Support for bibliographic software?

Druid & Martin have said much that I would say, so I’ll give my thoughts based on my personal usage.

Papers for PDF storage, reading and bibliographic maintenance. Amazing application, although more targetted at the science community and journal articles (rather than, say, book chapters). It will automatically retrieve most of the bibiliographic detail from the relevant website while you are there, can import various citation formats and you can manually enter whatever detail you need later. You can export any information you want to a dedicated reference software later if needed (see below).

DevonThink for storing non-journal PDFs and looking for actually using/searching my ever-expanding library of references. All of the PDFs in Papers are synchronised with DevonThink (DT indexes the Papers folder and includes all the documents within it. Means that I don’t need to duplicate these documents). If your budget (with academic discounts) will stretch far enough, I’d recommend DT over DevonNote.

I use EndNote for my reference software, mainly because my university has a licence that enables all students to install it for free. I only use it for tracking references in large documents in Word. Even then I sometimes find it easier to manage it manually. It has hardly been used in 3 years, most of my time is in Papers or DevonThink. If you’re not writing anything substantial for a while, I’d live with Papers and DT and just manually enter references until budget allows otherwise.

For writing, I am learning to use Scrivener. Working well so far. :slight_smile:

For editing and submission, Word or Pages. I prefer Pages, but mainly use Word for compatibility with my university computers. This enables me to work on my documents when I don’t have my MBP at hand, and allows me to print when on campus (no network printing from wireless devices at my campus).

I hope this helps (and I hope I haven’t repeated myself from earlier posts).

Tim

After seeing once again how much people love DevonThink, I decided to give it another shot. A question arose: I clicked the “Duplicates” smart folder. Now: if I simply delete everything there, am I deleting the original too? If so, is there a way to leave one copy behind? DT made me realize how many damn duplicates I have!

thanks,
s

The smart folder ought to show both (or more, if there are more) copies of the duplicated file. When I started out, I went through the duplicates one by one to check they really were duplicates, and deleted one copy of each by hand. Long-winded, but I didn’t want to lose anything. I have to say I was surprised to find that some files with different names were, in fact, duplicates. I’m not sure how you’d do a mass delete of duplicates – I’m too new to the program. Try Devon’s own forums.

Best wishes,

Martin BB.

Sorry to have to follow up on this - I am trying Endnote with Scrivener and I am getting stuck on the insert citation command. It is currently disabled (i.e. grey) in my Endnote. I tried to set up a keystroke in my systems preferences for scrivener and insert citations and that does not seem to work either.

Could one of you kind souls out there kindly walk me through how exactly I can use that universal insert citation command or what to do to make it active?

Many thanks.

Mareike,

One of the following “clarifiers” might sort something out: a) The Insert Citation command we are talking about is the one to be found (universally) on the Services menu – not to be confused with the Insert Selected Citations menu item in Endnote. b) The time to /use/ the Insert Citations menu item is when you are (frontmost) in Scrivener, not when you are (frontmost) in Endnote (though, of course, Endnote needs to be running and there needs to be one or more citations selected in it). c) The menu item in the Services menu will not be enabled unless you are clicked into a text field in the frontmost application. So, for example, if the Binder has focus in Scrivener, not the Editor, then Insert Citation will not work. d) After using Sys Prefs to assign a keyboard shortcut for application ‘Scrivener’ for menu item ‘Insert Citation’, the new key command will not be available in Scriv until you relaunch it. (If you assign the shortcut to ‘All Applications’ you might have to log-out/in or restart your Mac; can’t remember.) e) The services menu item is ‘Insert Citation’ (not ‘Insert Citations’) and needs to say exactly that in the Sys Pref setting.

To double check my earlier sketch of the process, I just re-followed my own advice (see below) from scratch and everything worked happily.

Hope something here helps. Let us know how it goes. --Greg

P.S. As a sporting diagnostician, I am going to hazard that (b) or (c) will resolve this one.

Greg, thanks so much.

