apologies for the continued pestering but I'm hoping to grab some attention here. ;)
  • adamsmith
    Have some patience - dev is reading all of this. But it is Sunday...
  • noksagt
    I'm not sure if EndNote supports importing files when using any of the open/standard bibliographic exchange formats (RIS,Refer,BibTeX, etc.). Seems like a question for their forums, unless you are already able to get EndNote to import file attachments for you in some way that Zotero could tailor the export filter to.
  • Peter100
    edited November 10, 2009
    Endnote can import another EN library (append) and copy/paste individual EN references from one EN library to the other with the attached pdfs. Perhaps the command under References/PDF/Convert PDF Links to Relative Links could be utilized somehow. If the pdf links are exported with the reference it seems that Zotero could be made to locate and re-link to the pdf (especially if the pdf is on a local drive.) There is more info here: http://www.library.uq.edu.au/endnote/new_in_endnoteX.html. Does this help?

    As other forum members have noted the Endnote techies are not that responsive, but I can certainly post this issue on their forum. Still, it seems to me that Zotero might have invested interest in finding a workable solution since Endnote is one of its primary competitors and reference-linked pdfs are increasingly standard practice.
  • dstillman
    As noksagt noted, it would have to be in the standard exchange formats that Zotero supports (RIS, Refer, BibTeX, etc.), not "EndNote XML" (which changes by version, isn't documented, and isn't something we support).
  • Peter100
    As I understand it the Zotero export RDF option exports any attachment including pdfs. I am curious to know how it was assumed that this feature would be used when it was introduced? I mean if I want to access the attachments in Zotero the most direct way is drag & drop them into a folder (but of course I loose the link with the reference info). Surely the developers had more complex RDF export ideas in mind, like the scenario I am concerned with. I guess my point is that I'm a little confused by what I sense as a lack of interest in my problem... or does it all boil down to shrewd business interests (albeit in an open source context)? Another way to phrase this is: what was the intended use of the Zotero RDF export? However, I do not want to shift this too far off-topic so please only answer if it can be interpreted in relation to Zotero export for Endnote import (or other bib ref apps). I hope you understand what I'm after here... In the meantime I have posted my query on the Endnote forum.
  • dstillman
    EndNote doesn't support Zotero RDF (and almost certainly won't), so it's irrelevant.
  • Peter100
    Okay. (The RDF scenario question could perhaps be followed up elsewhere.) In the meantime I'll hope for a reply from Endnote.
  • adamsmith
    @noksagt and Dan
    in one of the threads discussing import into endnote, someone describes successfully adding a link to a pdf (manually) in .ris and importing the pdf to endnote. So it is possible in a standard format.

    @Peter - don't be silly. RDF allows exporting items and files to other zotero users in a relatively lossless way. It's also an open format, so other software could take it up (what about Mendeley, maybe even possible already?) And i can only repeat what I tell other people - it's probably a bad idea to antagonize the developer whose help you seek out.
  • Peter100
    edited November 10, 2009
    @adamsmith - excuse me, but my aim is not antagonistic or silly but rather a naive attempt to flesh out how best to make use of Zotero (which by the way I think is a fantastic piece of open source software in most other respects). For instance, I did not realize that RDF was intended for import back into Zotero. Instead I would have instinctively thought some kind of backup or copy feature would be used for that (something like described here: http://www.zotero.org/support/zotero_data)... so....

    Second point: is manually adding a link to the ris file feasible without it taking more time than attaching each pdf by drag and drop into Endnote (or whatever the application at hand)? I still have yet to find the discussion you refer to. The ones I've found refer to importing into Zotero but perhaps I've read too quickly.
  • noksagt
    As of EndNote X, 'L1' from RIS is imported as a URL in EndNote (not as an explicit attachment). Don't know if this has been fixed in later versions.
  • dstillman
    I took no offense—Peter may fairly have wondered whether Zotero RDF was included in the "etc." that noksagt and I mentioned above. But it's not, since EndNote doesn't support RDF. Being RDF, however, it uses a number of ontologies designed for open data exchange, and in the not-too-distant future it will use BIBO, which means that any software supporting BIBO will be able to import fairly complete metadata from Zotero. But it'd still be up to other applications to support RDF/BIBO, and file support would still be a separate issue.
  • Peter100
    Oh, the prospects of a fertile future.... ;)

    Clarification: No, I didn't realize that RDF was Zotero's own format. I'm a humble social scientist not a software developer so please pardon my ignorance.

    So, if I may ask, what is the take away from all of this? While we all anticipate BIBO are we still stuck or are there potential workarounds to be found with URL/RIS/RDF for Endnote X (and other bib software)? A brief summary of this exchange with some indication of next steps would greatly be appreciated.

    Thank you.
  • adamsmith
    I found it - the problem is it's not endnote but papers that imports pdfs in L1 correctly:
    http://forums.zotero.org/discussion/7961/export-in-ris-format-link-to-pdf-file/
    so while it may not help with endnote, including the L1 pdf link (or at least giving the option to) would still be a good idea, as it works with other programs.

    @Peter, as for your questions - sorry for the "silly" - it was just the "shrewd business interest" part, not the question itself that I thought was unnecessary.

