How organized are your pdf files

radek42 · Jul 3, 2012

Hello fellow scholars,

I am finally gonna bite the bullet and enter my library of scientific papers (pdf files) into a database (Papers or BibDesk). I plan to use it with LateX as well as copy-paste references to MS Word (yuk!)

Until now, I have all my papers stored in not-so-sophisticated hierarchy in various folders by topics so I can find them easily (actually, it's still quite hard to find anything

. Since both Papers and BibDesk can link pdf files to individual entries I was wondering if any folder structure is even needed to keep files organized; any search query will be handled by the databes anyways.

So my question is: do you, in any way, organize your files when/if they are lined to the database? My feeling would be no ... there is no need.

I'd likt to hear/see your arrangement ...

Cheers, R>

jahala · Jul 3, 2012

I still organize my pdf files even though they are in a database just in case I need to find them without the database some time.

radek42 · Jul 4, 2012

What "scheme" do you use? Do you go by topic, author, or something else?

R>

jahala said:
I still organize my pdf files even though they are in a database just in case I need to find them without the database some time.

jojoba · Jul 4, 2012

For a long time, I've had a folder based system on my work pc which is duplicated on to dropbox, and from there I access it on my Air and my iPad. On my iPad, my entire research library is synced to iAnnotate. In many ways, this works quite well for me, and for the most part I find that I can locate the documents I need when I need them.

Having said that, I'm in the process of setting up a library in Papers, which is going a bit slowly because I'm partially questioning the need for it. Initially, I wanted to use Papers as a cite while you write tool, so my purchase was motivated by that. For pdf management, I think the main advantage of Papers versus my current file folders is the opportunity to tag documents. Even though I find that my current thematically organised file groups work quite well for my purposes, a lot of the articles could potentially belong to more than one category. So, by adding multiple tags in in Papers, I can place the same document in more than one category without duplicating the file, and I can also have a more fine grained categorical system because adding more tags doesn't mean adding more versions of the same document.

If I didn't work in a Windows environment, I would probably have no hesitations switching to Papers as my main pdf organisation app. However, since I will need to work cross platforms for the time being, I'm in two minds about whether to make the full switch to Papers on my mac/iPad. That hesitation is reinforced by the fact that the iPad version of Papers has very limited annotation capacities compared to iAnnotate or PDF Expert.

The Mercurian · Jul 4, 2012

I use Mendeley for this.

Precisely because Mendely allows you to dictate a file structure to it. As you import papers into its library it renames them. In the setting you can choose whether to name them via author, journal, year whatever way you want to.

Then within the Mendeley application itself I make project folders and drag papers into the relevant project. One paper can be in more than one project and remain linked to the same file.

Anyhow with this setup its easy to navigate either using Mendeley itself or using Finder to search the library file structure manually

radek42 · Jul 4, 2012

Thanks for posting your thought and working arrangement.

jojoba said:
For a long time, I've had a folder based system on my work pc which is duplicated on to dropbox, and from there I access it on my Air and my iPad. On my iPad, my entire research library is synced to iAnnotate. In many ways, this works quite well for me, and for the most part I find that I can locate the documents I need when I need them.

Having said that, I'm in the process of setting up a library in Papers, which is going a bit slowly because I'm partially questioning the need for it. Initially, I wanted to use Papers as a cite while you write tool, so my purchase was motivated by that. For pdf management, I think the main advantage of Papers versus my current file folders is the opportunity to tag documents. Even though I find that my current thematically organised file groups work quite well for my purposes, a lot of the articles could potentially belong to more than one category. So, by adding multiple tags in in Papers, I can place the same document in more than one category without duplicating the file, and I can also have a more fine grained categorical system because adding more tags doesn't mean adding more versions of the same document.

THIS! The fact that you can often place papers in number of different groups makes folder system cumbersome and potentially hard to managed. I suppose one can create links/shortcuts to place documents in different directories without duplicating files, but that just sounds silly. Database is certainly way to go.

The main reason for me to use Papers/BibDesk is managing pdf files AND .bib file for Latex.

If I didn't work in a Windows environment, I would probably have no hesitations switching to Papers as my main pdf organisation app. However, since I will need to work cross platforms for the time being, I'm in two minds about whether to make the full switch to Papers on my mac/iPad. That hesitation is reinforced by the fact that the iPad version of Papers has very limited annotation capacities compared to iAnnotate or PDF Expert.

You might want to check JabRef which java-based system working on any platform that runs java.

