Zotero Alternatives

QwertyFive

I have been looking for a program like this for a very long time, and stumbled across it while looking at FF's campus edition. I don't use firefox (opera) so using Zotero is a bit of a problem for me, although I have been opening FF up everynow and then to play with Zotero in preparation of potentially using it for upcoming research projects.

Anyway, I am wondering what zotera-like applications exist (commercial or free). Mostly, I am interested in the following features: the ability to add notes to a document, especially with good formatting capability, and the ability to have documents organized by author or field. I don't mind creating folders or tags for these sub divisions, or inputting the bibliographic data myself. Zotero seems to have this except for a few problems - extremely basic note taking capability, and an apparent inability to attach notes to folders locally stored.

So, if any Zotero like alternatives exist, particularly as stand-alone desktop clients, I would be very interested in knowing about them.

bdarcus

Zotero seems to have this except for a few problems - extremely basic note taking capability ...

This isn't really true. The existing Zotero note functionality is much more powerful than the alternatives that I'm aware of (say Endnote). Allowing rich text is, in my view, not a feature that s important, and in many cases is counter-productive.

As for being able to attach a note to a local file: create a reference, then a link to the local file, and attach the notes to the reference.

noksagt

Anyway, I am wondering what zotera-like applications exist (commercial or free).

Comparison of Reference Management Software and Comparison of notetaking software (also see the programs listed on the talk pages for those articles).

extremely basic note taking capability

Most apps specialize in being either reference mangement or in note taking & you may not be any happier with the way these two are combined in any other program. You can use a lightweight markup language for rich text now (converting it if you need to take your notes into another program for document composition).

and an apparent inability to attach notes to folders locally stored.

I'm not sure what you're asking for....do you mean to save it as a separate file in the file system (as opposed to being stored in the database)?

QwertyFive

I should have said "an apparent inability to attach notes to *files* locally stored" (not folders). Sorry about that. The workaround bdarcus mentioned worked (thanks), but still, I wish that I could directly attach notes to files imported. In my view, rich text formatting is important, especially for some fields in academia. I am not talking about LaTeX capability here, just the ability to bold, italicize, underline, make a bulleted list, and perhaps change the color of the text (although block quoting would be nice to, since one would naturally be referencing the attached article).

Noksagt: thanks for the links. I take it you mean to say/imply that since Zotero doesn't use a markup language, I could write my note in markup, and then export it, where it would then be formatted. Was this what you were suggesting or was it something else? Sorry, I didn't quite understand your comment.

I'm still open to suggestions. I suppose my emphasis is more on the note taking, not the reference-making. I read quite a few journal articles every week and keep regular notes on them (that sometimes extend for several pages). It would be great if I could keep up the same habit in Zotero -- better still for my future projects.

raf

I don't use firefox (opera) so using Zotero is a bit of a problem for me, although I have been opening FF up everynow and then to play with Zotero in preparation of potentially using it for upcoming research projects.

I have heard this several times: people do not use Zotero because it is tied to firefox (which is not entirely true, given the fact it also operates in some other browsers). In any case, the remark does not make much sense to me.

When one wants to open a specific Endnote file or database, one uses the Endnote programme. When one wants to open a specific Zotero database, one uses Firefox (with the Zotero add-on). For any reference manager, one opens the file or database with a specific programme (Endnote, Procite, etc.) In the case of Zotero, the programme is Firefox. Why is it not a problem to use the Endnote programme, yet a problem to use any other programme (Firefox in this case) to open your bibliographic database?

In fact, one could look at it this way, for people who do not use Firefox to browse the internet, Firefox becomes a reference manager (like Endnote). At variance with Endnote, your reference manager now has an integrated browser.

raf

You can use a lightweight markup language for rich text now (converting it if you need to take your notes into another program for document composition).

Noksagt: could you please elaborate upon this? I would find especially italics but also bold in the notes very useful. As for me, it would be great to have them in the notes. Looked at the wiki page but did not figure out how this works in Zotero notes. Thanks.

noksagt

I take it you mean to say/imply that since Zotero doesn't use a markup language, I could write my note in markup, and then export it, where it would then be formatted.

Yes.

could you please elaborate upon this? I would find especially italics but also bold in the notes very useful. As for me, it would be great to have them in the notes. Looked at the wiki page but did not figure out how this works in Zotero notes. Thanks.

