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Connecting Open Notebook data to a peer reviewed paper

6 February 2008 4 Comments

One thing that we have been thinking about a bit recently is how best to link elements of a peer reviewed paper back to an Open Notebook. There are a number of issues that this raises, both technical and philosophical about how and why we might do this. Our first motivation is to provide access to the raw data if people want it. The dream here is that by clicking on a graph you are taken straight through to processed data which you can then backtrack through to get to the raw data itself. This is clearly some way off.

Other simple solutions are to provide a hyperlink back to the open notebook, or to an index page that describes the experiment, how it was done, and how the data was processed. Publishers are always going to have an issue with this because they can’t rely on the stability of external material. So the other solution is to package up a version of the notebook and provide it as supplementary information. This could still provide links back to the ‘real’ notebook but provides additional stability and also protects the data against disaster by duplicating it.

The problem with this is that many journals will only accept pdf. While we can process a notebook to provide a package which is wrapped up as pdf this has a lot of limitations particularly when it comes to data scraping, which after all we want to encourage. An encouraging development was recently described on the BioMedCentral Blog where they describe the capability of uploading a ‘mini website’ as supplementary information. This is great as we can build a static version of our notebook, with lots of lovely rich metadata built in. We can point out to the original notebook and we can point in from the original notebook back to the paper. I am supposed to be working on a paper at the moment which I was considering where to send. I hope we can give BMC Biotechnology or perhaps BMC Research Notes a go to test this out.


  • I don’t think it will be a big issue. All you are doing is linking to a web page (a wiki page in our case), which is done all time these days. You could also point to a document with a doi (like Nature Precedings) that points to the data. It will be interesting to see what gets accepted. One of the advantages of linking directly to the notebook pages is that we can tell that visitors got there through the paper.

  • I don’t think it will be a big issue. All you are doing is linking to a web page (a wiki page in our case), which is done all time these days. You could also point to a document with a doi (like Nature Precedings) that points to the data. It will be interesting to see what gets accepted. One of the advantages of linking directly to the notebook pages is that we can tell that visitors got there through the paper.

  • Very true. I also wasn’t being clear. We have been thinking about how to make ‘snapshots’ that can be archived and show the state of the system at a particular time. Also the idea of neatly wrapping up all the relevant posts to tell a specific story, so this nicely allows us to do that for a paper. We would still link everything back to the original posts I think for consistency.

  • Very true. I also wasn’t being clear. We have been thinking about how to make ‘snapshots’ that can be archived and show the state of the system at a particular time. Also the idea of neatly wrapping up all the relevant posts to tell a specific story, so this nicely allows us to do that for a paper. We would still link everything back to the original posts I think for consistency.