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Published online 30 April 2008 | 453, 12 (2008) | doi:10.1038/453012b
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Programs promise to end PDF paper-chase
Software makes article control a virtual reality.
Researchers are buzzing about a new type of software that allows them to manage their research paper downloads from online journals much more effectively.
One of the most popular programs is Papers, a commercial offering released last year with a similar interface to iTunes, Apple's successful music-file organizer.
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Looks like a nice idea. The area of data management in science is an ongoing quest for better tools. One way to shortcut development time is to use acknowledged 'standard' interfaces (like iTunes, or email clients). What needs to come next for Papers is something like that implemented in Geneious, which runs automated searches of databases and can be trained to sort relevant from irrelevant articles as they are downloaded. At this time Geneious only downloads the reference not the PDF files.
In the meantime, use of the Mac OS Spotlight in tandem with an bibliographic application such as Bookends, which attaches pdf and other files to references with little effort, and is fully indexed, comes very close the the objective of the dedicated apps. Spotlight uses metadata as well, so PDF and other file types containing the search phrase are grouped.
I like to use mind mapping software (i.e. FreeMind, Mind Manager) with links to the PDF files. This way the file is connected directly to the idea I have associated with it. In many cases a single file is connected to more than one idea. This is a great way to see how your ideas relate to one another.
Oh yes, Pubmed should include many more interactive functions. In the meantime, I am using citeulike.org as Nature's connotea.org has some annoying bugs. These web-based bibliography managers are getting better and better, they allow comments, are organized around tags and you can also upload your PDFs now. Like all webtools, you don't need any backups and it's accessible from everywhere. However, the interface is by far not as responsive as Papers and PDFs are not integrated very well yet.
Another open source tool to manage literature, references, pdf files or whatever content of the WWW is Zotero. What I like most is that it lives straight were I need it - directly in firefox. While browsing pubmed or your favorite journals, you can add publications of interest to your library and take notes without starting an external program. When you want to re-read your papers, the program automatically locates the corresponding website / the pdf file. And it comes with integrated processors for MSWord and Openoffice. Weak point: import of large datasets is slow.
A year ago I was looking for a software to manage my growing scientific literature in PDF format. I am currently using Porfolio 8.1 from Extensis. There is certainly a strong need for a PDF managing software, such as Papers. I would love to try it.
Google Desktop is free and indexes ALL files that contain text, including PDF, DOC, TXT, PPT, email. It can find PDF articles and any notes on hard drives or in email folders, so that notes and articles do not have to be archived in the same location. It is also fast and works with the familiar Google search interface, providing brief excerpts of the found files with titles and links to access the file itself, or the directory where it resides.
I use A.nnotate from a.nnotate.com (of course I would: I helped develop it). We are concerned with exactly the problem of making and sharing annotations on PDF files in such a way that you can easily get back to a particular phrase or paragraph you have read. The current focus is on tags and notes, though we are working with groups who want to do much more structured curation. But what is really needed here is for the journals to provide richer, standardized, machine readable, versions of their content. Then you would get many more good tools to work with it. It is crazy the lengths we have to go to sometimes to get even the words and the text flow order out of a PDF!
If we had a large, decentralized database for all sciences, cross-referenced, with full-text search and all the web 2.0 bells and whistles, we would not need any special software for managing papers - we would all have our personal, fully customizable bibliographies. And as an added benefit, there would be no more Thomson Scientific, PubMed, Current Contents, Google Scholar or any such thing. While I'm at it, such a merged database would of course also provide a customizable citation, download, link, trackback, comment, rate, etc. count/rank. Basically, we'd get all the information we produce ourselves under our own control all in one place. So why don't we have anything like that already? It's not like the technology needed to be developed...
I use Google Desktop to search files (including PDF files and their contents). It works fine with Win-XP, but I have no exp. with the Mac. Unlike Papers it is free to date. It takes a while for indexing your files (do not forget to mark in-text search by installation), but then it is very fast and as efficient as google itself.
Corrigendum to my previous post: do not forget to enable content indexing...
Corrigendum to my previous post: do not forget to enable content indexing...
Corrigendum to my previous post: do not forget to enable content indexing...
Björn: while a great prospect for users that'd be quite a big database that somebody would need to pay to maintain. ;)
I like this. I have been using itunes to manage my pdf's though it does not allow a user to read and view the pdf's in the same screen.
I have used Papers and really like many aspects of it. But PDF management in Sente (my primary reference manager, mentioned in the article), is just as powerful and Sente handles all types of references (not just journal articles) and it generates bibliographies. Now if access to articles in all fields were just as easy as it is in PubMed...
The upcoming version of EndNote [for Windows & Macintosh] version X2 - will include the ability to automatically locate, download, and attach full text files to EndNote libraries using several technologies, including: DOI, PubMed LinkOut, ISI Web of Knowledge Full Text Links, and OpenURL linking. Version X2 will be available for Windows in June and for Macintosh at the end of the summer. www.endnote.com
EasyArticles is an excellent software available since several years for the WINDOWS platform. It not only manages PDF files in virtual folders but also nicely integrates into PUBMED thus allowing rapid download of PUBMED records and associated PDFs. Although some minor improvements (inlcuding an update of their website) would definitely make it more user friendly it is an excellent tool to work with. I use it since several years. http://www.synaptosoft.com/EasyArticles/index.html
I have written a program for my personal use that is more "journal-centric." The software facilitates reading scientific journals on a weekly basis and contains the tools needed to organize and process article information (including PDFs) in the context of one's research. A brief description of the program is available at: http://journalexplorer.xhifin.org/index.html
You will only know how important it is when you miss it! Papers is a no-frills program made by a scientist for scientists. I love the handy built-in search tool. You get so much unreliable info in Web search engines these days, that I started using Papers as my search engine (using my reliable article library!). It is like an aspirin when you are writing a review.
Literature management tools typically either require that you type in the whole bibliography by hand, or that the PDF reprint you want to import is downloaded from a site that is supported by your software. Yet things would be much easier, if the bibliography could be retrieved automatically from arbitrary PDFs without any user intervention necessary. For Pubmed indexed papers there is already an open-source tool available to do so: http://bioinf.boku.ac.at/bibglimpse Including this feature into PDF managers is definitely an improvement in ease of use!