Totally Unorganized, too many references, papers printed out, CHAOS!

[yoyo17]

Okay so maybe it's not bad as other people I've seen.  But I have a hard time lately managing a lot of papers/references.  I'm learning and working on 2 and maybe 3 projects.  I'm trying to keep all my references separate and divided by topic but still...incredibly difficult/painful to do this. 

 

First what I did was use Endnote and search up references.  I would read and then import.  Then use the "Groups" function on the left to divide it up.  Problem is this...I can't make notes on it, highlight or write comments on it and not as flexible to write on it how I want.  Even if I find the pdf on Endnote, it's kinda hard to read as it only looks at a screen shot of the paper and not the whole paper like a printed copy would.  The other problem is I really like paper format.  There is something therapeutic about flipping a page, writing on the margins that makes absorbing the information much easier.  It also allows me to focus better and not get side tracked by being on the computer and wandering off.  It also gets easier to lose track of all the refernces and finding them..i don't know.

 

Then I printed out all the articles but this becomes a waste of paper and money.  It's also difficult to organize because some papers fall under multiple categories.  But I feel so much better and get more out of reading a hard copy.  I can also bring a hard copy anywhere like lunch and read it.  I can't bring a computer everywhere and read it.  Hard copy for me is much more flexible.

 

So how do you organize references?  Is there a way to "star" references on Endnote as being important to use and look back on?  A way to at least organize my groups and pdfs inside on computer hard disk and not just on Endnote? How do you organize?

 

FWIW, I'm a science research background.  I'm open to all others, just I don't know if there's differences in how humanities/social sciences do things versus science. But I'd like to hear from everyone.  Thanks!

Edited June 15, 2015 by yoyo17

[TakeruK]

I use Mendeley (https://www.mendeley.com/). Ignore all of the "social media" / LinkedIn type stuff they have (well, you can use it if you want, but don't feel like you have to, I mean). 

 

Here's my general workflow:

 

1. I find the paper online, in PDF form. I download it to a special folder that is "watched" by Mendeley. (alternatively, I can download it anywhere and import it to my Mendeley library).

2. I open up Mendeley, and find the paper in the "Recently added" section. I then move it to various folders for the projects I am working on. They're like Gmail folders--you can put a paper in as many folders as you want.

3. I then double check the bibliographical information. I can use DOI lookup, PubMed ID, arxiv ID, etc. if necessary

4. I also have certain tags that I use for various methodologies or papers that are specific to certain experimental samples. I usually add these tags right away (these tags are searchable)

5. I then read the paper and make electronic annotations as necessary (also searchable)

6. Ultimately, when it's time to write the paper, I can export all of my library into a .bib file and use BiBTeX to add it to my paper (which I write via LaTeX).

 

The main advantages to Mendeley, for me, are:

1. It's free.

2. It's platform independent and stores papers on your machine as well as the cloud. This means my work computer and my home laptop are always sync'ed. More importantly, the electronic annotations are also sync'ed between all machines!!

3. Although I always access papers via the Mendeley interface, you can also go through your folders and find the actual PDF too. Within Mendeley, you can tell it to rename and reorganize your Papers folder any way you want (e.g. folders for years, subfolders for journals, and then files named as author_title.pdf if you want). You just click and drag little bubbles in your setup screen and you can change your mind and redo it at any time and all of your papers are moved and renamed as necessary. This is very similar to iTunes for music organization!

4. You can "star" papers like in Gmail. You can extend this by use of tags as I mentioned above. You can see all your tags on the left hand side and then click on the tag you want and you'll see all papers with that tag, across all of the folders you have. I use this to tag certain methods that are used in more than one project (I use folders for projects) to help me find something that might help me in Project X even if I had originally only saved it in Project Y (and not realise the connection at the time).

5. Finally, everything is searchable/organizable. I can click on a tag for an author name (these are automatically generated with the bibliographical information) if I want to see what else this person wrote that I already have in my library, or if I remember a paper but not the title or first author etc.

[yoyo17]

I use Mendeley (https://www.mendeley.com/). Ignore all of the "social media" / LinkedIn type stuff they have (well, you can use it if you want, but don't feel like you have to, I mean). 

 

Here's my general workflow:

 

1. I find the paper online, in PDF form. I download it to a special folder that is "watched" by Mendeley. (alternatively, I can download it anywhere and import it to my Mendeley library).

2. I open up Mendeley, and find the paper in the "Recently added" section. I then move it to various folders for the projects I am working on. They're like Gmail folders--you can put a paper in as many folders as you want.

3. I then double check the bibliographical information. I can use DOI lookup, PubMed ID, arxiv ID, etc. if necessary

4. I also have certain tags that I use for various methodologies or papers that are specific to certain experimental samples. I usually add these tags right away (these tags are searchable)

5. I then read the paper and make electronic annotations as necessary (also searchable)

6. Ultimately, when it's time to write the paper, I can export all of my library into a .bib file and use BiBTeX to add it to my paper (which I write via LaTeX).