    As a summary - as of now it is not looking great.
    I think getting Zotero to include links to pdfs in RIS as "L1" should be feasible and is desirable for interoperability with Papers (and perhaps other software) - Dan, any reason it couldn't do that?
    But if Endnote doesn't deal with that properly, you're back at square one for your problem.
    Everything else - RDF/BIBO support as well as importing PDFs from RIS correctly - depends on Endnote then, so you'll have to see what the friendly folks over at Thompson Reuters have to say.
  • Peter100
    Well, closure is nice, even if partial. Thank you for that. Whatever response I get from Endnote I'll be sure to post it back here. In the meantime I remain curious about what if anything comes from thinking more about RIS and URL links. If a workable sollution is found for Zotero --> Papers perhaps Papers could be used to mediate Endnote.
  • noksagt
    I remain curious about what if anything comes from thinking more about RIS and URL links.
    What do you mean by this?
    If a workable sollution is found for Zotero --> Papers perhaps Papers could be used to mediate Endnote.
    Perhaps, but only because Papers claims EndNote XML export support. I don't know how good that is. Again: it seems that EndNote doesn't properly import PDFs for formats they did not, themselves, create.
  • Peter100
    edited November 10, 2009
    @noksagt "What do you mean by this?"

    - I was simply referring to adamsmith's comments: "I think getting Zotero to include links to pdfs in RIS as "L1" should be feasible and is desirable for interoperability with Papers (and perhaps other software) - Dan, any reason it couldn't do that?"

    - and your comment, "As of EndNote X, 'L1' from RIS is imported as a URL in EndNote (not as an explicit attachment)."

    It seems to me that there is potential lurking somewhere here for a workaround (i.e. revising the Zotero RIS format to include URL links to pdfs which is then read by Endnote, Papers, etc.) but perhaps I'm mistaken...

    "Again: it seems that EndNote doesn't properly import PDFs for formats they did not, themselves, create" - yes, I agree, but somehow I'm still optimistic that Endnote could be fooled... but again I know too little about the tech side.

    PS - what is 'L1' anyway?
  • noksagt
    edited November 10, 2009
    Zotero can be modified to include information about file attachments when exporting RIS.

    But EndNote will still get that wrong when it imports them. You can see for yourself by exporting an RIS from EndNote (which will contain attachments) & re-importing it into EndNote (which will put the attachment information into the generic URL column, rather than the file attachment column; also note that EndNote's peculiar pseudo-URI scheme ('internal-pdf://') means that the links won't even work).
    but somehow I'm still optimistic that Endnote could be fooled...
    Nope. RIS will not, by itself, get file attachments into EndNote as working attachments unless they improve their importer.

    Until that happens, the only way in is through one of their proprietary formats & I really can't say how strong support for that is in software that has better import functionality.
    PS - what is 'L1' anyway?
    The tag in the RIS specification used to denote PDF attachments: http://www.refman.com/support/risformat_tags_07.asp
  • dstillman
    Does Papers support relative paths in L1, or just absolute file:// URLs? To do this properly, you would want to have an Export Files option for RIS identical to RDF exporting that created a 'files' subdirectory and copied exported files into it, but that would only work if relative paths worked. Otherwise we'd have to use absolute file:// URLs to the Zotero storage directory, which would be a rather fragile (and unportable) solution.
  • Peter100
    edited November 11, 2009
    I'm sure others with more tech experience as well as Papers experience (of which I have little to none) will want to comment here.

    In the meantime, just one question. If Zotero RDF creates a 'files' subdirectory in the export process, and relative paths are discovered an unworkable route, couldn't an absolute path be created on c:\? -- alt. the user is offered a choice of where to put the directory (if the 'c' drive is unavailable)?
  • dstillman
    Well, yes, we could still copy the files and use an absolute path to the export directory instead of the Zotero storage directory. But the main reason to include the files would be so that you could copy the entire directory to another computer and import them, and then you'd almost certainly have to do a find-and-replace on the paths before importing. Better than nothing, I guess.

    Not much point in speculating on this until we have more technical details on what Papers and other programs actually support, though.
  • adamsmith
    sorry - can't help on papers beyond the thread I linked to - it's Mac only _and_ for pay, so doubly not for me.
    I'm not sure I agree on the relative paths as a prerequisite - people who want to move from endnote to Zotero are happy that endnote is putting absolute paths (kind of...) into its RIS export. My thinking is that Zotero should do the same. But I very much see all the reasons that might be problematic.
  • Peter100
    edited November 11, 2009
    Perhaps there is a 'baby step' before tackling computer to computer export. For instance, an absolute/relative export could first be designed for same machine export where both Zotero and the client program (e.g. endnote, papers) are installed. Once the new library has been created in the other program it could be 'packaged' for copy/move to another computer. This is not optimal of course... but perhaps it's better to start somewhere than nowhere. - again, just a thought and am unfamiliar with all the techy details. ;)

    (I use a PC with endnote and Zotero/Firefox installed but for various reasons anticipate moving to a mac with Papers (and possibly Office). Is Zotero a PC only application? I just assumed it was cross-platform. Of course there is the possibility on the Mac to move between OX and Windows.)
  • dstillman
    I'm not sure I agree on the relative paths as a prerequisite
    I wasn't suggesting that they were a prereq—just that, if Papers (or other programs) supported them, it'd be preferable to use them, since absolute paths to either the Zotero storage directory or the export directory would be unportable.
  • adamsmith
    OK - with that I agree 100%. I'll see what I can find out.
  • adamsmith
    I've taken a look at Mendeley -
    L1 in an RIS is imported (and exported) as a link to the respective file - i.e. the pdf would stay in the Zotero storage folder - which seems intuitive, but hardly ideal for the given purpose.

    Mendeley does claim Endnote XML Export as well as Zotero library import, though - that may be a possible route to explore for Peter - it's free (as in beer, not in speech).

    How would I test for relative links? I tried ~/ (in linux) that didn't work.
  • dstillman
    A relative path would just be, for example, "files/foo.pdf", where 'files' was in the same directory as the RIS file.
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