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Great pdf/literature organizing app for (life-)scientists

post #1 of 14
Thread Starter 
For all you scientists on AI:
I just came across the 'Papers' app after reading a glowing Ars Review.
I've been playing with it for the last hour and it is hands on the best literature organizing software I've come across thusfar, and it's not even at 1.0!
post #2 of 14
AWESOME FIND!

As a medical resident, it is damn near impossible to keep track of all the articles and papers that our attendings want us to read. This software is going to be a lifesaver! It has some bugs and some minor shortcomings, but I am impressed so far. Thanks for posting this.
post #3 of 14
Thank you, Thank you, Thank you. Good find! I've been looking for this kind of App for years. So far, so good on first use for me.
post #4 of 14
Quote:
Originally Posted by dutch pear View Post

For all you scientists on AI:
I just came across the 'Papers' app after reading a glowing Ars Review.
I've been playing with it for the last hour and it is hands on the best literature organizing software I've come across thusfar, and it's not even at 1.0!

Wow! The Read n Full Screen feature of Papers alone may make this product worth the price. I'm now collecting a lot of metadata for many of my papers--just great. Hopefully, they'll expand beyond PubMed.

I read in the comments to the Ars Technica article a reference to another similar App called Bookends. Have you used that one? I gave up on EndNotes years ago --too much work.

For the non-scientist readers here, this App emulates the iTunes model of searching the web , retrieving the metadata and storing it in its database. Papers searches and retrieves metadata for scientific articles in PubMed. I can see the further extension of this model for law, arts, history, literature, etc.

Apple's brilliance ( the iTunes retrieval and database model) strikes again!
post #5 of 14
Maybe you guys can answer a question for me... I checked out Papers, and it looks very nice. But I have almost a thousand PDFs I'm accumulated over the years from my field; when I tried importing them into Papers, it found very little useful metadata, not even journal names for >90% of them. It wasn't obvious how/if Papers can automagically fetch metadata from PubMed, the way iTunes does from CDDB. Is there any way? Or would I have to manually find each manuscript using Paper's PubMed search function?
post #6 of 14
Thread Starter 
Quote:
Originally Posted by Towel View Post

Maybe you guys can answer a question for me... I checked out Papers, and it looks very nice. But I have almost a thousand PDFs I'm accumulated over the years from my field; when I tried importing them into Papers, it found very little useful metadata, not even journal names for >90% of them. It wasn't obvious how/if Papers can automagically fetch metadata from PubMed, the way iTunes does from CDDB. Is there any way? Or would I have to manually find each manuscript using Paper's PubMed search function?

Unfortunately it does not automagically find and import all metadata for all articles in one go yet. What you do is select an article and then click the 'match' button. You select some text (title works great), select what it is by clicking the green + sign and then search it. Double the correct result to import the metadata.
Seems like a hell of a job for hundreds of articles, but you get real quick at it, and once you're through this part you really will start enjoying papers enormously.

Supposedly importing endnote-data should also work, but I have no experience in that as I've always been too lazy to keep an endnote-library for all my pdf's
post #7 of 14
Quote:
Originally Posted by dutch pear View Post

Seems like a hell of a job for hundreds of articles, but you get real quick at it, and once you're through this part you really will start enjoying papers enormously.

I might plow through all that if I can extract the metadata later, keeping it associated with PDFs, and use it outside Papers. Just in case Papers vanishes in a few years or something. Looks like Papers does at least create a copy of the matched PDF files in ~/Documents/Papers with the PMID right in the filename, which is convenient enough. I can always use that to import metadata into another application later, keeping it associated with the correct PDF. It's unfortunate, though, that the metadata database itself (Library.papers) appears to be binary.
post #8 of 14
I used it about 45 days ago. While its a nice app, I've found its easier to use spotlight. I might give it another try, since I DL'ed it the week it was released, and they have done a number of bug fixes. BTW, they also make a another great app called EnzymeX, and its free.
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post #9 of 14
Thread Starter 
Quote:
Originally Posted by Bacillus View Post

I used it about 45 days ago. While its a nice app, I've found its easier to use spotlight. I might give it another try, since I DL'ed it the week it was released, and they have done a number of bug fixes. BTW, they also make a another great app called EnzymeX, and its free.