 

The main advantages to Mendeley, for me, are:

1. It's free.

2. It's platform independent and stores papers on your machine as well as the cloud. This means my work computer and my home laptop are always sync'ed. More importantly, the electronic annotations are also sync'ed between all machines!!

3. Although I always access papers via the Mendeley interface, you can also go through your folders and find the actual PDF too. Within Mendeley, you can tell it to rename and reorganize your Papers folder any way you want (e.g. folders for years, subfolders for journals, and then files named as author_title.pdf if you want). You just click and drag little bubbles in your setup screen and you can change your mind and redo it at any time and all of your papers are moved and renamed as necessary. This is very similar to iTunes for music organization!

4. You can "star" papers like in Gmail. You can extend this by use of tags as I mentioned above. You can see all your tags on the left hand side and then click on the tag you want and you'll see all papers with that tag, across all of the folders you have. I use this to tag certain methods that are used in more than one project (I use folders for projects) to help me find something that might help me in Project X even if I had originally only saved it in Project Y (and not realise the connection at the time).

5. Finally, everything is searchable/organizable. I can click on a tag for an author name (these are automatically generated with the bibliographical information) if I want to see what else this person wrote that I already have in my library, or if I remember a paper but not the title or first author etc.

Wow thanks for the reply! 

 

I've heard of Mendeley.  Are there pros and cons of Mendeley vs Endnote?  From what I heard, Endnote is better for Citing While You Write.  What are your experiences and thoughts between the two?  Example, I'm having trouble synching Mendeley's Groups from my computer to the cloud.  It takes the references well but I'd have to do the Groups all over again.

 

What are your thoughts on hard copy or why do everything electronic?  Aren't there risks to keeping eveything digital?

Edited June 15, 2015 by yoyo17

[St Andrews Lynx]

You can also annotate the PDFs in Mendeley, or highlight portions of the PDF text in a fetching neon yellow. In addition to the tags that TakeruK mentioned, you can write a short Note on the 'coversheet' page (e.g. "This paper has totally cool methods I want to use for Subproject X."). 

 

Maybe instead of printing out the whole document, you could create several folders with just the first pages of your journal articles? Then you could write some notes on the back of the page to remind yourself about what was important in this paper. Now you have the 'prompts' for the articles all together, and if you need to read the article in detail you can go back to Mendeley to look at the PDF?

[TakeruK]

St Andrews Lynx makes a great suggestion! Also, this will generally let you have all of the abstracts, which, if well written, should remind you everything about that paper!

 

To answer your questions:

 

I've never used EndNote so I can't compare the two directly.

 

Citing While You Write: You capitalize that so it seems like you mean something special and specific. I don't know what this is though, but I can respond to the general concept of citing while writing. Yes, I cite while I write! I typeset my papers in LaTeX, and use BiBTeX as the backend for generating my references. I use Mendeley to create the "database" of references for BiBTeX and LaTeX to use. So, for example, if there is a paper that is by Smith et al. (2002), published in the Awesome Journal, vol 888, p. 25, I would use Mendeley to associate this paper with a "key" like "Smith2002" (this is the default unless you change it). Then in my paper itself, I might write a sentence that looks like:

 

Previous studies~\citep{Smith2002} show that the moon is made of cheese.

 

When I compile this LaTeX document, it will search the Mendeley-produced BiBTeX file for the reference with the key "Smith2002" and then automatically replace my ~\citep{Smith2002} with the actual reference in the correct in-line citation style for my journal. It will also add this reference to the paper's Bibliography at the end, in the correct citation style required by the journal.

 

Hard copy vs. digital: I do print a few key papers that I regularly reference and store them in my filing cabinet. Sometimes there are tables with detailed figures or large tables that I want to cross reference with my screen instead of having to switch between two windows. Or, I just want to really draw on it and/or take it with me on planes, coffee shops etc. 

 

But in terms of risk, I actually fear more for my hard copies than my digital copies. I can lose or damage hard copies! Mendeley backs up all of my papers on the cloud, so in theory, the PDFs exist on my work computer, the cloud, and my laptop. I also do regular backups to an external hard drive so I should always have access to at least 4 copies (my work computer is also backed up by the IT staff in my department). So, I always consider my digital copy as my "main" one and I won't really feel much loss if I accidentally damage a hard copy, or leave it in an airport etc. If I had made really important notes on a hard copy, I always transcribe it onto the electronic copy ASAP.

[rising_star]

Cite While You Write is an EndNote feature (can also do this with Zotero) that lets you insert citations into your paper directly from EndNote and have them properly formatted. I used it eons ago when I still used EndNote but stopped after a glitch. Basically, I deleted a sentence. Somehow, all my other references got bumped up one place, which then meant nothing was properly attributed. I had to go back in and fix it all manually (in a like 20 page paper). It was so irritating that I haven't used Cite While You Write since then.

