This week’s tip is a bit off-topic (as in genomics databases), but it is science/biology-related and something we all need. There are a lot of reference management software possibilities out there like EndNote, some great web 2.0 social networking sites like Connotea (Nature Publishing) and CiteULike (Springer) and some PDF management tools. Mendeley wants to be all three. I like the idea a lot. Instead of having 2 or 3 separate applications, desktop and/or web, etc., you have one to rule them all. Of course EndNote has EndNote web, but it’s not free (Mendeley is free, and the features they offer now will stay free. They will offer new features for professional users later with a fee). You can export your references in Connotea and CiteULIke, but it’s an extra annoying step. My first experiences with Mendeley have been quite positive, so I thought I’d introduce them to you here.
As one of the tools (along with Connotea, Faculty1000, MyNCBI, HubMed, etc) to keep abreast of the fire hose of literature that is published, I also use RSS feeds to keep up-to-date on the latest publications from journals of interest. There are a lot of journals out there that publish a lot of data interesting to me, but subscribing to them all IRL of course is cost prohibitive (and environmentally unfriendly). Many will send updates by email of new issues, but the last thing I need is another email in my inbox screaming for my attention. Getting an RSS feed from a journal is a good way to keep up-to-date on new issues (if you haven’t used RSS feeds, read up on them here, find a reader here). Many journals include RSS feeds to new content, others don’t. Another way to get RSS feeds to a specific journal is to use HubMed in a nice feature that allows you to get an RSS news feed for a ‘search.’ I’ll show you how to do that here.
That’s the title of a recent paper in PLoS Computational Biology paper I read. This paper is a good read on two levels. It discusses the problems and difficulties (and solutions) with the rising number of digital libraries, published papers and research. Difficulties like identity (identifying papers in a persistent and standard way) and metadata (being able to pull out publication data from a paper in a standard and simple manner, if at all) and solutions like simple and persistent URIs, exposing metadata and identifying people and publications.
It was also a good read on another level, here, now and me. The authors discuss several digital libraries and their scope (the graphic here is a representation of some and their overlap) and tools to ‘defrost’ these libraries at a personal level. Many of these tools I use or know about (MyNCBI, CiteULike, Connotea and HubMed) and some I’m not particularly familar with (Zotero, Mendeley and Mekentosj Papers-Mac only! :), but the paper did give me a pretty decent understanding on some better ways for me to start to get a handle on the growing body of literature.
Now I should go do two things… reorganize and reinvigorate my references (back to Connotea! and try out Papers!) and to add the DOI link from CrossRef to this post, you know to standardize!
Looking through the results and discussing it briefly with others, I would say that there is nothing particularly surprising from my experience in the bioinformatics field. The survey reflects what I see today. What is notable is that many bioinformaticists in the survey have commented that they see the future of bioinformatics moving toward more integration with other fields and more cross-disciplinary needs, as illustrated by this comment by one (and many others):
“bioinformatics will be incorporated into cross-disciplinary work by scientists that will learn to use computational tools and insights as a commonplace part of their experiments, part in silico, part wet bench”
I would agree, though of course I could well be wrong :), with that and along with that will come the need less for ‘bioinformaticists’ and more for biologists trained in bioinformatics. A quick look of some of the analysis is also not particularly surprising, BLAST is by far and away the most cited application of use (lots of alignment and phylogeny stuff there too) as can be seen by the chart (left ) on the results analysis site. Asked which web application/site they use most, it’s an interest mixture between utility sites Google Docs (hmm, maybe there’s something I should look at there :), Gmail, Twitter, WordPress and biological resources like NCBI, UCSC Genome Browser, Ensembl, BLAST, Connotea and PubMed. I think the questions here might have been designed better. Those are two entirely different categories and I would love to see the results (of course for the resources if that was more explicitly asked. Perhaps next survey (btw, that those 5 biological resources made the it in the graph is no surprise to me).
It will be interesting to go through this data in some more detail!
I use Connotea (though not enough, I need to make it a habit) and like it. It’s a ‘social bookmarking’ reference management system. I just noticed a new feature added recently in beta that allows you to put your references on your web site. This could be useful and allow readers to see some of the stuff you find interesting and useful. We’ll have to consider adding it here. CiteULike is another such service, but I haven’t seen this feature.
If you have a blog or a lab web site, thought you might find it interesting.