Well, although working with pdf's works all right using the finder and spotlight I find that Papers does give me way more power in organizing and working with literature, similar to the the advantage iTunes has over working with music using the finder and spotlight.
One problem with spotlight and articles in pdf format is that it doesn't distinguish the different parts of an article: to spotlight the abstract, main body, title, authors and references are all the same thing. Thus, when you search for an article by a certain author, spotlight also gives you every article that has the author in its reference list. There is a wealth of metadata just based on WHERE in the pdf file a certain word is located and spotlight simply cannot use this wealth. Papers lets you sort/search/organize by title, authors, year, journal, keywords, abstract and so on. Extra power over spotlight. Combined with easy in-app pubmed searches, fullscreen viewing, grouping options, smart groups, tabs and more Papers really does wonders for working with literature for me.

Slightly off topic: writing the above made me see why i actually don't use spotlight a lot: It is just too general a solution, since each type of data has it's own relevant metadata and within a certain data type, specific apps are often way better at leveraging the unique metadata of the data-type in question. iTunes for music, iPhoto/Aperture for pics, and Papers for scientific pdf's.
post #10 of 14
Quote:
Originally Posted by dutch pear View Post

Well, although working with pdf's works all right using the finder and spotlight I find that Papers does give me way more power in organizing and working with literature, similar to the the advantage iTunes has over working with music using the finder and spotlight.
One problem with spotlight and articles in pdf format is that it doesn't distinguish the different parts of an article: to spotlight the abstract, main body, title, authors and references are all the same thing. Thus, when you search for an article by a certain author, spotlight also gives you every article that has the author in its reference list. There is a wealth of metadata just based on WHERE in the pdf file a certain word is located and spotlight simply cannot use this wealth. Papers lets you sort/search/organize by title, authors, year, journal, keywords, abstract and so on. Extra power over spotlight. Combined with easy in-app pubmed searches, fullscreen viewing, grouping options, smart groups, tabs and more Papers really does wonders for working with literature for me.

Slightly off topic: writing the above made me see why i actually don't use spotlight a lot: It is just too general a solution, since each type of data has it's own relevant metadata and within a certain data type, specific apps are often way better at leveraging the unique metadata of the data-type in question. iTunes for music, iPhoto/Aperture for pics, and Papers for scientific pdf's.

Great post dutch_Pear. I've had the same experience with Papers. Also agree with your comments on Spotlight.

I've also been comparing it to Bookends. I asked a great cs guy at Bookends to tell me the difference between the 2 programs. Here is his response.

Hi,

It depends on what you want. Both are good for finding articles
online and downloading the pdfs. Papers is certainly pretty, but
doesn't do bibliographies and document scanning, though, and is of a
much more limited scope than Bookends.

You might actually consider both, though (Papers is only ~$25). The
guys who make Papers and I have collaborated to create an exporter in
Papers -> Bookends (direct, no files), which includes links to any
pdfs in Papers. So if you really like the Papers gets articles, you
can organize them there, then pipe the reference info over to
Bookends for citing in manuscripts.

I'd definitely try both, with this information in mind.

Jon
Sonny Software
post #11 of 14
I use Sente as my reference manager and citation app.

http://www.thirdstreetsoftware.com

It also organizes and names your PDF files etc. It can download PDF files from the web with a quick key stroke (as long as the PDF files are freely available or your working at a university that has access to the journal in question).
post #12 of 14
Thread Starter 
Papers is now at version 1.0. Seems to have matured quite a bit!
post #13 of 14
I've been using this for some weeks and it's good. I think I'm going to pay.
post #14 of 14
Thread Starter 
An already great software I use throughout my working days keeps getting better and starts to expand beyond the life sciences. Also there is support for plug-ins and a SDK available.
According to the developers, version 2.0 will be tailored to take advantage of the improved pdf-kit and other developer goodies in Leopard and enable things like note-taking and highlighting within the pdf.

New in Papers 1.5:

Search Engine plugins, including Google Scholar, Scopus and Web of Science.
Full compatibility with Mac OS X 10.5 Leopard.
Much better integration with other applications.
A streamlined and improved user interface.
Over 100 more new features and bug fixes...
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