I have been trying to work through this, but I still can’t get it to work.
Assigned a key stroke command for scrivner and all applications for insert citation–and restarted Scrivener. I am not sure I have found it in the services menu but that should do the trick, right? Am in foremost scriver in an editor field (and have also tried the command in Word which ought to work if it is universally assigned, right?) and no reaction so far.

I have never consciously used the services menu before, maybe I am doing something wrong there?

Sorry and many thanks for your help.

M

If you have not actually located the Services menu item, it may be that the problem is not assigning the command at all, but that the menu item is not being enabled as expected. Let’s try using the Services menu item the old fashioned way (by pulling down menus) and get that working before we worry more about assigning a key command to it.

Bring Scrivener up, and then look on the application menu (i.e., the menu entitled ‘Scrivener’). On that menu open the menu item called Services, and in the resulting submenu, there should be an Endnote submenu. the Insert Citation menu item is in there.

In short: the menu item you are looking for is in down the following menu path: Scrivener > Services > Endnote > Insert Citation.

Make sure the Insert Citation menu item is there, and see whether it is greyed out or enabled when you know you had your cursor clicked into some doc text in Scriv. Also, if there is a key command associated with this menu item, you should see it showing there. If the menu item is enabled, pick it and see if a citation inserts as expected. (Of course, we need you to have Endnote open in the background and some cite selected there for this to work.)

Let me know what you find and we’ll work from there.

–greg

Thanks, Greg. I really appreciate it.
Yes, found the services menu, yes, command is enabled in there and active, yet no keystrokes are associated with it. Went back to keyboard system preferences, assigned a keystroke to “Insert Citation” to both Scrivener and all applications and neither seems to work.

Many thanks,

Mareike

This thread has been very useful, I’ve picked up quite a few tips that I’ve implemented in my writing routine immediately. So thanks!

But with regards to getting references from eg. EndNote - let me ask - why don’t any of you simply arrange things so that you can see both your text in Scrivener and your EndNote-database and then drag’n’drop the references you want to wherever you want them in Scrivener? It works smoothly for me…

I’ve started using BibDesk a few months ago, and have found it really good for my needs. It interfaces with several online databases very well, and the UI is nice.

The only minus is that it does not have a scanning system that can work with Scrivener, Nisus or Mellel. But it is not really a problem for me, since I work this way:

  1. In BibDesk, create a new group/folder for the current research.
  2. Collect all sources in the dedicated group/folder; they are also automatically included into the general database for future researches.
  3. In BibDedsk, setup and select the citation formats for export. I use a custom format, typical of semiotic and linguistic studies here in Italy, that is rather similar to the APA citation style so common in the USA.
  4. When a citation is needed in my wordprocessor, I just copy it from BibDesk, and paste it into my wordprocessor. The pasted citation has the final appearance, ready for printing/exporting.
  5. If I delete a citation from my document, I also remove it from BibDesk’s group/folder (but not from the general database: something I’m starting to do is to create a second group/folder for the removed citations, in case I need them again in the current research).
  6. When it is time to generate the final bibliography, I copy the whole group/folder in the due format, and paste it into my wordprocessor with the final appearance.

Paolo

I don’t have the screen real estate to work by drag-and-drop like chefpogo does, but it is probably well to remember that getting a key-command for the Insert Citation service menu item is saving you one and only one key stroke. If you were to simply type command-c before flip back from Endnote to Scrivener, you could just use command-v to paste the citation into your text–instead of using the service menu item at all.

So, if the mystery of the key command that won’t stick continues, you will not have lost much. Truth to tell, I use the copy and paste way not the services menu way, because copy and paste are simply second nature, so the workflow is unfailingly intuitive–no thinking required.