Zotero currently has no ability to process markup languages. But one reason people use lightweight markup languages is because they can provide a standard way to denote markup in any plain text input.

If using Markdown, you may encase a term between two single asterisks or underscores for _italics_ (really the semantic 'emphasis') and two for **bold** (really 'strong').

You would need to use a third-party tool to convert it to the format you want (although there has been talk of having Zotero use a lightweight markup language & there may be some small chance that you'll pick the same one they choose if they decide to have one).

QwertyFive

Raf: the comment must make sense to many people if it is a frequent comment on Zotero. The reasoning, at least on the surface, makes sense, since someone is likely to see Zotero as being tied with a piece of software one does not use, either because one already uses the default and thinks its ok (IE) or thinks that whatever alternative is better for whatever reason. In general, one sees FF as a browser, with Zotero being just another add-on, albeit a good one. (Being tied to FF means it is tied to all of FF's flaws as well, plus it seems to have a lot less screen real-estate even in full screen mode, and, in my view, UI issues that might be resolved with more space to work with.) I would prefer that Zotero be a standalone program, with plugins for each browser. I read that this wasn't possible in the FAQ though (at least, making Zotero *itself* (and not some minor plugin variation that communicates back to a client) a plugin of IE, Opera, etc), which is very surprising to me.

In anycase, my approach from the beginning has been similar to what you spoke of: view FF as an extension of Zotero, not Zotero an extension of FF. I would be willing to bet I am not the only one who (may) use FF only for Zotero. Right now I am looking at ways to make FF more amendable to Zotero, but that is for another thread. My purpose here is to try to find more about the capabilities of Zotero and if they match my needs. So far there have been major disavantages along with advantages of going with Zotero, but Zotero is still high on my list. When I am done going through the program and seeing what I like and what I think could be improved, I will post my comments on the feature request thread and hope the major ones go through in later editions. That's the great thing about open source, afterall.

Nevertheless, I am looking for alternatives and suggestions for alternatives -- programs designed with academic purposes in mind, specifically, research management, and academic-oriented note taking. If anyone has further suggestions, please post them here.

Matthias

I don't know whether you're on a PC or a Mac, but if the latter, Scrivener might be worth a look, it has solid note taking & writing capabilities:

http://www.literatureandlatte.com/scrivener.html

QwertyFive

Sorry, should have specified -- I have a PC. Thanks for the suggestion anyway,

scot

Note that if you plan to make use of your notes in MS Word or OpenOffice, you can use the following conventions in your plaintext notes, and use your word processor's 'Auto Format' feature to convert them to WYSIWIG formatting:

Word will Auto format the following:
*bold* and _italics_
Ordinals (1st) with superscript
Fractions with fraction character
Double hyphens with m-dash
URIs with hyperlinks

There is also some facility in Word for auto-recognizing lists and headings, but one would have to experiment to see if it produced consistent enough results to be usable. You can adjust each of the options individually.

OOo has a similar set, with slightly different markup. I think it's **bold** and *italics.*

To use in Word 2003:
(1) Check to see which options are set in: Tools/AutoCorrect Options.../AutoFormat
(2) Import or type text with *bold* and _italics_
(3) run "Format/AutoFormat.."

Neither WP lets you change or expand that list. One could write a macro in Word/OOo to implement a more elaborate set of conventions (a la Wiki-languages or Markdown or Markdown's beefier little siblings Pandoc and Multi-Markdown, both of which include simple footnote support).

The other options for converting marked-up plaintext notes would be an external application. Most , but I haven't yet discovered a slick way to get plaintext notes to something a word processor can parse under Windows. There's a drag-and-drop application for Multi-Markdown on the Mac, and Linux makes such things pretty easy with pipes. I'm sure Windows has the functionality but I have not seen it implemented for plaintext markup languages. (By this I mean, something like a single keystroke/click method of changing the contents of my clipboard from a lightweight-markup-language-plaintext paragraph to something Word can grok).

Italics is far and away the most important piece in my own work, since it is common to academic writing and needs to be 'stored' in any mechanism that wants to keep quotations for later use. So for now, a person can use _italics for Word_ or *italics for OOo* to make due.

