Upgrade StorageMaking the Switch - And what stands in the way...
I have been using Endnote for a long time, and have watched the evolution of Zotero with great interest. I've tried it out several times, too, and have watched these forums. So, is it time to switch from Endnote to Zotero? Humbly, I think it is not quite yet time. For the average, pc-using academic or researcher, a few things stand in the way. My view of those which are most important (that is, the issues that have kept me from migrating from endnote to zotero) are listed below. The great thing about Zotero is that it is a rapidly-evolving tool, and the user community is quite vibrant, so it seems likely that these issues will be resolved.
1. The organization of zotero-stored files in the zotero folder is obscure. By placing all imported PDFs into randomly named folders, zotero prevents the use of the PDFs through the operating system. Zotero becomes the only gateway to accessing those PDFs. This will require users to either rely exclusively on Zotero for access, or to maintain two separate libraries of PDFs, one for access through Zotero, and one for access via the OS. See http://forums.zotero.org/discussion/2160/is-there-any-automatic-renaming/#Item_28 for discussion of this.
2. User-modifications of bibliographic styles is still difficult. Creating styles requires use of the citation style language (a somewhat involved process requiring xml-editing), or must be done using an on-line process that is still not very amenable to user-manipulation. Furthermore, existing styles can not be modified. Without the ability to easily create your own style or modify an existing one, most users should be worried that they will not be able to use zotero to format their bibliographies--when it comes time to submit a publication and a specific style is required, zotero may not work, and the user will need to make editions manually.
3. While perhaps not a 'make-or-break' issue, I have long hoped to be able to make notes on, and assign keywords to, specific sections of text in PDFs. This capability does not yet exist in Zotero. If it did, it would revolutionize the way we use PDFs, turning them into a digital source for coded data-analysis. Although the ability to do this seems to be limited (see http://forums.zotero.org/discussion/4574/tagging-pdf-content-text-sections-images-annotations/), this seems to be the direction that several efforts are moving, among them the program Papers, (http://mekentosj.com/papers/), and perhaps Endnote (http://forums.thomsonscientific.com/ts/board/message?board.id=en-suggest&thread.id=59).
Given how farm Zotero has come in such a short time, perhaps it is not too much to think that these and other issues will be resolved in coming versions...
1. The organization of zotero-stored files in the zotero folder is obscure. By placing all imported PDFs into randomly named folders, zotero prevents the use of the PDFs through the operating system. Zotero becomes the only gateway to accessing those PDFs. This will require users to either rely exclusively on Zotero for access, or to maintain two separate libraries of PDFs, one for access through Zotero, and one for access via the OS. See http://forums.zotero.org/discussion/2160/is-there-any-automatic-renaming/#Item_28 for discussion of this.
2. User-modifications of bibliographic styles is still difficult. Creating styles requires use of the citation style language (a somewhat involved process requiring xml-editing), or must be done using an on-line process that is still not very amenable to user-manipulation. Furthermore, existing styles can not be modified. Without the ability to easily create your own style or modify an existing one, most users should be worried that they will not be able to use zotero to format their bibliographies--when it comes time to submit a publication and a specific style is required, zotero may not work, and the user will need to make editions manually.
3. While perhaps not a 'make-or-break' issue, I have long hoped to be able to make notes on, and assign keywords to, specific sections of text in PDFs. This capability does not yet exist in Zotero. If it did, it would revolutionize the way we use PDFs, turning them into a digital source for coded data-analysis. Although the ability to do this seems to be limited (see http://forums.zotero.org/discussion/4574/tagging-pdf-content-text-sections-images-annotations/), this seems to be the direction that several efforts are moving, among them the program Papers, (http://mekentosj.com/papers/), and perhaps Endnote (http://forums.thomsonscientific.com/ts/board/message?board.id=en-suggest&thread.id=59).
Given how farm Zotero has come in such a short time, perhaps it is not too much to think that these and other issues will be resolved in coming versions...
I do believe we need better ways to add new styles and correct/update existing ones, but the Endnote approach is actually a step backwards. because it effectively forces users to have to maintain their own styles.
I did a quick, WAY incomplete, skeleton of a demo of what I'm hoping to see in terms of a better online style creator and editor here. What software does support this functionality? Certainly Endnote doesn't.
Another factor that's reducing the importance of this is that Zotero gets better in renaming attached files and desktop searches on computers are getting better.
