Posts Tagged ‘PubMed’

20 December 2013 by William
mobile 2  Read and add Pubmed papers to Mendeley on your Android device with Pubchase

If you’re a life science researcher, you’re in luck. There’s now a way for you to search PubMed and add to your Mendeley library from your Android device. Pubchase is a new Android app from Zappylabs, a mobile development company that specializes in life science. Here’s what the app offers:

  • Search PubMed and add papers to your Mendeley library from your Android device (works on iOS too).
  • Read your Mendeley papers* on your Android device
  • Get life-science specific recommendations from PubChase, based on your Mendeley library, with no need to build a separate library in PubChase.

PubChase also has a neat section with essays written by other researchers about papers which may be of interest to you. Please note, however, this is just a way to get PubMed papers from Android into Mendeley and Mendeley papers into PubChase. PubChase isn’t a Mendeley app. Here’s what Lenny from PubChase has to say:

The forte of ZappyLab is mobile and web technology. We have no plans to build citation management plugins. So, from the beginning, we wanted to make it easy for our users to import their libraries from Mendeley, Papers, Endnote, and other software. However, adding newly recommended papers to your PubChase library means that you then have to export your PubChase library to the other software when writing a paper. The Mendeley sync greatly simplifies this process. Though our Endnote and Papers users keep asking for a similar integration, those tools do not have open APIs, so it is not an option for us. Therefore, we will be focusing our developmental efforts on deeper integration with Mendeley.

The conclusion of that paragraph is precisely why we make the Mendeley API available and we’re happy to feature them on our Developer Portal. We hope to see great things from PubChase and from all the other talented developers using our platform to serve their constituents.

To get started with PubChase and the Mendeley Sync, follow the instructions at Pubchase.

*I know many of you are disappointed we don’t have an official Android app for Mendeley. We’re working on it for the new year and think PubChase and Mendeley will be a nice pair for life science researchers who use Android.

31 May 2012 by William

tipstricks  11 free tools for discovering researchFinding research is often frustrating. You’re always running into paywalls and the interfaces to most library databases look like they were designed sometime back in 1980. To make it just a bit easier, we’ve assembled a collection of free tools to help you in your research. We discuss both databases and newer social tools for discovery.

6/7/2012 Updated to include Microsoft Academic Search
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24 April 2009 by Victor

progress update  One million articles uploaded to Mendeley!We passed a landmark today: As of 16.50h GMT, our users have uploaded one million articles to their Mendeley accounts! Including the cited references which Mendeley also extracts from research papers, we now have over 14 million metadata sets in our database. Even we were surprised by the speed in which this has happened!

For the record, the millionth article added to our database was “The somatic marker hypothesis: A critical evaluation by Dunn et al. (2006) in Neuroscience and Biobehavioral Reviews – as luck would have it, that’s a topic related to my personal research on the role of emotions in decision making! The closest publication by one of our users, Joaquin Rivera, was added at 17.01h – a maths paper titled “On the exact multiplicity of solutions for boundary-value problems via computing the direction of bifurcations”, available for download on Joaquin’s Mendeley profile.

90% of these one million articles have been uploaded since January 2009, and our database is currently doubling in size every 6 weeks. For comparison, venerable PubMed – the largest database of biomedical literature – contains 18,813,527 records as of today. Assuming we managed to keep up our growth, we could surpass the size of the PubMed database within the next 6 months!

Roughly 43% of the papers in our database are in the biological and medical sciences (even though only about 27% of users are working in these academic disciplines). Computer and information science comes in second with roughly 11% of all papers, followed by engineering with 7%, and chemistry, physics, psychology and other social sciences with 4-5% each.

As we’ve said before on this blog and elsewhere (e.g. see my talk at the Plugg Conference), we’re not hoarding all that data just because we can, no Sir! Our vision is to create the largest open, interdisciplinary and ontological database of research – as crazy as that sounds, remember that Last.fm (whose former chairman and COO are our co-founders and investors) pulled it off in the space of music within just three years, using the same user data-aggregation model that Mendeley is built on.

We’ve already begun to report real-time “usage-based” research trends – a nice discussion of Mendeley statistics showing the most-read journal in the biological sciences can be found here (we’ll be writing more about this soon!). Analogous to Last.fm, we will provide APIs to let others mash up the research statistics we’re generating. Moreover, our database will be the basis for our upcoming collaborative filtering recommendation engine: Based on the articles in your Mendeley library, we will be able to tell you about articles you don’t know yet, but which have been read and recommended by researchers with similar interests. You can read more about these plans in our recent IEEE e-Science paper.

