Monday, May 11, 2009

How do you manage your PDF's?

Okay, so I have always printed out my journal papers and read them. I will continue to do that, because there is something about reading a paper, writing notes all over it, with a nice cup of tea which makes the information stick. However, putting together a proposal I still need to quickly glance over the paper to ensure that I am describing the data and/or its implications correctly, that I am referencing the right paper etc. Which means I either have to drag a crap load of papers back and forth with me or I can actually save the pdf on my laptop...since I am of the weak lazy type I will be saving the pdf from now on. The question becomes how do you name the files? Normally I file my papers by the first author, however many first authors have more than 1 paper so I can just name the file after the first author? I'm thinking first author and year? Or maybe first and last author, but that would be long. What do you more technologically advanced folk do? I use endnote as my reference manager, in case that information is needed.

30 comments:

Mrs. CH said...

For myself, I just name it by author, journal, date (i.e., smith_jones_journal_date.pdf). However, that doesn't always work if I can't remember the topic they wrote about!

I have heard of this program called "papers" and I've only heard amazing things about it! It basically organizes your PDFs for you. You can even put it on your iPhone or iPod (I believe it's only for Mac, but I may be wrong). It does cost $$, but it might be worth it. Here's the link:

http://mekentosj.com/papers/

Fia said...

I second Mrs CH, - papers is what saved my life (and will make me never switch to Windows or Linux ever ever again).

It makes my live so much easier. We just moved home to a place overseas and I don't have to bring all my printouts with me, - I have my library on my laptop, nicely ordered (it does it automatically into neat folders, year-author-journal, or what ever constellation you prefer).
You can read onscreen (or print), full screen. You can scribble (electronical) notes, they get attached to the paper and later you can do a fulltext search (within the notes and the pdf). You can find papers within all usual repositories (including PubMed, WoK, Googlescholar), download it (using th proxy of your uni-library), - they get named and filed automatically. You can make lists of papers (like playlists in itunes), and these lists can be exported in your reference program format of choice (like, endnote or reference manager). No more typing titles, authors ect. It's brilliant.

And I realize I should get paid by either one of them (Mac and Papers) given all the praise I write.

Nat Blair said...

This is a total pain in the rear, that's for sure. I'm not sure I've really gotten things as organized as it could be, but here's what I do.

I have always used the convention for pdf naming of FirstAuthorLastNameTHREELETTERJOURNALABBREVYear
So you might have something like BeanNAT89.pdf.

Then I stick all of these into one giant folder. The trick now is how to figure out how to search that effectively. One way is Papers, as people have mentioned, assuming you're using a Mac.

Another way is to make entries for those papers in a bibliographic management program, and link the pdfs to the appropriate entry. I've done this with EndNote. I've stopped doing this though, because it's slow. I may do it for papers I actually want to reference in a paper, but not for the entire range of papers I download and read. What you really want is something that will scan the pdfs in a chosen folder, and automatically pulls out the info from each.

Other possibilities for Windows based people are Mendeley (www.mendeley.com) and Zotero (which works through Firefox). I've tried both, but in the versions I tried, both didn't really like the EndNote library I imported (1800 entries). But I'm about to go back and retry both.

Maybe that's helpful, maybe it's just more blathering on my part.

Professor in Training said...

I used to number them with their EndNote catalogue number and first author: #007Stupidname.pdf however, the new version of EndNote allows you to attach pdfs to each record number.

Becca said...

I save them as LastnameFirstAuthor...LastNameLastAuthorTitleJournalYear
Possibly I am compulsive.
The dots don't go in if it's only a two-author paper. Sometimes I add in a key middle author if that's the main reason I found the paper.
Titles of papers often get substituted for keywords if they aren't descriptive enough; journal names get abbreviated.
I also group similar papers in endnote libraries, but have yet to put together a MasterList. Sometime before the thesis it will have to happen...

Nat Blair said...

I also group similar papers in endnote libraries, but have yet to put together a MasterList. Sometime before the thesis it will have to happen...I'd recommend against having multiple different EndNote libraries. It always seems to be a pain later. Perhaps it's better to have just one master library, and you can add Keywords in a field in the EndNote record. Then delimiting your search by this keyword you can filter the papers that apply to that keyword. This helps when you get to those papers that straddle the lines between the separate libraries, as you can add multiple keywords to each record.

