del.icio.us bioinformatics
January 7th, 2007Heard about how the internet is revolutionising science and bioinformatics? The semantic web is giving meaning to your data, life, as well as writing grant proposals for you? Well, not quite. The party may just be getting started, but there are already some great sites for taking advantage of the web science buzz.
The social bookmarking site del.icio.us is excellent for managing your own bookmarks, and searching those of others. Here’s a tutorial using delicious to find links on topics you’re interested in.
Here’s the del.icio.us frontpage.
I’m interested in a bioinformatics topic, such as multiple sequence alignment. So I enter this in the search box in the top right corner. Highlighted by the red circle.
This returns a list of web pages that delicious users have tagged in relation to this topic. Each entry gives a link to the result, and a link to save the page to your own delicious bookmarks. Beneath each result are the keywords that the user has used to describe the site. Finally there is link to the other delicious users who have this bookmark in their collection.
I’m interested in the tool MUSCLE (red box), but I’d also like to see what else people are interested in. I click on “saved by 10 people” (green box) to jump to this.
This page summarises the delicious links for the MUSCLE tool. On the upper right (red box), is summarised the words that all the users have tagged the link with. As you might expect, bioinformatics is the most commonly used word. Clicking on this will take us to other pages tagged with bioinformatics.
Below this (green box), are the users who have bookmarked the MUSCLE tool. Clicking on one of the users’ names will take me to their delicious page.
This user’s page shows a list of the links in their collection. I refine this to topics I am interested in by clicking on one of the tags (red and green boxes). Here, I have selected the pages marked with “sequence alignment”. This then gives me a set of links related to the topic I am interested in, as seen in the list.
More information can be found at delicious help as well as a page on discovery using tags
February 26th, 2007 at 9:50 pm
You could also have a look at Connotea and/or citeUlike which are two bookmarking tools tagging academics papers (e.g. connotea recognizes a pubmed URL , a doi….)
Pierre
February 28th, 2007 at 9:09 pm
I tried out Connotea. I know that it gets a lot of attention in the bioinformatics blog community. However, I never really became enraptured with it, in the way I have with delicious. I think this was partly to do with how to use it, which I wasn’t really clear on.
March 2nd, 2007 at 2:47 pm
Yeah, del.icio.us is simpler to use because there is a firefox/epiphany extension which help to post bookmarks to the system.
It would be nice to have something similar for connotea or CiteULike..
March 2nd, 2007 at 4:45 pm
Yes, del.icio.us is nice to use. I really like the way the tagging system works which makes search really transparent. I like the idea behind connotea though, literature searching is always important. Novel ways to do this will help us all.
June 8th, 2007 at 7:36 pm
There are browser buttons for Connotea, and they work great. They actually scrape citation data from a publisher’s site or a pubmed page and pre-fill the form with it. All you have to do is add tags and, optionally, a comment.
Take a look at my Connotea page in action here. I also use the RSS display widget for Wordpress to display a list of what papers I’ve been reading on my blog.
June 11th, 2007 at 11:39 am
Thanks for the tip Mr Gunn. Connotea definitely is popular. Adding get more so. Browsing around their website you can see that Nature is taking how scientists can use the web seriously.