For the longest time I struggled with fining software solution for different platforms. I have work PC (office/lab), mac mini at home, and linux laptop (work) ... don't ask

Every individual piece works and I don't even mind switching, but trying to find one software that works on all three is tall order at times. So I ditched my office computer and switched to apple laptop. Since then I worry less about cross-platform stuff ... if it works, use it!

I am trying to learn little more about Papers vs. BibDesk. Since one of my primary uses will be .bib file management, I think I'll go with BibDesk. We will see.

Cheers,
R>

jojoba · Jul 4, 2012

The Mercurian said:
I use Mendeley for this.

Precisely because Mendely allows you to dictate a file structure to it. As you import papers into its library it renames them. In the setting you can choose whether to name them via author, journal, year whatever way you want to.

Then within the Mendeley application itself I make project folders and drag papers into the relevant project. One paper can be in more than one project and remain linked to the same file.

Anyhow with this setup its easy to navigate either using Mendeley itself or using Finder to search the library file structure manually

Can you tag documents in Mendeley? And do you also use it for cite while you write?

----------

radek42 said:
You might want to check JabRef which java-based system working on any platform that runs java.

For the longest time I struggled with fining software solution for different platforms. I have work PC (office/lab), mac mini at home, and linux laptop (work) ... don't ask Every individual piece works and I don't even mind switching, but trying to find one software that works on all three is tall order at times. So I ditched my office computer and switched to apple laptop. Since then I worry less about cross-platform stuff ... if it works, use it!

Thanks for that tip, I hadn't heard of JabRef before. I'll check it out. Do you have any personal experience with it?

PC, mac an linux??? My work flow all of a sudden seems simple

I was planning to use Papers as a cross plat form tool, since there also in a windows version and apparently the library can be synced with DropBox across platforms. But setting it all up and that takes time... and I got into some formatting issues with the cite while you write function which can probably be sorted, but I didn't have additional time right then to really look into it and just finished the paper I was working on with EndNote.

The Mercurian · Jul 4, 2012

jojoba said:
Can you tag documents in Mendeley? And do you also use it for cite while you write?

Yes you can add your own tags.
You can download plugins for various word processing programs to provide citing functions but honestly I've yet to use that feature.

I will be trying it out soon though.

radek42 · Jul 4, 2012

It looks like an interesting option. Can it export .bib files for use with Latex?
R>

The Mercurian said:
I use Mendeley for this.

Precisely because Mendely allows you to dictate a file structure to it. As you import papers into its library it renames them. In the setting you can choose whether to name them via author, journal, year whatever way you want to.

Then within the Mendeley application itself I make project folders and drag papers into the relevant project. One paper can be in more than one project and remain linked to the same file.

Anyhow with this setup its easy to navigate either using Mendeley itself or using Finder to search the library file structure manually

----------

jojoba said:
Thanks for that tip, I hadn't heard of JabRef before. I'll check it out. Do you have any personal experience with it?

I did use it in the past, but it's been couple years. IIRC it's similar to BibDesk; it builds around .bib file (latex bibliography file) to store relevant data. It could also link pdf files. It was OK, but I did not spend enough time with it to be more specific.

R>

The Mercurian · Jul 4, 2012

radek42 said:
It looks like an interesting option. Can it export .bib files for use with Latex?
R>

Honestly I don't know. I haven't use any reference management software since Endnote shuffled all 56 references on an important paper a few years back

Die endnote die.

anyhow....let me check

Yeah can export .bib .ris and .xml

Its free anyhow so donwload it and have a play.

THere are some others you moight want to look at.

Readcube, Zotero, CiteULike to mention a few. I chose Mendeley for the pdf managment aspects mainly as I felt it was stronger at the time. ITs a fast developing field after years languishing.

radek42 · Jul 4, 2012

Thanks, I'll give it a try.

Honestly, I would not touch M$ with 8-foot pole on any important document such as thesis. I did couple shorter papers in Word ... needles to say, it messed up reference

I just play with BibDesk importing some old papers from Web of Knowledge and it was pretty painful

As a matter of fact the resulting .bib file did not compile :-( Gonna try Papers next.

Cheers, R>

The Mercurian said:
Honestly I don't know. I haven't use any reference management software since Endnote shuffled all 56 references on an important paper a few years back Die endnote die.

anyhow....let me check

Yeah can export .bib .ris and .xml

Its free anyhow so donwload it and have a play.

THere are some others you moight want to look at.