As for actual paper copies, I've always written the EndNote record number on the top right in red ink. Before the advent of pdfs, I had hanging folders of "Papers 1-10", "Papers 11-20" etc. From EndNote, I could find any paper I knew I had in 15 seconds or less.

It got to the point my thesis advisor would come to ask for papers he knew I had.

I still save the paper copies for those few items I don't have a pdf for. But I'm working on phasing everything into pure digital form.

@PiT - It's still manually linking the pdfs to EndNote record, right? (Or has is changed in X2?) Cause that's what kills me. It actually takes some time to do this, which led me to have folders with hundreds of papers I thought I wanted to get into EndNote. I want something that will do it for me, extracting the metadata in the pdf headers. In principle that's what Zotero and Mendeley can do (papers as well) but like I said, I have to go back and try them again.

Schlupp said...

Use a Mac, get "papers".

Dr. J said...

At the moment I don't actively store PDFs in any kind of systematic way. I can see a tipping point arriving very soon - the desk is overflowing now with papers and I would like to print a little less and carry a little more with me. I've tried Mendeley, but only in an early form and it's lack of decent word integration was a real problem, plus like others I store my papers by EndNote cat# and it had no support for importing that.

I cannot believe how short sighted the owners of Papers are. Most people still use PCs, most are desperate for something better than EndNote and yet they say they have no intention of making a PC version. I for one am not buying a mac (how much do they think post-docs get paid!?)

Professor in Training said...

Nat: I'm using X2 on a Mac and yes, you have to manually import the attachments (unless I'm missing something). I'm considering trying Papers though as I've lost my former admiration for EndNote because it's latest version sucks.

Dr J: I shelled out the cash for an iBook while in grad school and I've only just replaced it (5yrs later). They are definitely worth the extra initial outlay ... and they look supercool :)

Dr. J said...

PiT: I just bought a Dell XPS, which I'm very happy with, so no Mac for me. Plus all the licences for Office and all sorts are geared for PC at our place (happily!) so I'm not going to be changing - and I would lose a lot of face as the anti-Mac person!

Cath@VWXYNot? said...

Papers really is tremendous!

I don't have to really track too many papers any more, but when I did, I used Nat's method of filing hard copies by Endnote number. During thesis (and, to a lesser extent, paper) writing I ended up learning the important ones off by heart, just because of how often I referenced them ;)

ScientistMother said...

You guys rock! Papers isn't too expensive, its $51 for a single person license (which gives you 2 licenses - one for lab one for home!) plus as a student they'll give me 40% off. My only concern is that they recommend a minimum 1.5 GHz processor. I have a 4 year old G4 so its processor is only 1.42 Ghz. I'm downloaded a trial version to see if how it works.
Dr.J - you totally have to get a Mac! Even Cath has converted! My 4 year old G4 works totally fine. its only problem is that the processor is getting slow for all the new programs. I will be replacing it with a powerbook when its time to write my first paper.

ScientistMother said...

Oh and Schlupp, welcome to the blog! Definitely agree with the Get a Mac! Dr. J will eventually see the light.

Cath@VWXYNot? said...

Yup, I've gone Mac and will never go back.

Except at work, where I'm still using a PC.

Digger said...

Biblioscape runs on Windows. I use the free BiblioExpress just for bibliographic references; but the full Biblioscape will grab .pdfs also.

http://www.biblioscape.com/

JLK said...

I use the last name of the first author and either a brief description of the paper or the first half of the title. So for example, if you went into my journal articles folder and into the appropriate sub-folder by subject, you would see "Murphy - Signaling Threat" and that's it.

I used to love going through hardcopy articles, but then I discovered the annotation feature in my pdf reader. Now I can highlight, add notes, etc., and when I open the file the right-side pane previews the pages so I can scan to the ones that show highlighting and note bubbles. No more wasting paper!

Nat Blair said...

*sigh* Sad to see so many nice smart people caught up in the Cult of Mac.

I'm with Dr. J!

I'd never heard of biblioscape, and I'm gonna have to put that on the list of apps to try.

@JLK - what pdf reader are you using? I was adding notes and such for a bit with pdfXChange, but the notes weren't searchable by anything. So those notes were still kinda convenient to take, but ultimately not a useful as before.