–Greg

Hi,
anyone out there who found a way to integrate Zotero and Scrivener so that we can use write&cite like we do with Bookends & Co., or like Zotero does thru the plugins with OpenOffice.org and Word?
If not, any clever workaround to avoid forgetting to convert the citations on the draft when compiling the draft for the final touch in the wordprocessor of choice?

thanks,

brunus

I’m loving Scrivener. In fact, between it and Curio I’m almost completely redefining my workflow. My only limitation is in handling the citations, since I use Zotero and I’m in a technical field that uses lots and lots of citation. I’m using RTF-scan now, but it isn’t playing very well with word (which I detest) for me.
So, I’d like to second the request for citation from Zotero while using Scrivener.

Hi,

What exactly is the problem with Zotero? Doesn’t it place things on the pasteboard in the same way as Bookends and Endnote et al? It may just be that Zotero doesn’t provide that convenience, but if you describe the problem or difference, I’ll take a look.

EDIT: Actually, looking at their site it seems that it’s necessary to write a plugin, but the documentation on doing something like that looks scant (at least for someone with my low level of experience in doing something like that - and double that with the fact that I’m no java-scripter). They provide plugins for Word and OpenOffice, but it’s up to other developers to provide plugins for their programs, and I’m not sure how big a job it is. If any of you can find any solid information or more examples around that might give some indication of how to do something like this with a Cocoa app, feel free to post the links here and I’ll have a look at it.

Thanks,
Keith

Could you say more, perhaps in the Other Software section, about how you use Curio in writing? I keep looking at it and wondering how or if I could use it. I’m not a mind-mapper; prefer to arrange my notes in top-down outlines. But I use images, films and links a lot when teaching; and Curio looks like it might be a decent presentation tool.

Hi, Keith. Thank you for your willingness to take a look.

The team I’m working with now is madly trying to find a tool that will work for our collaborative style and mass document production, and it’s been hard. So far, Scrivener is the closest. I’ve already lost the LaTeX fight, which isn’t surprising, and I really don’t want to lose the Zotero fight since it’s organization works well for me and we can have multiple users on the same library with it synced against our own server. I’m predisposed to like Zotero (bibtex-friendly, free, open, developer-friendly, …) but I’m also not a Java or Cocoa person (I like fortran). So I’m not readily able to write a plugin. If I can help with testing or anything along the way, though, I’m entirely willing!

As to where things are going wrong for me, really it’s a sort-of-works-but-with-extra-steps. To use Zotero with Scrivener, it’s 1) write in Scrivener and use {Author YYYY} for citations; 2) export to RTF; 3) use Zotero’s RTFscan; 4) import file into word (blech) and finish formatting. Along the way somewhere is add or fix EndNote references for the other sections. I realize this is an anomalous workflow.

Zotero dumps citations into the clipboard just fine, and I can dump them in as complete citations that way. Unfortunately, I need to manage on the order of 100 per article, and they change location as one expects, and (here’s the big issue) the other main contributor uses EndNote. So, I need to be able to drop in the in-line citation and then have everything work together at the final compilation. Taking the document out to RTF and then scanning isn’t going to fly for us.

I’m new to Scrivener, so it may be that I just don’t understand how to put the references in, but I think that when I dump a citation in from something in my Zotero library, I’m literally putting a note at that point and the formatted citation information, not something that will be processed into a bibliography later. I should also point out that I’m fairly new to using anything other than vi-latex-bibtex, so I’m a bit out of water.

And, Druid, sure, I can talk a little bit in the other thread about how I’m using Curio in writing. The short answer, though, is managing the supporting research - lots of image files (data plots or figures I or others have made) with comments and notes and their sources. I never thought I was a mind-mapper (I am now, completely and devotedly), and that’s what got me into Curio originally – it’s very flexible.

Thank you guys for your help!

-Caroline

Hi, Caroline,

Mere Scrivener and Endnote user here, but I thought I might be able to usefully pitch in:

If Zotero and its rtf scan function is anything like Endnote and its rtf scan function, then you and your team should definitely be placing only “temporary citations” into your Scrivener text. Your bibliography software has the task of scanning the rtf, replacing the temporary citations with propertly formatted in-line citations, and tacking on a generated bibliography list at the end. It sounds like you are trying to manually manage the bibliography-making, so you must not be doing things this way right now and that is likely the source of your trouble. Notice: The automatic bibliography generation is entirely dependent on your only putting in the “temporary citations”, not fully formatted in-line citations – this is how the software recognises what sources the document is appealing to and from this builds the bibliography.