Readcube, Zotero, CiteULike to mention a few. I chose Mendeley for the pdf managment aspects mainly as I felt it was stronger at the time. ITs a fast developing field after years languishing.

ozaz · Jul 4, 2012

I've been using Mendeley for a while. Here are my thoughts.

Mendeley is very good for pdf management and it is a good choice for cross-platform and multi-machine use because it has mac, pc, and linux versions and it handles syncing itself via their own server (instead of having to faff around with a dropbox solution).

It can do one-way mirroring to a .bib file
http://blog.mendeley.com/tipstricks/howto-use-mendeley-to-create-citations-using-latex-and-bibtex/

Its main weakness, I would say, is relatively poor functionality as a tool for adding citations and bibliographies into documents. It has cite-while-you-write plugins for MS Word and LibreOffice but does not support RTF scan and temporary citations, which is a problem if you wanted to write in other writing apps like Pages, Scrivener, Google Docs etc that do not have cite-while-you-write plugins. However, if you will be using LaTex and the .bib file for writing, I guess this won't be an issue.

I've settled on Mendeley due to its strong cross-platform and syncing support. I've never used Papers, but it looks to me like both excel at pdf management and pdf annotation, Mendeley is better for cross-platform and multi-machine use, and Papers is better as a writing aid. Papers also seems to have better iOS app than Mendeley.

The Mercurian · Jul 4, 2012

radek42 said:
Thanks, I'll give it a try.

Honestly, I would not touch M$ with 8-foot pole on any important document such as thesis. I did couple shorter papers in Word ... needles to say, it messed up reference

MS Word wasn't the problem it was Endnote. Since then I've used MS all the time with its only internal footnote and crossreferencing tools with no problems

jojoba · Jul 5, 2012

Hm, maybe I should give Mendeley another look. I really like the cross platform/ sync features, but I had bad experiences with it in terms of cite while you write and inserting bibliographies. It messed up the formatting.

I've had no problems with Word and I need to stick to it because I work in a Windows environment and do a lot of collaborative writing both with Word and PowerPoint. I once experienced the same shuffling of references as someone reported above, and this happened when I tried to bring my EndNote library with me while travelling.

I'm slowly accepting that I can't have everything I want in one app:
- strong cite while you write functionality
- good PDF management with tags options
- good syncing options when working cross platforms

So I need to figure out how to best cut that cake in light of the available choices.

radek42 · Jul 5, 2012

A quick update:

I spend couple hours last night and this morning trying to make either Papers or Mendeley work "properly". In either case I was not able to automatically search and download pdf into the application :-(

In Papers I could search and import and create an entry, but I could not retrieve pdf file. I saw the link, but it always opens in new window when in browser (IE, Chrome, Firefox) and it did not work in Papers.

I could not really get search and import going in Mendeley. I started my database last night by downloading pdf files from my browser and I set Mendeley to watch appropriate folder; that worked nicely by importing nearly all metadata properly. Still, pain in rear end ... I was hoping to do this from within the application.

I am sure this must/should work better than this. I am still not quite decided which one to use.

Btw, I am not completely giving up on BibDesk, but since I could not use its .bib file in Latex due to some improper data fields .... I must see.

I'd really appreciate some deeper insight into these applications especially if somebody could clarify issues I raised above. Thanks.

R>

------

Papers could display only first 30 hits from WoS. I should say that this is under Wins using trial version.

The Mercurian · Jul 5, 2012

You can use Zotero for directly downloading I believe (at least my buddy swears by it). But personally I don't like Zotero being in the browser and its not great for file management.

I have it but rarely use it.

However you can also do something a little clever here - you can use Zotero for the import/download capabilities and then set Mendeley to watch the Zotero download folder thus automatically importing them to Mendeley for its superior file management. I have done this set up on mine but since I almost never use zotero I don't use it much

radek42 · Jul 5, 2012

Thanks for the comment. It's too bad you cannot do it directly. However, it seems that mac version might have more features than wins one. I'll try it at home again.

I seems to me that it does not make much sense to you Zotero just for "downloading" pdf files. I could do that just as easily from WoS directly; save file in proper directory that's being watched by Mendeley with proper name. Most metadata will be taken care of. Actually, I am a bit disappointed that article keywords are not parsed properly :-( . Also, unfortunately, moving or renaming files breaks a link. Move/rename function within Mendeley would be handy.

Oh well, it seems I still need to do more testing .... it never ends

As always, comments are welcome!

R>

The Mercurian said:
You can use Zotero for directly downloading I believe (at least my buddy swears by it). But personally I don't like Zotero being in the browser and its not great for file management.

