iTunes-esque App for PDFs?
 

Not sure if this is the best forum to post this in, but here goes.


I'm just starting a PhD, and one of the (many) things I'll be doing over the next 3 1/2 years or so is reading a lot of scientific research papers. My feeling is that I will accumulate a very large number of them, some more useful than others.

I wanted to ask if anyone knows of an app which works as a database front-end that would allow me to view each PDF from within it, as well as attach meta-data such as author(s), title, subject area, conference, date published, links to citations, inline comments, etc. such that it was searchable.

At the minute, I'm stuck using my own hierarchy via Finder, and hoping that my memory is sufficiently jogged by the time I reach the bottom-level folder. Once Leopard comes out and you can preview PDFs from within the OS, my system may work a bit better, but I would still ideally want a purpose-built app.


Thanks in advance.

I don't know about applications, but pdf files are indexed by Spotlight. It doesn't help with meta data, but it's something.

I found this on MacUpdate by searching for "pdf library":

http://mekentosj.com/papers/

It looks exactly like what you want.

You can also use Get Info to add Spotlight Comments to any file or folder you wish. I've recently started doing this for applications that I seldom use but when I want to use them have to do a hunt and peck method to find what I'm looking for as I've long forgotten the original name of the app. It has been a tremendous help.

Not sure if this will benefit you but I thought I'd chime in with this oft overlooked tool.

you might also look at skim, which I just noticed in another thread. it has the advantage of being free, which I know (from experience) has value for grad students. :)

Skim is awesome
 

really, really awesome

Thanks for the ideas guys...
 

Papers and Skim both look exactly like the kind of thing I had in mind. Unfortunately, they both require 10.4 and I'm still using 10.3 :( . It's a similar story for iPapers as well (although I prefer the look of Papers).

Out of the three, Skim looks the best (I'll keep it in mind when I update my OS). Also, the other two include PubMed searching which is of no use to me at all -- my PhD is in Informatics, not medicine. EngineeringVillage would be of greatest use to me (it searches through Inspec, Compendex, and Referex).

Thanks for the help though. It's much appreciated.

hmmm...
 

on reflection, I'm going to throw out one caution. if you're going to pursue an academic career, you're going to want access to these notes 10, 20, and 30 years from now, and I would worry a little bit about that. for all we know, Skim won't work under Leopard (or os XI), and you'll find yourself in a minor (or major) crisis.

low-tech as it sounds, nothing beats scribbling in the margin of a printout for portability and longevity...

Why not use iTunes?
 

iTunes actually supports PDFs. There's no need to find another app that works like iTunes; just use the real thing. :) Plus, it's supported in Panther.

Edit: It would probably be best to create a separate library for your PDFs, to keep from cluttering up your music library, but it isn't actually necessary.

Also, you can use ⌘-i to add/edit tags, just like a music file. This allows easy implementation of smart "playlists" for easy sorting by appropriate criteria. Be aware that iTunes doesn't actually display the PDF files; it leaves that to Preview (or whatever application you have set to open your PDFs by default). iTunes just works as a database to keep them sorted.

Ditto, iTunes or iPDF is the way to go. But a way to annotate them is also important.

I did the same thing
 

When I was going through grad school. I used a php/mySQL setup to do this.

I had no idea about iTunes. Great idea.

You might also want to look at an application called TextCite:
http://textcite.sourceforge.net/

It will track citations for any format (although APA could still use some work).

Highlight the citation in Acrobat, then enter it in textcite. Tracking citations live was really the only thing I couldn't do off the shelf a few years ago, which is why I went with my custom system.

Good luck.

You should see if this has been published as a Hint, and submit it if it hasn't. :cool:

Take a look DEVONthink. I believe there is a free version as well as Pro version. Their tech support is fabulous, and you get really great help in their forums.
http://www.devon-technologies.com

You can try out the high-end product for 150 hours for free, and request more time if you need it.

You can create a database by importing the PDF's, or reference them inside DT with full access to the PDF contents via their interface, just as long as you dont move the PDFs from their folders in your Finder.

Read how people use it here:
http://www.devon-technologies.com/su...its/index.html

DEVONagent is one of the best search engines if you're doing serious research. Finds stuff from around the world that Google on its best days couldn't.