 

Zotero, btw, might be another option for you. It's a different program that works similarly to EndNote and Mendeley. If your school subscribes, Proquest FLOW (previously known as RefWorks) could also be a good option for you. 

[knp]

I use Zotero, although it does not let you annotate PDFs, if that is important to you. It lets you organize things into lots of subfolders in a way I find generally sensible and intuitive, and a decent tagging system. It doesn't have a starring system, but I use a "favorites" tag as a solid workaround. It's free and open-source, so occasionally it's a little more glitchy than I think paid corporate projects tend to be (I use a lot of foreign-language works, and have issues with capitalization about 1/3 of the time, which has been my biggest problem). Its equivalent "Cite While You Write" feature is really good, though. It has a Word plugin—I don't know if or how well it works with other text editors—that lets you move things around amazingly. I always use footnotes or endnotes, rather than in-text citations, and the Zotero links all talk to each other and update according to what the other ones do. So, for instance, if I am citing Book Longtitle: The Practice of Academic Titles Always Having Colons in Them twice in a row, it'll make the second note an "ibid." for me automatically. If I decide to change the order, the notes will flip, too, so that the second note is always an "ibid.", and I don't have to spend a lot of time doing that.

 

Its primary notetaking feature is "notes", which are simple text boxes that attach to a bibliographic record. They're basic, but pretty effective. The search feature is solid, except that it won't show you where in a note your search term shows up, just which note it attaches to. My one concern is I don't know how often/whether it backs up: I have pretty much uploaded my entire brain into this program through various notes on things I've read, so I need to figure this out myself.

 

Like many of these things, it has a bit of a learning curve, but I personally figured it out in about two days and have never looked back.

Edited June 15, 2015 by knp

[TakeruK]

From reading the descriptions of Cite While You Write, it seems like it is possible to use Zotero and EndNote to do, within one piece of software, what I do separately with Mendeley and LaTeX/BibTeX. I do know that Mendeley has Word plugins that might allow for the same behaviour, but I have never used it, since my field writes most of our articles in LaTeX! (i.e. LaTeX+BibTeX has all of the features knp mentions, which is especially useful to me because I never have to worry about writing these things in the correct style, I just tell it I want to cite a certain paper and the journal's own style file determines how it should appear).

[Eigen]

Just to comment, you can annotate papers from within Endnote (at least in X7), and you can view the PDFs natively within the program. 

 

If you want extensive notes, there are two primary ways I'd suggest going about it:

 

1) Annotate the PDF. This is good, especially if you want to highlight a few specific things. 

 

2) Write a quick summary, export said summary as a PDF, and attach both the PDF summary/notes and the paper to your reference in Endnote.

 

Endnote (as well as most other citation managers) lets you attach multiple files to a given reference- I usually have the reference, any supplementary information, and then any extra figures I've downloaded/made based on the reference, and if I have them, notes on the reference/importance. 

 

I've only briefly used Zotero and Mendeley, but aside from base design choices (and price), I've found the feature set of EndNote, Mendeley & Zotero to be pretty similar- one will come out with a feature first, then the others fairly quickly adopt or one-up it. For instance, you can do pretty much everything TakeruK suggests in Endnote.

 

I used Endnote X2 for a very long time before upgrading, and I'm glad I did- a lot of the bugginess of some of the earlier releases is definitely gone. 

 

From a back-end perspective, I appreciate the flexibility in being able to design your own input/output styles easily- it makes going from Endnote to BibTeX pretty easy, as well as to any other citation manager. 

 

Cite-while-you-write is nice, but I prefer using the in line unformatted citation codes, and not updating/making the bibliography until the end- it saves having the issue Rising_Star mentioned. You can also convert the bibliography to plain text when you have your final paper, and then make any small edits you want to it directly. 

 

Editing in a response to TakeruK:

 

Endnote's cite while you write is pretty much exactly the same thing as cite keys in bibtex. The coding is even very similar. Endnote uses a ref ID (numerical) and author/year bracketed and inserted in the text, then at the end compiles and creates a bibliography from those IDs. i.e. Smith 2007 with a ref ID of 742 would be {Smith, 2007 #742}. When you get used to it, you don't need to drag/drop from endnote, you can just type them in as you go. Multiple references just get tagged together with semicolons {Smith, 2007 #742;Smith, 2008 #743} which will reference the two in one place. 

 

Especially with the recent editions, I find Endnote the closest commercial equivalent to JabRef/BibTeX, and the underpinnings of how it does citations via compile are very similar to BibTeX.

 

Endnote also supports natively an export of a library (or subset of references) to a BibTex file, and you can script in what you would like as the cite key from each reference.

[mop]

The Word plugin for mendely to cite papers is very easy to use in my experience. Can select many types of citation styles or  create your own custom citation format, and then inserting a citation in text automatically adds the article to a bibliography at the end. If you want to change the citation style after writing (say to change the journal you submit to) it just takes a few clicks and then everything is automatically reformatted.