I have it but rarely use it.

However you can also do something a little clever here - you can use Zotero for the import/download capabilities and then set Mendeley to watch the Zotero download folder thus automatically importing them to Mendeley for its superior file management. I have done this set up on mine but since I almost never use zotero I don't use it much

The Mercurian · Jul 5, 2012

When I was looking into all this like 8 or 9 months ago I came to the conclusions that no application really does all this very well.

Staggering really, given how useful it would be. Mendeley was the best compromise I could find.
Like i said I rarely use the Zotero thing

radek42 · Jul 5, 2012

Have you tested Papers and/or BibDesk?

As I said before, I will be using .bib (latex bibliography database) quite a bit, which would make BibDesk natural choice. However, since BibDesk uses .bib file to store EVERYTHING it breaks latex functionality sometimes; this is from my limited experience as well as according to some on-line reading.

R>

The Mercurian said:
When I was looking into all this like 8 or 9 months ago I came to the conclusions that no application really does all this very well.

Staggering really, given how useful it would be. Mendeley was the best compromise I could find.
Like i said I rarely use the Zotero thing

Consultant · Jul 5, 2012

Great book about paperless office (including document sorting), available as both iPad book or PDF:
http://www.macsparky.com/blog/2012/5/9/my-new-book-the-macsparky-paperless-field-guide.html

jojoba · Jul 5, 2012

radek42 said:
A quick update:

I spend couple hours last night and this morning trying to make either Papers or Mendeley work "properly". In either case I was not able to automatically search and download pdf into the application :-(

In Papers I could search and import and create an entry, but I could not retrieve pdf file.

I find that in relation to journal articles, downloading PDFs work well. I open the relevant web page in Pages, then I import the meta data (this is a bit of a hit and miss, though, and sometimes I need to take different approaches to this to make it work), and then I just import the PDF from there. I don't have my air with me right now so can't double check exactly what I clicked on. I'll run away check both on windows and mac versions tomorrow. I have to say that in terms of retrieving meta data correctly and consistently, I have yet to find anything that beats EndNote.

radek42 · Jul 5, 2012

I actually had a colleague complaining about EndNote messing up references (in Word I believe ... and it got published). I'm just not gonna use it

I actually had some luck downloading some pdf files in Papers, but not from WoS which I use the most to look up papers in my browser. I am not sure if Papers can get author names, title and other stuff from pdf meta data like Mendeley can. I could make WoS search work, but I could not get through all hits (only saw first 30; see my earlier post). I haven't tried extensively other search options. "Omni" search on mac might work better. But if I have to first import meta data and then go to web site, download, save, and link pdf file that would be pain. Mendeley would be better: download and save file into watched directory, check meta data, annotate, done. That might actually work

Actually, how about using a spotlight? Metadata in pdf files should be indexed, so looking for authors or keywords might be all right? I have couple coworkers who do just that on wins boxes ....

Cheers,
R>

-------

I downloaded Papers on my mini at home .... what a difference! I can download pdf files from the search and it's significantly faster than wins counterpart (which was painfully slow). Populating metadata was pretty weak; Mendeley is much better (at least from pdf files downloaded from WoS).

I gotta say it's gonna be hard to decide.

R>

jojoba said:
I find that in relation to journal articles, downloading PDFs work well. I open the relevant web page in Pages, then I import the meta data (this is a bit of a hit and miss, though, and sometimes I need to take different approaches to this to make it work), and then I just import the PDF from there. I don't have my air with me right now so can't double check exactly what I clicked on. I'll run away check both on windows and mac versions tomorrow. I have to say that in terms of retrieving meta data correctly and consistently, I have yet to find anything that beats EndNote.

jojoba · Jul 6, 2012

Do you know if your colleague was using EndNote cross platform or from difference machines at the time?

radek42 · Jul 6, 2012

The same platform (wins; not sure which version). He usually sync all his stuff from office PC to his laptop. He most likely worked form the desktop. R>

jojoba said:
Do you know if your colleague was using EndNote cross platform or from difference machines at the time?

jojoba · Jul 6, 2012

radek42 said:
The same platform (wins; not sure which version). He usually sync all his stuff from office PC to his laptop. He most likely worked form the desktop. R>

Yes, IME it's the syncing that messes up EndNote. If EN could find a way of working across computers, I really think it would be reliable. It is not my favourite app by far in terms of interface, but I have yet to find something that consistently imports meta data correctly from a very wide range of data bases.

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