To get around that, I've been adding notes for papers in some googly flavored thing, either gmail (with a label to easily segregate those messages), or as a google doc, or as a page in google sites. That way, the search is so good, I can easily retrieve the most applicable notes for things.

chall said...

I store my pdfs under lastnamejournalnameyear... and then crossref to Endnote. Without endnote I am a lost puppy...

Before I saved many papers as pdfs I always numbered them and kept the number in endnote. Now, I fear to say I store them in some piles in different subjects. I guess I will hate myslef when I finally write the manuscrips later on?!?!

ScientistMother said...

I am in LOVE with papers. I even got my PI excited about it. But seriously people, you guys actually NUMBER your papers and rename them? I am way too lazy to do that, which is why I have never saved PDF's. Papers has changed my life..BEST THING EVAH!

Mrs. CH said...

Yay!! I'm so glad you like it! I might have to lay out the cash for it...hmmm.

EthidiumBromide said...

For those of you who do not have Macs (I use one at work, and have a PC at home... and MUCH prefer the PC), I suggest Mendeley for managing PDFs. The newer version is much improved than what Dr. J has tried, it works on both PC and Mac so I am able to sync between both my computers, and I actually prefer it to Papers because of that, even though I have Papers on my lab computer. Plus, I love that it syncs all my papers to the web, so if I am traveling without my laptop (i.e., visiting Husband for the weekend) and want to access a paper but don't remember enough to pull up the immediate paper from PubMed without doing a huge search and looking through all the papers... all my papers, with all my tags/labels in the appropriate folds are all right there on the web and I can access them that way.

ScientistMother said...

Oh mrs.ch if you can buy all those summer clothes, you can shell out $31 for a program. What I really liked is that a single user licence comes with two licences as the de elopedz recognize that alot of science folk have more than one computer that they work ie a home and lab computer

EtBr - one day you will see the erroroc your ways and join the force

ScienceGirl said...

Also a devout Papers user, I even got most of my lab mates to use it as well. My mac is nearly 4 years old (but it is 1.5GHz), and Papers doesn't seem to stress it out at all. My bibliography is in bibtex, and I add notes to my pdfs by Skim (seamless to use with Papers).

Dr. J said...

It was actually the most recent version of Mendeley I tried (Beta 0.6), it still has a bit to go - but I they know that. If the word integration becomes as good as EndNote then it has every chance of being much better.

Mrs. CH said...

LOL SM - fair enough! Even better though, I got DH to look at it and he wants it now. So, he'll pay for it and it can be a tax write-off for him since he's an independent contractor! Woohoo!!

We are using the free trial (30 days) to see how it works before buying the license. I couldn't get it to work properly last night (it would find papers, but wouldn't link me to the sites properly). I'll play with it this weekend :)

Phagenista said...

I name .pdfs with the last name of the first (or both, in the case of two author papers) author, the year and then a string of keywords associated with the paper. Only occasionally do I add an abbreviation of the journal name, mostly to distinguish reviews from novel data papers by the same author.

I haven't purchased Papers yet, and I dislike Endnote enough to want to circumvent it for all but the papers I actually cite in manuscripts. I rely on the excellent search capabilities of the mac (spotlight) to search the thousands of pdfs on my hard drive for the appropriate keywords in the file names or within the full text of the pdfs. This strategy also allows me to have the papers in as many different folders/smart folders as I wish instead of one giant folder.

Anonymous said...

Papers sounds awesome, but no way I'm going mac. I organize by 1st author, last author, YEAR, keywords or running short title. I put all of my PDFs into a folder called "library" and also make shortcuts for them that I then place in additional files according to subject matter.

Nat Blair said...

I put all of my PDFs into a folder called "library" and also make shortcuts for them that I then place in additional files according to subject matterNow that is super clever!

The knowledge within the Hive Mind is awesome.

Brenda said...

I upgraded to Endnote X2 a couple months ago - it'll download fulltext pdfs at the click of a button. Doesn't work for every paper, especially when I am off campus but I like it and it worked for me - my thesis is printing as I type.

Kent M said...

Might I suggest a free, cross-platform bibliography manager called JabRef?

http://jabref.sourceforge.net/

Thanks for all the useful links though, Zotero especially!