@2: I think this currently is a bigger issue than Bruce says it is - making easy adaptions to existing styles should be feasible without asking for help on the forums - although I agree that there is a bunch of us here who are always happy to help.
@3: I think the original point of the author was to say that other programs are moving into that direction and that Zotero shouldn't miss the train. Qualitative research tools for the social sciences, I believe, do provide that functionality.
Generally I agree these seem to be relatively minor issues, that for many researchers should be outweighed by Z's advantages (and, since I do have free (as in beer) access to Endnote I think I can reasonably make that claim).
I think there are other issues - e.g. the current problems Zotero faces in including formatting in citations (italics etc.) that - depending on your discipline - might be bigger issues - and I believe they are currently being addressed.
Thanks for the response.
Regarding #2, I think it is commendable that the community will respond by creating bibliographic styles. Even so, I'd like to be able to manipulate styles myself, without needing to be xml-savvy. My fear is that I will be racing to a deadline, attempting to output a document, and unable to get commas to appear in place of semi-colons, as required by a publisher... I liked the look of your hypothetical online style creator, btw.
Regarding #3, currently Papers offers some of this functionality (ie writing notes to a page view of a PDF; see this discussion for some limitations: http://mekentosj.com/papers/forum15/viewtopic.php?id=1407 ). Skim is pretty much there (http://skim-app.sourceforge.net/). The Endnote forum discussion linked in the initial posting contains a statement from a member of the Endnote development team that they are heading in this direction, too ( http://forums.thomsonscientific.com/ts/board/message?board.id=en-suggest&view=by_date_ascending&message.id=386#M386) .
Regarding "this is overblown", sorry if my post seemed like an attack on Zotero--that was certainly not my intention. I was interested in suggesting some of the reasons why, in my opinion, it is perhaps not yet time (for me, at least) to make a complete switch from Endnote to Zotero. I'd be very happy to be able to see Zotero as the solution that will allow me to do what I (and other similar users) hope to be able to do with a reference management program. It looks like Zotero is on the way there, and my intervention was merely to suggest a few items that could be improved so that zotero can arrive there...
Jon
The other two programs, as correctly noted on the endnote forum - are MacOS specific and only possible because of the (terrific) pdf features of MacOS - but Zotero is _actually_ cross platform (as opposed to Endnotes fake cross-platform) and that does make everything involving pdfs a _lot_ harder.
E.g. in Linux, pdfs in general are very poorly handled.
As for your concern about deadlines and such, I hear you, but a) as I said, generally people can help you, and b) if the worst case scenario is you have to spend 30 minutes on the final document cleaning up some minor details, is it really that bad; particularly if you save hours elsewhere in the process because of the superior design and functionality of Zotero?
@adamsmith: It's not that it's trivial; it's that sometimes particular solutions to the problem are worse than none at all.
Example 1: adding support for reading Endnote styles, while I strongly believe perfectly legal, nevertheless brought a lawsuit. Baseless as it is, it's still a distraction.
Example 2: simply recreating an Endnote-like approach to a style editor in Zotero would have significant downsides in my view: much more difficult to create and more complex to use, specific only to Zotero, result in styles that are likely to be harder to maintain and debug, and so effectively require users to do it themselves, etc., etc.
I used to find this a problem, and posted about it early on. But I'm reconciled to zotero's placement now as (a) desktop search finds them for me for any other purpose and (b) if I ever move away from zotero it will be easy enough to do a quick search through storage and dump all the pdfs elsewhere. As for automatic renaming, zotero's automatic pdf download hasn't worked for me in a long time, so I name them myself.
#3:
I just use one of the pdf readers that allows annotations. Though the ability to link through keywords to zotero would indeed be marvellous.
I do always use a proxy, and guess that must be the problem. I did post a number of threads in the relevant category about the translators involved a while back.
CB, if you're having trouble with Z translators and doing manual PDF download instead, I highly recommend the Zotfile plugin. If you highlight an item in Z and hit the Zotfile button, it grabs the most recent file from your downloads folder (or other specified directory) and brings it in to Z under the highlighted item and even renames it. It also deletes the file from your downloads folder, so that the next-newest downloaded file is now the newest. This means that as long as you work in reverse chronological order, you can download a stack of PDFS and then bring them into Z one by one using Zotfile. IF you use Zotfile, take a few minutes setting the config files, it'll save you time later.
http://www.columbia.edu/~jpl2136/zotfile.html