So, right now, I am not yet seeing why the workflow cannot work for your project. (If you do not have all the needed sources in a single database–Zotero or Endnote–then you might have to scan the rtf twice to process all the references. That is definitely an extra trip around the block, but really that would be an hard-to-work-around artifact of your team using unshared databases.)

–Greg

P.S. If Zotero (which I have not used) does not provide this kind of bibliography-from-in_text-citation function, I personally think you should take a more serious look at using a program which does–since the documents you deal with have lots of bibliographic data to manage.

Hi Caroline,

Yes, as Greg says, it’s quite normal to scan the exported RTF - this is what users or Endnote, Sente and Bookends do too. You certainly wouldn’t want to scan the Scrivener project itself. Scrivener is intended for hammering out the draft, so presumably the time you are ready to process the citations and bibliography etc, you are at a stage where you will want to take the work to a word processor for formatting anyway.

Of course, you don’t have to import into Word - there are better options, such as Nisus Writer.

All the best,
Keith

Also, isn’t there some kind of Zotero/OpenOffice integration? So you may be able to export to rtf, open with OpenOffice and scan from there. (OpenOffice is probably no better than Word, but it’s no worse, either, for most things…)

Thanks for the replies. I’m certainly not trying to be obtuse. I just am not used to non-commandline approaches to these things, or to working in groups that won’t use commandlines. And I know that we’re trying to do something non-standard (if I could force a single library, I’d do it, but I can’t, and it would be Zotero anyway, for reasons enumerated below). I’m very appreciative to you all for your comments and insights.

There aren’t any issues with using RTF-scan itself (and yes, I mean scanning the compiled draft in rtf form). That is straight-forward. But, if my playing with EndNote is correct, Scrivener+Endnote(+Word) users are not using RTFScan because a plugin exists to use write-and-cite and generate the bibliography at compile. Am I not correct in that understanding?

If I am correct in that understanding, then I would guess that the citation information from the write/cite insertion commands is somewhere, and a plugin for X_bibprog could dump into that list and the whole thing could be program agnostic, and I might be able to code some of that. If I’m incorrect, then the whole discussion is different (and I may have just made the traditional newbie bloomer of thinking something really, really hard is easy, for which I apologize).

I wasn’t very clear about what we’re trying to do. We’re using both libraries (EndNote and Zotero) simultaneously. We need the document and bibliography to be compiled once, with (apparently) a single step. I say apparently because it can be several steps hidden in a wrapper, and that’s fine, but if I have to ask the other contributors to go through multiple steps to generate the final public document it’s over. This is for a long-term solution, not a single document. It’s not a fun position to be in. For the purposes of this discussion, Word, OO, et al. are interchangeable, I think. I am desperately trying avoid managing the references manually.

As a side note, if anybody has suggestions for a collaborative tool that allows shared editing, non-external-server storage, simple templating (with figures and captions), non-markup editing, multiple bibliographic packages, version control, export to word (not my fault!) and any other flourishes (I know I’ve forgotten some of the list), I would love-love-love to hear about it. As I said, Scrivener is by far the closest currently. Plus, I think it’s fun.

As for what Zotero does(n’t) do – as far as I can tell from using it for the past 18 months it does literally everything (including inline citations, and generates bibtex keys) that any other package does - except have a plug-in for Scrivener - but in a free and open manner. No downside to that. Oh, it may have something most others don’t, and that’s working from within the browser, so that whenever you trip over something it is a single click to store it. For most scientific articles, that includes grabbing the pdf and all the citation information. And it allows for multiple users of a shared network-accessible library (on our own server) that also stores the pdfs. And works on all platforms. I’m amazingly pleased with it – it’s efficient and effective, and the best collaborative library I’ve seen.