OpenWetWare and Supplementary Material
There has been a lot of discussion about how OpenWetWare can best get involved with scientific publishing. One of the ideas that has been tossed around is to develop OWW as a place to publish supplementary material. In the spirit of my ongoing experiment with OWW as a publication platform (see other posts one, two, three,four, five), I’ve played around with using OWW as a repository of supplemental material.
The idea is simple - there is a lot of extra information gleaned in the course of an investigation that just doesn’t make it into the final paper. We all know of it under the blanket term ‘Supplementary Material’, but what it consists of can vary quite a bit from paper to paper. Most of the time it contains tables and figures that describe some technicalities that don’t fit in with the story line of the article, but are required if anyone wanted to reproduce the results of the investigation. There is no reason it couldn’t be more, which is where OWW could step in to revolutionize the supplementary material business.
Being wiki based, OWW has a unique opportunity to offer the most up-to-date version of supplementary material possible. Even though articles and papers are fixed time snapshots of a work, research has a life of its own and is often on-going. What’s to say that a regularly updated supplemental material section of an article wouldn’t be useful? Furthermore, since wikis support almost any kind of content imaginable, why not explore alternative supplementary materials such as videos that don’t fit in with the current pdf-based supplementary material model?
The problem is that we haven’t figured out how best to get OWW plugged into the mainstream publishing venues. Luckily some journals - namely the Public Library of Science (PLoS) journals - have created a way we can play around with some of these ideas.
Here’s the setup: I recently published a comparative genomics study in PLoS Computational Biology (link (trackback)). During this study, I used python to do ALL of the computations in the work. I thought it would be a good idea to write a small companion paper on how I did this so that other scientists could learn how great python is as a complete scientific programming environment. You can see this article through OWW here. This little companion article can easily be viewed as supplementary material to my original article. I contacted the PLoS people and asked them if I could add a link to this OWW article from the original article and they said ‘Sure, you can even do it yourself!’ You see, PLoS has a commenting system, much like the one on this blog - all I had to do is to create a comment linking to my OWW article (see image below) and voila, we have the first OWW supplementary material! What is even more interesting is that the supplementary article was written AFTER the original article was published - a great example of how OWW facilitates the evolution of supplementary materials over time.
The conclusion is that we actually don’t have to do much at all to start using OWW as a supplementary material repository - just start using it, and figure out a way to link your OWW pages to your official journal article. If you have published in a PLoS journal, then do the above. I encourage you to write other journals and request that they manually place a link to your content if they don’t offer a commenting system.
Please, let me know what you think and share your experiences in using OWW for developing supplementary materials by leaving a comment below.
Posted: April 14th, 2008 under Publishing.
Comments: 7
Comments
Comment from jason
Time: April 14, 2008, 4:55 pm
wow, this is great julius. we should email PLoS, maybe they could add an “authors links” section to the side of the article, where the author could post links to any website that they thought would provide useful info to supplement the paper. This is a great way to get ball rolling though.
Comment from Julius
Time: April 14, 2008, 6:24 pm
That’s a good idea. They kind of already have that with the commenting system actually - you can just add a bunch of links in your particular comment and mention that you are an author of the paper. Or even better you could make your author links on an OWW page and link to that!
They also have a way to add a note to a specific part of the article, but I haven’t used it yet.
I am hoping that a bunch of people start linking to OWW in this way - easy to do and immediately useful.
Comment from Cameron Neylon
Time: April 15, 2008, 5:08 am
PLoS ONE is supposed to enable trackbacks so you could use that potentially, but I never got it to work properly. The notes are fine but I think its a bit limited because it doesn’t know what the link means. Somehow we will need to get some semantics into this.
Look forward to seeing you on Sunday!
Comment from Jean-Claude Bradley
Time: April 15, 2008, 8:52 am
That is a great suggestion. Supplementary sections in most journals are limited in format. In organic chemistry NMR spectra are key to characterizing compounds. Presenting the spectra in an interactive format (like through JSpecView) would be far more useful than a scan of the paper printout we usually get in supplementary sections.
Comment from Cameron Neylon
Time: April 16, 2008, 6:40 am
I would argue that for spectra it is much better to do what you are doing with chemspider and have a central purpose built repository but the broader issue keeps coming up. Should supplementary data be housed with the journal or stuck wherever. I see a paper as a ’snapshot’ that ought to contain all of the appropriate data wrapped up as one package (with links out to the ‘raw’ data which may change, or at least be reassessed over time). Maybe I’m just old fashioned?
Comment from Evie Browne
Time: April 17, 2008, 6:31 am
Hi Julius, I didn’t have any luck getting through to your email, so will leave a comment instead!
We were very pleased to read this post on your addition to your PLoS Computational Biology article of your supplementary OWW website – this is exactly what we were hoping to achieve with the addition of our commentary features! We were wondering if you were aware of the trackback feature we also have, which allows you to add a URL for the PLoS article to a blog post, which will link your article with the blog post. If you use this, your blog post will appear under the ‘Trackbacks’ listing on the right hand side of your article, and so people will be able to navigate back and forth between your blog and the article. If you’re interested in adding this, your trackback URL is:
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000001/trackback
(I’m not sure if this will work in a blog comment - it might need to be embedded in the post text)
You might also be interested in reading and/or commenting on this month’s Editorial, Open Access: Taking Full Advantage of the Content (http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000037), which explores some of the applications available for using the full corpus of Open Access material.
Your thoughts on Open Wet Ware are very interesting to this community, and we’d love to hear more from you – via email or commenting.
All best,
Evie
Evie Browne Publications Manager PLoS Computational Biology ploscompbiol@plos.org
Comment from Julius
Time: April 17, 2008, 12:12 pm
Hi Evie,
I am delighted that PLoS Computational Biology is interested in these type of ideas! I actually did try to use the WordPress trackback system when I originally wrote the post through the author’s console, but it doesn’t seem to have worked. I have not added the trackback link within the text - let’s hope that works.
OpenWetWare is very interested in identifying aspects of the publishing process that can be expanded and revamped (such as Supplementary Materials) and changed from an ease-of-use perspective. I personally think PLoS has made great strides in some of these areas, and would love to talk to you more about how OWW can interact with you to further the progress!
Julius
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