Take a look at Yep: http://www.yepthat.com/

I think this is exactly what you're after.

Leopard will have a function called core animation (which is more than a GUI front end, its also a set of APIs) which allows you to organize and browse documents much like the itunes interface built into the OS. This will be a standard feature in Leopard which is going to be released really soon.

So, if you planned on upgrading anyway, you also get what you are asking for.

Great "how to" article right here using iTunes

http://lifehacker.com/software/pdf/g...nes-240447.php

It has been around for some time , if I remember right, its also documented. ;)

the hint

Cool! Thanks for the search, and thanks to Kirk for the Hint.

J Christopher:
I hadn't realised that PDFs can be imported into iTunes. It never even crossed my mind! However, the inabitlity to view PDFs from within iTunes is a major drawback.

gdap:
Yep's not quite what I'm after, but thanks for the suggestion anyway (plus, it's also Tiger only).

rumirocks:
I've downloaded DEVONthink, and although there is no way to add comments to specific parts of a PDF, it does most of the rest of what I'm after. I've played with it for a short while and it looks promising (the only downside so far is that some PDFs have the top 1/2 cm cut off, unless they are zoomed out far enough). Cheers for the pointer!

tlarkin:
I'm keeping all my fingers crossed for Leopard. I've been holding off upgrading ever since the features began to be publicised. A new Mac is top of my list for Santa this year...! :D

roninuta:
I'll keep textcite in mind, thanks. It looks very useful too. EDIT: It appears to require Tiger, so it's yet another program I can't run. This is getting frustrating!


As I said before, all your suggestions are greatly appreciated. Thanks.

Is viewing the PDFs in iTunes critical? They can be easily opened from iTunes via double click. I think (I've not tested.) that as long as the filename and location do not change, iTunes will still easily access the PDFs after any comments are added.

Do you have an application in mind for modifying the PDFs with comments? Preview in Leopard may have some editing tools. For that matter, iTunes may be updated to open PDFs, considering that capability already exists in Quicktime.

[QUOTE=rumirocks;413969]The PDF cutoff is something that can be alleviated with a setting. Everyone had that problem with the penultimate version. That was a year ago and I can't remember what it was. Check the forum?

As for comments, hit the "i" icon and add everything there. Then it makes search, WHICH YOU SHOULD BE DOING FROM THE TOOLS MENU because it has more choices, much faster and better. Pose your question to the forum for suggestions. I barely know how to use the program but I dump everything into it.

Do the short online tutorials and look for Bill de Ville's comments in the Forum. Their forum is a goldmine. Check out the Devon Academy.

Lots of freebie programs to download that helps you with DT. Their firm is very security-conscious and they're conscientious.

I would think that if they are scientific papers, then a person should know how to select them from a list of keywords similar to selecting photos out of iphoto.

You can put tags on the pdfs and then recall them based on the tags YOU define. What could be more convenient than that?

Maybe 'critical' was too strong a term. It's really more of an inconvenience when viewing (or searching) through multiple papers. iTunes' inability to search through the text of the PDFs is more of a problem.

I know that Spotlight can do that, but I'm still running Panther (Sherlock may be able to do it too, but I want an app that organises the papers as well). DEVONthink can do that, plus I like its ability to automatically suggest appropriate groupings based on how existing papers were grouped. The only problem is that it isn't designed with scientfic papers in mind, so there is no way (other than the gerneric comment field) to include multiple authors, journal name, pages in the journal, date published, etc. I've gone with making lots of groupings to cover these fields, but it's very time-consuming!


I think the Panther version is older than the Tiger version, so it may still contain bugs which no longer appear in the Tiger one. I'll check the forums though to see what they say.


Skim lets you write comments anywhere on the PDF, as if you were writing on a paper copy. Unfortunately, it requires Tiger.


There is a high likelihood that any given scientific paper may contain a lot of things I'd like to recall. While using comments to add general topics of the paper is useful, anything more would become cumbersome. Also, I don't really want to spend a lot of time adding keywords and tags to a paper, when the majority of the information is already contained within the document itself.



For what it's worth, I'm also using BibDesk now to do my BibTeX database -- I used to do it manually, which was OK when I had less than 50 papers. The downside is that it can't search through the content of the PDFs, only the tags.