I like simple interfaces similar to itunes which is why I’ve stuck to using both PDF Stacks and Papers to manage my collection of medical articles and journals. They all do the job.

if you like mendeley our software “sciplore mindmapping” might be interesting for you. sciplore mindmapping is a mind mapping application that allows you to integrate your pdfs and references with mind maps. the big advantage of this approach is that you do not only have a list of your PDFs but a mind map in which you can add additional information and arrange PDFs more flexible. And in case you really like Mendeley, you even can use Mendeley in addition to SciPlore MindMapping.

For a short demonstration of sciplore mindmapping see
http://www.youtube.com/v/jRHqLktIMWw&hl=en_GB&fs=1&rel=0&hd=1

To try the software (open source, Java): http://www.sciplore.org/software/sciplore_mindmapping/

and to read about how to write a phd thesis (or academic papers in general) with sciplore mindmapping see http://sciplore.org/blog/2010/03/02/how-to-write-a-phd-thesis/

Eli — I think this is possible by dragging and dropping the duplicate author name onto the form you want to use in the “Filter By Authors” frame. It should then ask if you want to replace e.g. all instances of “Richard Scalzo” with “R. A. Scalzo” or whatever, and when you confirm, it will do a search-and-replace which is what I think you’re asking for.

I would definitely like to see improved metadata extraction from PDFs. For example, I find that the ApJ bibliography format is inscrutable to Mendeley and I get a lot of extractions where e.g. “Mnras” is the title (when titles aren’t usually given) — this is true even for recent IOP PDFs as well as astro-ph offerings. But the format is regular and if I could give Mendeley some kind of template for parsing them, just for a given journal, it ought to do much better. I don’t know whether this capability is already available (Gus, how did you get it to work?), or whether they’re planning on adding something like it. It’s probably not that crucial, just annoying — if they have that information available in the library, it ought to be correct without me manually entering every citation.

Modulo things like that, though, I really like the browser.

Eli – Mendeley has joined the Open Researcher and Contributor ID initiative, which is a community effort to establish an open, independent registry to resolve the systemic name ambiguity by means of assigning unique identifiers linkable to an individual’s research output. The researcher name issue is a complex one, but there is finally some progress in this area. We’re hopeful this will lead to a real and lasting solution to the problem.

Kelle – No worries Just trying to help.

Eli

Thanks for looking into this in more depth and posting your comments. I understand why it is tricky for Mendeley to grab the PDF from ADS. That would be great, but I’m not holding my breath.

I was referring primarily to Gus’ scenario (b). I want improved duplicate checking or at the very least a way to manually tell Medeley — hey, these are duplicates, merge the entries (according to some preferences). That seems like it would provide an acceptable work-flow for me. Anyhow, this discussion would clearly be more productive on the Mendeley support forums…

I first thought that Jonathan was referring to the Bibdesk like behavior(s) that (a) allow one to drag and drop a PDF onto a citation, adding the link and paper for storage and (b) looking for and flagging/repairing duplicates.

I really like feature (a) of Bibdesk, and no matter how I try, no field in a citation on Mendeley reacts to the drag n drop of a PDF. So one must use the manual “add” button do this, as Jonathan stated. This feature is the #5 most requested on Mendeley’s feedback page.

On to Bibdesk feature (b), Mendeley appears to try to duplicate check when one adds the PDF after a citation import via the bookmarklet. It flashes, “looking for duplicate” or something like that. PDFs dropped in twice will not twice import for me. Yet actually improved duplicate checking is the #1 most requested feature/improvement.

I tried as an example, “Mid-Infrared Extinction and Its Variation With Galactic Longitude” by Gao et al 2009 both from ADS and arxiv via the bookmarklet and from parsing the IOP PDF. Mendeley did not find or prevent duplication even though the ADS and PDF resulting entries have matching DOI! That should be a bright flashing light in my mind. Interestingly, Mendeley does not pick up the arxiv key from ADS, which I would personally like to see.

The second scenario is based on Tom’s feedback note and has to do with auto following PDF links on parsed web citations. When I went to the arxiv page for Gao et al, I found that the Mendeley bookmarklet does result in a linked PDF for the paper that I could view on either the Mendeley website or Desktop.

The Mendeley admin’s response on their feedback forum indicates that the issue of auto-following PDF links is not dealt with on a per site basis as Tom requested. You could argue that they should add the PDF linkages where ever one exists and let the user figure suffer the consequences if they cannot get to that PDF…

I would like to hear comments on the PDF citation parsing capabilities of Mendeley versus say Papers. The IOP ApJ Gao et al PDF from 2009 parsed perfectly, while another from 2008 ApJ article (DOI 10.1086/590364 — from UChicago originally I think) is a serious mess. I have my guess as to why but wonder if Papers would do better.

Also, if you use Chrome, there is an extension that works like the bookmarklet.

Jonathan: I looked into this a bit and it turns out someone had already requested this in the feedback forum (http://feedback.mendeley.com/forums/4941-mendeley-feedback/suggestions/275394-automatically-fetch-the-pdf-from-an-online-source). The issue seems to be that Mendeley would import the PDF directly without passing through your computer, so they could only import freely available PDF files with the ‘import to mendeley’ link. However, at the moment, it doesn’t even import the free PDF files on ADS, so I left a comment to that effect in the above feedback post. Feel free to log in to their forums and vote for this issue!

If you have a set of papers where this consistently doesn’t happen, drop a line to support@mendeley.com and they’ll tweak the recognition algorithm.