I wonder if Zotero could implement a copy-selected-text to clipboard function which would optionally intercept the text and convert it from some LML subset to RTF or HTML, or whatever Word processors can easily accept? This might be a quick way to get some of this functionality, even if the LML concept is not gorgeous enough to convince everyone... If it's of any use as a beginning, I see that Markdown has been ported to Javascript here. The main page of the project is here, with a nice list of the benefits of simple semantic markup over WYSIWYG, and even a GUIimplementation for Markdown entry, which, if it were stable (GUIs for markup being notorious for trouble) and re-usable (the code is available and distributable, though not GPL), might be a useful way for Zotero to add this stuff. Not that I think a GUI is *at all* essential to the matter, but a who would complain if we could have our cake and eat it too?

The next step (we users are insatiable!) would be a nice *import* for web text to our ZoteroML notes. After that, some inter-note linking and citation referencing features would round things out nicely.

For reference, here is the most extensive previous discussion of using markup in notes.

bdarcus

Yeah, scot, I saw the JS Markdown and editing widget recently. It's got me thinking it could not only serve as a nice basis within Zotero for this example, but also maybe as a nice browser-based authoring solution ;-)

Matthias

Markdown is very nice and, from my experience, works great for basic note taking as well as for academic citations.

For people who aren't familiar with Markdown: paste the contents of e.g. this Markdown sample text into the form of the Markdown Dingus (online preview) page.

From an academic POV, though, I have one long-standing gripe with the core Markdown language which doesn't offer any Markdown elements for super- or subscript text. Instead raw HTML syntax has to be used for that. I've raised this issue on the Markdown-Discuss mailing list but, AFAIK, nothing has be done about it. OTOH, there are Markdown derivatives (such as Pandoc) that support Superscripts and subscripts as well as stuff like document metadata (title, author, date), footnotes, tables, inline LaTeX math, etc.

Anyways, for Zotero, I would greatly prefer a simple semantic markup language (such as Markdown) over any WYSIWYG styling methods. If the Zotero interface gives some hints about the basic markup constructs (or uses GUI tools to insert the markup), I don't think it won't be an issue for Zotero users.

magg

Personally, I would like to have a few basic formatting possibilities in Zotero while writing notes. For instance, I use it for grabbing the vocabulary from the web pages I visit. And I would like to emphasize words of particular interest in my notes to fasten my learning process. Take e.g. Google Docs - they offer a very limited yet useful set of basic formatting tasks (bold, italics, font color, lists). If you don't want to use it, then simply do not use it. That's it. But other people may find it very useful in their daily routines with Zotero.

bdarcus

If you don't want to use it, then simply do not use it. That's it.

It's not that straightforward. I'd say dumb bold/italic/underline is actually counter-productive. In my experience, these "features" actually get in the way, and they're difficult, if not impossible, to ignore.

I'm in favor of richer markup of notes, but just want something better than the typical rich-text support (which hasn't seen improvements in 20+ years, and that's not for lack of need).

mark

Just a note for who's reading this topic and wondering about its status: there is WYSIWYG editing of notes since the Sync Preview version of Zotero.

awenner

Forking the thread a little, I'd like to point out that while I'm mostly very happy with Z, it's attachment to FF leaves a lot to be desired. It can be rather slow, and it uses a lot of screen real estate, but most fundamentally my feeling is that it's not always a good idea to repurpose one functional object into another. This is recognizing that Z is trying to combine the aspects of web browser and citation manager into something with the best parts of both.

What I would really really love is a stand-alone browser, a stripped-down FF, that runs Z exclusively. Z would utilize large detachable windows and maximize its screen real-estate (rather than just allowing you to increase text size). It would still be able to access the internet, but wouldn't have or need the extensibility that the entire FF package would have.

This is probably possible right now, perhaps by compiling FF separately and creating a dedicated skin for Z.

alexuw

Not exactly what you have in mind, but you can do something like a dedicated instance of firefox for zotero by running it a separate profile. Create a new firefox profile, install zotero, and run your zotero-firefox in a separate instance with a command like (this is linux, not sure about windows):

firefox -P zotero-profile-name -no-remote &

That will run an instance with the zotero profile rather than your default profile. You can run both simultaneously.

I'm currently looking at doing this in order to have two completely separate zotero databases.