Tuesday, September 06, 2011

Calling all authors, bloggers, reporters - please help with aggregating discussions of scientific papers

There has been a lot of hand wringing over whether we should and if we should how should we link discussions about scientific papers with the papers themselves.  For example, if someone writes a news story about a paper in BMC Genomics - should the online version of the paper show links to the news story?  I think so, as so many others.  If someone writes a blog post discussing the paper, should there be a tracked link on the journal site?  Again, I think so.  I think this is even more important in social media discussions of papers, which I find fascinating much of the time.   Very few people go to journal sites and post comments and open up discussions of papers.  But lots of people post comments to twitter, facebook, and other social media sites.  So why not bring those posts into the fold?

Now there are lots of efforts out there to collect comments about papers.  Faculty of 1000.  The Third Reviewer.  Research blogging. And much more. For other discussions of the issue see:
I am not really going to get into a discussion of all the ideas out there in this area.  Some are good.  Some are bad.  Some are probably both.  I personally think aggregation is going to be a very useful tool in post publication sharing and discussion and searching.  But that is not per se what I am here to talk about.  What I am here to talk about is what anyone can do right now to help with this in a very simple way.

My simple suggestion:
If you see ANY online discussion of a paper - a news story - a blog - even some smaller thread somewhere.  Find the journal article online and use the comments function is the journal has one to post  a comment saying "There was a news story discussing this paper in the New York Times.  See ...."  Or something like that.  And presto, people who go see the paper online will also have potential to find the link you post.

I have been doing this for a while.  It is relatively easy for PLoS Papers.  For example for my paper on "Stalking the Fourth Domain in Metagenomic Data" I posted all sorts of links using the PLoS One comment function.  I posted links to my blog.  I posted links to positive news stories.  I posted links to critiques.  Anything I could find.

And this worked out pretty well.

I then started posted links for other papers, even pretty old ones (I just posted a few for my PLoS Biology paper in 2006 on the Tetrahymena genome).  I have now done this for many PLoS papers as well as my recent Nature paper on a "Phylogeny driven genomic encyclopedia of bacteria and archaea".  Now, mind you, this works best when the papers are open access or at least freely available, so that people can read the paper as well as the discussions.  But you could do this for any paper in principle if the journal has a commenting function.

Now - I am not alone in starting to do this.  PLoS One has even launched this as a formal "media tracking" project: see PLoS ONE’s Media Tracking Project | EveryONE.  Not sure how well their system will work, but any aggregation is good.  Of course, in the long run, systems that aggregate automatically using trackbacks or DOIs or other tools will be best (e.g., some journals link to Research Blogging posts but not all do), but those do not always work perfectly and some journals do not seem to like the automated approaches.  So please - link and comment away.  Become part of the aggregation solution.  I know this is not all we need to do and this is a relatively minor thing - but if we get everyone engaged in doing it, I believe there will be a catalytic effect whereby people will then understand why this might be useful to do broadly ...


  1. Great idea. But say I wanted to link your paper on Mauve Assembly Metrics to my blog post on the software, does that mean I have to write an "e-letter" to Bioinformatics?

  2. Like I said "But you could do this for any paper in principle if the journal has a commenting function. " --- and part of my point here is to encourage people to write to the journals that don't have such functions to try and open them up

  3. Right. Just clarifying whether you thought "e-letters" were appropriate or not. I think probably not, so I've emailed Alex Bateman to ask if he'll allow commenting on articles in Bioinformatics.

  4. Please do. Meanwhile I submitted a comment in their electronic letter to the editor system pointing out your blog post. We will see if it get's posted ...

  5. Good idea. Shall try to do as suggested and hope this will lead to good academics and not leg pulling.

  6. Well, one can never prevent leg pulling and other complications. But we need to do a better job of aggregation so maybe this will help

  7. I am going back to all my past PLoS Papers and posting comments on the site if there was a news story or blog post ... gonna take some time but should be useful ...

    See for example

  8. This comment has been removed by the author.

  9. This is a great idea. I think it would be really helpful if someone would come up with an app that integrates all the popular links that you're talking about and original publications. If my new cell phone can integrate gmail, facebook, twitter, and whatever into one feed, and merge everyone's multiple identities into one, surely we can come up with something similar.

  10. Note - Mary and Trey at Genomes R Us suggest that people also post links to original papers wherever they are missing from stories. Great idea.

  11. I think I won't be doing this for non- OpenAccess papers. Not much point in that.

  12. That last comment is either link spam, or a very subtle critique of this idea ...

  13. I like being subtle - really I do - but that was too subtle for me

  14. Yes, but notable that the Tetrahymena paper you mention has now had 28000 views and not a single comment or rating in the past 5 years. I think it's time to think more seriously about this issue than just asking the 0.001% of blog-happy scientists to spend uncopious free time manually tagging their own papers (will look like narcissism) or other papers (near-sisyphean).

  15. Well, I have said previously that I think the PLoS Commenting system is fundamentally flawed. Who would go to the PLoS site when they have blogs, twitter, facebook etc. What I am asking for here is for people to show the power of aggregation so that it wil help encourage those out there with time , $ and ideas to develop better aggregation systems.

    So this effort is kind of a hijacking of the commenting system.

  16. "So this effort is kind of a hijacking of the commenting system". Very subtle :)

    My $0.02

    1) Science Bloggers are generally very good in terms of linking back to Manuscripts. The same cannot be said for many media outlets. I raised this (and other stuff) when hosting a podcast at the HQ of the Guardian last week. It should be online tomorrow so I'll post a link once I have it.

    2) One example that I brought up (as Jon will recall) was a front page article in a UK newspaper about Cancer research published in PLoS Biology about 2 years ago. It's not exactly everyday that science reaches "the front page" so I went on 'a bit of a mission'.

    I went online but alas, no link to the Paper (which was OA for heavens sake), so I left a comment with a link to it during my lunch-hour. A few hours later and the link appeared 1/2 way through the article. RESULT.

    2) Many Publishers/Journals such as BMC/PLoS/BMJ to name a few have adopted a policy to make it very easy to share content using social media. In the case of PLoS, I personally politely asked them to do so (about 4 years ago) and they agreed straight away.

    What we need is something similar, a bit like reverse engineering to aggregate the online discussions back to the source. I don't know the answer(s) but blog posts and comments gathered (like this) are most helpful IMO.

  17. As alluded to, our Guardian Podcast is now online here:- http://poddelusion.co.uk/blog/2011/09/09/chatting-with-the-guardian-science-podcast-a-pod-delusion-special/


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