So I was watching my twitter feed today and saw this tidbit come along:
….The Genome Viewer utilizes a genome browser developed by NCBI (the National Center for Biotechnology Information at the National Institutes of Health). Elsevier collaborated with the NCBI as it was developing the browser, and is the first publisher to incorporate the technology into an application for viewing detailed information about the gene sequences that are mentioned in articles.
When an author of an article tags a gene sequence, Elsevier matches this gene with information in NCBI”s databases and pulls this information into the article. This allows readers of the article to get specific information about each strand by hovering over it, and also offers functionality such as flipping the strands, zooming to a sequence, or going to a specific position to define a track of interest within the sequence….
There’s nothing I love more than exploring a new genome viewer, or a clever new use of an existing one! The press release offered links to a couple of papers that were supposed to show this new feature. Um…I couldn’t find it.
Step 1: Locate genome viewer.
Step 2: Explore genome viewer.
Step 3: Write up blog post about new genome viewer.
So here we are, and I’m stuck at Step 1 still. But I’ve sort of hurdled over that to Step 3. I’m sure the folks at Elsevier are going to get me to this browser–I’ve already been in touch with them and they are going to help me out.
But in the meantime I’d like to say how cool an idea this is. I have always thought there should be more integration between the science publications and the databases. And not only because I firmly believe that, in large part, the data isn’t in the papers anymore.
We took a different approach. We recently partnered with BioMedCentral’s team to tag articles with the computational resources mentioned in their publication for which we have training. On their pages you’ll see a link to our site that looks like this, on a recent paper about CNVs in trypanosomes: http://www.biomedcentral.com/1471-2164/12/139
On our pages–such as this example of our landing page for the GBrowse tutorial–you’ll see recent papers that referred to this tool.
So if you were interested in GBrowse you could quickly see who is working with it, how, and it would help you to assess if GBrowse is the right tool for you needs. And you could use our tutorial to help understand ways to explore the data from a project that uses GBrowse. In many of the “big data” projects you aren’t going to get a gene list or a gene link. You’ll need to explore the set in toto at their sites. I’ve had my ranty pants* on about this before
Yeah. I have strong feelings about this.
I also think it’s a good idea for publishers. There’s a bit of pushback I’ve seen about subscription pricing, including this letter that has always stuck with me since I read it:
Profit margins of journal publishers in the fields of science, technology, and medicine recently ran to 30–40 percent; yet those publishers add very little value to the research process, and most of the research is ultimately funded by American taxpayers through the National Institutes of Health and other organizations.
I think that by adding handier access to the data in a paper, or to the tools needed to go further, publishers can add value beyond just the traditional publication.
If I could only find it…
*hat tip to Mike the Mad Biologist for my new favorite phrase, “ranty pants“