A big thank you to our wonderful users who have been helping us improve Mendeley with their constant feedback. After celebrating the millionth article upload tonight, we’ll get back to work on our next two releases, packed full with exciting new features!

30 March 2009 by Victor

It’s here! The Mendeley browser “bookmarklet” allows you to import documents from websites and academic databases into your Mendeley library with a single click. At the moment, the following sites are supported: ACM Portal, Amazon.com, arXiv.org, CiteSeer, IEEE Xplore, IngentaConnect, Google Book Search, Google Scholar, PubMed, NASA Astrophysics Data System, and ScienceDirect. We’ll be adding support for further sites continuously.

This is how it works: Say you’re on PubMed and you’ve just discovered an interesting paper. Now, all you need to do is click the “Import to Mendeley” bookmark in your browser – Mendeley does the rest: The paper is automatically added to your Mendeley Web library with metadata, abstract and (if available) the PDF. All of this happens in the background, so you don’t have to leave the PubMed page you’re on.

It also works on search results pages, so you can import multiple documents at the same time – a small pop-up allows you to choose which ones.

academic features  Mendeley Bookmarklet released! One click import from Google Scholar, PubMed, arXiv, ACM, IEEE etc.

And since your Mendeley Web library and Mendeley Desktop library are sync’ed, you’ll have the imported metadata and papers on your computer, too.

To get the bookmarklet, log in to Mendeley Web and go to http://www.mendeley.com/import. Install the bookmarklet by dragging & dropping it to your browser toolbar, or by adding it your bookmarks.

Now, surf to one of the supported websites and import happily!

4 March 2009 by Victor

community relations academic life  Ricardo Vidal joins Mendeley as Community Liaison

Today we can announce another bit of news that makes us very happy! For a while, we’ve been looking for help in better engaging the academic community, involving it more in our roadmap decisions, and also understanding the needs of life scientists better. Consider this: We’re all social scientists, computer scientists and engineers here at Mendeley HQ, and we couldn’t pick this guy PubMed out of a police lineup.

Ok, I’m exaggerating (our next release of Mendeley Desktop, due next week, will enable manual PubMed ID lookups, and the next release after that will do PubMed lookups for all your PDFs automatically). However, the help we’ve been looking for has now arrived in the congenial, talented and Portuguese shape of Ricardo Vidal, author of My Biotech Life! You can see his picture on the top right, and his “silly microbe” design down on the left.

community relations academic life  Ricardo Vidal joins Mendeley as Community LiaisonRicardo will become our first “Community Liaison”. While continuing on with his graduate studies, he’ll also devote a few  hours each week to interacting with other researchers on the blogosphere, Twitter, and other social media on Mendeley’s behalf.

I first came across Ricardo’s blog around June last year, because he had written an article about his research paper management needs. So I left a comment pointing him to Mendeley, and he asked for a few invitation codes to the then-ongoing private beta for his readers. We were happy to give him twenty, which were gone only hours after Ricardo offered them on his blog! We loosely stayed in touch ever since and were grateful for the continued support he’s given us over time.

For this announcement, I asked Ricardo to briefly introduce himself and describe why he decided to join us as a Community Liaison and what his hopes for Mendeley were. Here are his answers:

Introduction
Let’s see… I’m currently concluding my Master of Engineering degree in Biological Engineering at the University of Algarve, in Southern Portugal. I’ve been blogging since 2006 at My Biotech Life and am also the co-founder of the DNA Network, a leading network of DNA-related blogs.  I also produce (sometimes silly) biotech graphics and logos from time to time.

Why I joined
Besides the fact that I am terrible at keeping my digital papers in order on my laptop or online, I believe that Mendeley represents not only a two-in-one solution for research paper management but also comprises another aspect that I consider of extreme importance, networking. The ability to contact and share your work with researchers alike is invaluable.

Hope/vision for Mendeley
Looking at the progress that has taken place since Mendeley’s launch, I can only hope that things keep evolving as they are now. The roadmap looks promising and the user feedback can only make it a better piece of software as time goes by.

As it has been stated, I also envision Mendeley to become the “Last.fm for Research Papers” where user statistics and networking play a vital part in research, by providing easier access and interaction to scientific information.

Are you looking for a research job?